Lactobacillus crispatus is a commonly found species in the urogenital tract(UGT)of healthy females and can also colonize other niches,such as the gastrointestinal tract(GIT).Although its potential protective role in c...Lactobacillus crispatus is a commonly found species in the urogenital tract(UGT)of healthy females and can also colonize other niches,such as the gastrointestinal tract(GIT).Although its potential protective role in cervical cancer has been reported,the anticancer mechanisms involved are still unclear.In this study,we sequenced and characterized the complete genomes of two L.crispatus strains(Lc31 and Lc83)isolated from the UGT of healthy women of reproductive age.Phylogenetic and phylogenomic analyses of these two strains and 15 other L.crispatus strains with complete genome sequences revealed that strains from the UGT and GIT clustered separately.UGT strains had a larger genome size,higher GC contents,and more protein-coding sequences and insertion sequence(Is)elements,indicating the likelihood of active horizontal gene transfer in this niche.We found a universal presence of genes encoding bacteriocins and the absence of virulence factors and antibiotic resistance genes in UGT strains,suggesting the potential of L.crispatus as a urogenital probiotic.Comparative genomic analysis identified an ula gene cluster responsible for L-ascorbate catabolism exclusively in UGT strains,and carbohydrate fermentation experiments confirmed that this substrate supported the growth of L.crispatus Lc31 and Lc83.Our findings improve the understanding of how the genome determines niche adaptation by L.crispatus,providing a foundation for investigating the mechanisms by which urogenital-derived L.crispatus promotes female health.展开更多
Lonicerae Flos(LF)derived from the dried flower buds or opening flowers of four Lonicera plants(Lonicera macranthoides,L.hypoglauca,L.confusa,and L.fulvotnetosa),is a popular traditional Chinese medicine.Because the f...Lonicerae Flos(LF)derived from the dried flower buds or opening flowers of four Lonicera plants(Lonicera macranthoides,L.hypoglauca,L.confusa,and L.fulvotnetosa),is a popular traditional Chinese medicine.Because the four origin plants are very similar in morphology,it is difficult to control the quality of LF in actual production.Over the past decade,many reports have pointed out the differences among them,including the botanical characteristics and active ingredients.However,there is still a lack of rapid methods that can be applied to the identification of the four origins.In this study,comparative analysis of the four chloroplast genomes was performed,and they showed low diversity(Pi=0.00267),three variation hotspots regions(rbcL-accD,rps12-ndhF and rps12-trnN-trnG)were identified as potentially molecular marker of highly informative.Meanwhile,the most obvious difference in SSR comparative analysis is reverse and complement repeats were only identified in L.confusa and L.hypoglauca,respectively.Lastly,the phylogenetic tree showed that L.confusa is more closely related to L.fulvotnetosa,while L.macranthoides is closer to L.hypoglauca.This study systematically revealed the differences among the four chloroplast genomes,and it provides valuable genetic information for identifying the origin of LF.展开更多
The green seaweeds Ulva linza and U.prolifera are closely related species.They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone.In the Yellow Sea,...The green seaweeds Ulva linza and U.prolifera are closely related species.They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone.In the Yellow Sea,a genetically unique floating ecotype of U.prolifera even bloomed to cause serious green tides.However,there is still a lack of appropriate molecular markers to distinguish these two species,partially due to limited evaluations on the intraspecific variations in U.prolifera among dif ferent ecotypes.Since organelle genomes could provide rich genetic resources for phylogenetic analysis and development of genetic markers,in this study,the chloroplast genome from one attached population of U.prolifera was completely sequenced,and comparative genomic analyses were performed with other existing chloroplast genomes from U.linza and the floating ecotype of U.prolifera.The results showed that in spite of the high level of collinearity among three genomes,there were plenty of genetic variations especially within the non-coding regions,including introns and gene spacer regions.A strategy was proposed that only those signals of variation,which were identical between two ecotypes of U.prolifera but divergent between U.linza and U.prolifera,were selected to develop the interspecific markers for U.linza and U.prolifera.Two candidate markers,psa B and pet B,were shown to be able to distinguish these two closely related species and were applicable to more attached populations of U.prolifera from a wide range of geographical sources.In addition to the interspecific marker,this study would also provide resources for the development of intraspecific markers for U.prolifera.These markers might contribute to the surveys for Ulva species composition and green tide monitoring especially in the Yellow Sea region.展开更多
Rice blast caused by <em>Magnaporthe oryzae</em> (<em>M. oryzae</em>) is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To be...Rice blast caused by <em>Magnaporthe oryzae</em> (<em>M. oryzae</em>) is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To better understand genetic variations among different isolates of <em>M. oryzae</em> in the nature field, we re-sequenced and analyzed the genomes of three field isolates, QJ08-2006, QJ10-10, and QJ10-3001, which showed distinct pathogenicity on Xin-Yin-Zhan, an elite variety in South China. Genome annotation indicated that these three isolates assemblies have similar genome sizes with 38.4 Mb, 38.3 Mb, and 38.4 Mb, respectively. The QJ08-2006 assembly has 2082 contigs with an N50 of 127.4 kb, the QJ10-10 assembly has 2239 contigs with an N50 of 105.13 kb, the QJ10-3001 assembly has 2025 contigs with an N50 of 133.16 kb. A total of 10,432 genes including 1408 putative secreted protein genes were identified from the annotated isolate QJ08-2006 genome, 10,418 genes including 1410 putative secreted protein genes were identified in QJ10-10, and 10,401 genes including 1420 putative secreted protein genes were identified in QJ10-3001. There are as many as 11,076 identical genes in these three isolates and contained only a few unique genes among three isolates, of which 277 unique genes in QJ08-2006 and 264 unique genes in QJ10-10, and 213 unique genes in QJ10-3001. Most of the predicted secreted protein genes had been identified, and the three re-sequenced strains contained 371, 369, and 387 small Indel, respectively. <em>Avr </em>genes were analyzed in several sequenced <em>Magnaporthe</em> strains, the results revealed that <em>Avr-Pi9</em> and <em>Avr-Piz-t </em>were present in all the sequenced isolates. The isolates QJ08-2006 contained <em>AvrPib</em>, QJ10-10, and QJ10-3001 had an insertion of a Pot3 element in the promoter of the <em>AvrPib</em> gene. Our results showed that, the rapid dominancy of virulence mutant isolates via clonal propagation displayed in the field after the release of the elite variety Xin-Yin-Zhan.展开更多
Genomics research of Populus deltoides,an important timber species that is widely planted worldwide,is an important part of poplar breeding.Currently,the nuclear and chloroplast genome of P.deltoides have been sequenc...Genomics research of Populus deltoides,an important timber species that is widely planted worldwide,is an important part of poplar breeding.Currently,the nuclear and chloroplast genome of P.deltoides have been sequenced,but its mitochondrial genome(mitogenome)has not been reported.To further explore the evolution and phylogeny of P.deltoides,the mitogenome of P.deltoides I-69 was assembled using reads from Nanopore and Illumina sequencing platforms and found to consist of 802,637 bp and three circular chromosomes(336,205,280,841,and 185,591 bp)containing 58 genes(34 protein-coding genes,21 tRNA genes,and 3 rRNA genes).RNA analysis in combination with several species showed signifi cantly fewer RNA editingsites in the mitogenomes of poplar and other angiosperms than in gymnosperms.Sequence transfer analysis showed extensive mitogenome rearrangements in Populus species,and with evolution from lower to higher plants,tRNA transfer from chloroplasts to mitochondria became increasingly frequent.In a phylogenetic analysis,the evolutionary status of P.deltoides was determined,and the section Populus was supported.Our results based on the fi rst report of a multicircular conformation of the Populus mitogenome provide a basis for further study of the evolution and genetics of P.deltoides and other Populus species and for breeding programs.展开更多
Weeping forsythia (Forsythia suspensa,Oleaceae) is a deciduous broad-leaved tree species distributed in the warm temperate zone of China.However,the species still lacks a chromosome-level genome.In this study,the form...Weeping forsythia (Forsythia suspensa,Oleaceae) is a deciduous broad-leaved tree species distributed in the warm temperate zone of China.However,the species still lacks a chromosome-level genome.In this study,the former draft genome (Accession No.WIPI00000000) of weeping forsythia was assembled into 14 chromosomes with a 712.9 Mb genome size.Weeping forsythia underwent a and b whole-genome duplication events.After the divergence between weeping forsythia and Olea europaea,1 453 gene families had a significant expansion,and 1 146 gene families had a significant contraction.The enrichment pathways and ontologies of expanded genes suggested that the tillering,photosynthesis and growth capacity of weeping forsythia were enhanced after the divergence of weeping forsythia and O.europaea.The contracted genes suggested that the resistance of weeping forsythia to cold and drought was weakened.The last glacial period led to a significant decline in the effective population size of weeping forsythia.Forty-six candidate genes were identified for the synthesis of the forsythin and forsythoside A by genomic and transcriptomic data.In this study,we improved the previous draft genome of weeping forsythia.Our genome will provide genomic resources for the subsequent evolution and breeding research of weeping forsythia.展开更多
The Triticum-Aegilops complex provides ideal models for the study of polyploidization,and mitochondrial genomes(mtDNA)can be used to trace cytoplasmic inheritance and energy production following polyploidization.In th...The Triticum-Aegilops complex provides ideal models for the study of polyploidization,and mitochondrial genomes(mtDNA)can be used to trace cytoplasmic inheritance and energy production following polyploidization.In this study,gapless mitochondrial genomes for 19 accessions of five Triticum or Aegilops species were assembled.Comparative genomics confirmed that the BB-genome progenitor donated mtDNA to tetraploid T.turgidum(genome formula AABB),and that this mtDNA was then passed on to the hexaploid T.aestivum(AABBDD).T urartu(AA)was the paternal parent of T.timopheevii(AAGG),and an earlier Ae.tauschii(DD)was the maternal parent of Ae.cylindrica(CCDD).Genic sequences were highly conserved within species,but frequent rearrangements and nuclear or chloroplast DNA insertions occurred during speciation.Four highly variable mitochondrial genes(atp6,cob,nad6,and nad9)were established as marker genes for Triticum and Aegilops species identification.The BB/GG-specific atp6 and cob genes,which were imported from the nuclear genome,could facilitate identification of their diploid progenitors.Genic haplotypes and repeat-sequence patterns indicated that BB was much closer to GG than to Ae.speltoides(SS).These findings provide novel insights into the polyploid evolution of the Triticum/Aegilops complex from the perspective of mtDNA,advancing understanding of energy supply and adaptation in wheat species。展开更多
The high intraspecies heterogeneity of Baciillus coagulans leads to significant phenotypic differences among different strains.Thus,6 B.coagulans strains were tested in the present study using an irritable bowel syndr...The high intraspecies heterogeneity of Baciillus coagulans leads to significant phenotypic differences among different strains.Thus,6 B.coagulans strains were tested in the present study using an irritable bowel syndrome(IBS)animal model to determine whether the IBS-alleviating effects of B.coagulans strains are strain-specific.The results of this study showed that the ingestion of B.coagulans GBI-30,6086,and B.coagulans CCFM1041 significantly alleviated IBS symptoms in mice.In contrast,other B.coagulans strains showed no or limited alleviating effects on IBS symptoms.According to our experimental results,the two main common features of these strains were as follows:1)The resistance of vegetative cells to bile salts,and 2)ability to synthesize specific lipids and secondary metabolites.Screening strains based on these two indicators may greatly reduce costs and provide a basis for mining new functional B.coagulans strains.Our results also suggest that administration of B.coagulans could significantly regulate microbiota dysbiosis in animal models.Moreover,the close relationships between the gut microbiota,gut microbiota metabolites,and IBS were further confirmed in this study.展开更多
Cobetia marina is a model proteobacteria in researches on marine biofouling. Its taxonomic nomenclature has been revised many times over the past few decades. ~To better understand the role of the surface-associated l...Cobetia marina is a model proteobacteria in researches on marine biofouling. Its taxonomic nomenclature has been revised many times over the past few decades. ~To better understand the role of the surface-associated lifestyle of C. marina and the phylogeny of the family Halomonadaceae, we sequenced the entire genome of C. marina JCM 21022 ~T using single molecule real-time sequencing technology(SMR^T) and performed comparative genomics and phylogenomics analyses. ~The circular chromosome was 4 176 300 bp with an average GC content of 62.44% and contained 3 611 predicted coding sequences, 72 t RNA genes, and 21 r RNA genes. ~The C. marina JCM 21022 ~T genome contained a set of crucial genes involved in surface colonization processes. ~The comparative genome analysis indicated the significant diff erences between C. marina JCM 21022 ~T and Cobetia amphilecti KMM 296(formerly named C. marina KMM 296) resulted from sequence insertions or deletions and chromosomal recombination. Despite these diff erences, pan and core genome analysis showed similar gene functions between the two strains. ~The phylogenomic study of the family Halomonadaceae is reported here for the first time. We found that the relationships were well resolved among every genera tested, including Chromohalobacter, Halomonas, Cobetia, Kushneria, Zymobacter, and Halotalea.展开更多
Emerging evidence shows that some Lactobacillus fermentum(L.fermentum)strains can contribute to the prevention and treatment of ulcerative colitis(UC).In this study,105 isolates of L.fermentum strains were separated f...Emerging evidence shows that some Lactobacillus fermentum(L.fermentum)strains can contribute to the prevention and treatment of ulcerative colitis(UC).In this study,105 isolates of L.fermentum strains were separated from fecal samples of populations in different regions in China and their draft genomes were sequenced.Pan-genomic and phylogenetic characterizations of these strains and four model strains(L.fermentum 3872,CECT5716,IF03956,and VRI003)were performed.Phylogenetic analysis ind icated that there was no significant adaptive evolution between the genomes of L.fermentum strains and the geographical location,sex,ethnicity,and age of the hosts.Three L.fermentum strains(FWXBH115,FGDLZR121,and FXJCJ61)from different branches of the phylogenetic tree and strain type L.fermentum CECT5716 were selected and their anti-inflammatory and immune modulatory activities in a dextran sulphate sodium(DSS)-induced colitis mouse model were further investigated.Both L.fermentum FXJCJ61 and CECT5716 significantly alleviated UC by reducing all colitis-associated histological indices,maintaining mucosal integrity,and stimulating replenishment of short-chain fatty acids(SCFAs),while the other two strains failed to offer similar protection.The anti-inflammato ry mechanisms of L.fermentum FXJCJ61 and CECT5716 were related to the inhibition of nuclear factor kappa-B(NF-κB)signaling pathway activation and enhancement of interleukin 10(IL-10)production.Comparative genomic analysis of these strains identified candidate genes that may contribute to the anti-inflammatory effects of specific L.fermentum strains.展开更多
Objective To investigate the relationship between genomic DNA imbalance in oligodendroglial tumors and its different classification. Methods 16 oligodendrogliomas and 17 anaplastic oligodendrogliomas were investigated...Objective To investigate the relationship between genomic DNA imbalance in oligodendroglial tumors and its different classification. Methods 16 oligodendrogliomas and 17 anaplastic oligodendrogliomas were investigated by comparative genomic hybridization on Paraffin-Embedded tissue samples,and the chromosomal genomic DNA imbalances were analyzed. Results Chromosome DNA imbalance rates in oligodendrogliomas展开更多
Objective Campylobacter jejuni NCTC11168 is commonly used as a standard strain for flagellar biosynthesis research.In this report,two distinguished phenotypic isolates(CJ1Z,flhA mutant strain,lawn;CJ2S,flhA complement...Objective Campylobacter jejuni NCTC11168 is commonly used as a standard strain for flagellar biosynthesis research.In this report,two distinguished phenotypic isolates(CJ1Z,flhA mutant strain,lawn;CJ2S,flhA complemented strain,normal colony)appeared during laboratory passages for NCTC11168.Methods Phenotypic assessments,including motility plates,transmission electron microscopy,biofilm formation assay,autoagglutination assay,and genome re-sequencing for these two isolates(CJ1Z,flhA mutant strain;CJ2S,flhA complemented strain)were carried out in this study.Results Transmission electron microscopy revealed that the flagellum was lost in CJ1Z.Phenotypic assessments and genome sequencing of the two isolates were performed in this study.The capacity for biofilm formation,colony auto-agglutination,and isolate motility was reduced in the mutant CJ1Z.Comparative genomic analysis indicated a unique native nucleotide insertion in flhA(nt,2154)that caused the I719Y and I720Y mutations and early truncation in flhA.Conclusion FlhA has been found to influence the expression of flagella in C.jejuni.To the best of our knowledge,this is the first study to describe the function of the C-terminal of this protein.展开更多
Akkermansia muciniphila, one of the most promising next-generation probiotics, was reported to exhibit beneficial modulatory effects on the gut barrier. However, the strain-specific and underlying regulatory mechanism...Akkermansia muciniphila, one of the most promising next-generation probiotics, was reported to exhibit beneficial modulatory effects on the gut barrier. However, the strain-specific and underlying regulatory mechanisms of this species on gut barrier function were not well studied. Therefore, this study evaluated the protective effect of A. muciniphila strains on the intestinal barrier and investigated the mode of action and material basis of this modulatory effect. We first confirmed the strain-specific effects of A. muciniphila on intestinal barrier regulation and found that this phenomenon may be explained by the different abilities of strains to affect tight junction protein expression in enterocytes. Comparative genomic analysis proved that the ability of A. muciniphila to regulate the intestinal barrier was exerted in part by the functional genes(such as COG0438, COG0463, and COG2244)related to the synthesis of cellular surface proteins. The role of these surface proteins in intestinal barrier regulation was further verified by strain-comparative experiments in animal and cell models and surface protein removal trials. This study confirmed the different effects of A. muciniphila strains on gut barrier modulation and provided molecular and genetic targets for the screening of A. muciniphila strains with superior protection against gut barrier dysfunction.展开更多
BACKGROUND Chromosomal Xq28 region duplication encompassing methyl-CpG-binding protein 2(MECP2)results in an identifiable phenotype and global developmental delay known as MECP2 duplication syndrome(MDS).This syndrome...BACKGROUND Chromosomal Xq28 region duplication encompassing methyl-CpG-binding protein 2(MECP2)results in an identifiable phenotype and global developmental delay known as MECP2 duplication syndrome(MDS).This syndrome has a wide range of clinical manifestations,including abnormalities in appearance,neurodevelopment,and gastrointestinal motility;recurrent infections;and spasticity.Here,we report a case of confirmed MDS at our institution.CASE SUMMARY A 12-year-old Chinese boy presented with intellectual disability(poor intellectual[reasoning,judgment,abstract thinking,and learning]and adaptive[lack of communication and absent social skills,apraxia,and ataxia]functioning)and dysmorphism.He had no history of recurrent infections,seizures,or bowel dysfunction,which is different from that in reported cases.Microarray comparative genomic hybridization confirmed MECP2 duplication in the patient and his mother who is a carrier.The duplication size was the same in the patient and his mother.No prophylactic antibiotic or anti-seizure therapy was offered to the patient or his mother before or after the consultation.CONCLUSION MDS is rare and has various clinical presentations.Clinical suspicion is critical in patients presenting with developmental delays.展开更多
Diaphorina citri is a global citrus pest.As a vector insect,it can transmit the causative agents of citrus huanglongbing,causing irreversible losses to the citrus industry.The acquisition of genomic information can pr...Diaphorina citri is a global citrus pest.As a vector insect,it can transmit the causative agents of citrus huanglongbing,causing irreversible losses to the citrus industry.The acquisition of genomic information can provide a molecular genetic basis for effective control of D.citri.Here,the DNBSEQ™,Oxford Nanopore Technologies,and Hi-C technologies are applied to generate a high-quality chromosome-level genome of D.citri.The genome size of D.citri was 523.78 Mb with a scaffold N50 of 47.05 Mb distributed on 13 chromosomes.A total of 250.64 Mb(47.85%)repeat sequences and 24048 protein-coding genes were predicted.Genome resequencing of female and male individuals indicated that the sex chromosome system of D.citri is XO.Phylogenetic analysis demonstrated that D.citri and Pachypsylla venusta,which separated from their most recent common ancestor about 336.62 million years ago,were the most closely related.Additionally,we identified genes potentially involved in detoxification metabolism,pathogen transmission,and honeydew secretion for further investigation.The high-quality genome provides an important reference for developing effective management strategies of D.citri.展开更多
The Tibetan Partridge(Perdix hodgsoniae)is an endemic species distributed in high-altitude areas of 3600–5600 m on the Qinghai–Tibet Plateau.To explore how the species is adapted to the high elevation environment,we...The Tibetan Partridge(Perdix hodgsoniae)is an endemic species distributed in high-altitude areas of 3600–5600 m on the Qinghai–Tibet Plateau.To explore how the species is adapted to the high elevation environment,we as-sembled a draft genome based on both the Illumina and PacBio sequencing platforms with its population genetics and genomics analysis.In total,134.74 Gb short reads and 30.81 Gb long reads raw data were generated.The 1.05-Gb assembled genome had a contig N50 of 4.56 Mb,with 91.94%complete BUSCOs.The 17457 genes were annotated,and 11.35%of the genome was composed of repeat sequences.The phylogenetic tree showed that P.hodgsoniae was located at the basal position of the clade,including Golden Pheasant(Chrysolophus pictus),Common Pheasant(Phasianus colchicus),and Mikado Pheasant(Syrmaticus mikado).We found that 1014,2595,and 2732 of the 6641 one-to-one orthologous genes were under positive selection in P.hodgsoniae,detected using PAML,BUSTED,and aBSREL programs,respectively,of which 965 genes were common under positive selec-tion with 3 different programs.Several positively selected genes and immunity pathways relevant to high-altitude adaptation were detected.Gene family evolution showed that 99 gene families experienced significant expansion events,while 6 gene families were under contraction.The total number of olfactory receptor genes was relatively low in P.hodgsoniae.Genomic data provide an important resource for a further study on the evolutionary history of P.hodgsoniae,which provides a new insight into its high-altitude adaptation mechanisms.展开更多
Common wheat(Triticum aestivum) is a hexaploid plant(AABBDD) derived from genetically related tetraploid wheat T. turgidum(AABB) and a diploid goatgrass Aegilops tauschii(DD). Recent advances in sequencing technology ...Common wheat(Triticum aestivum) is a hexaploid plant(AABBDD) derived from genetically related tetraploid wheat T. turgidum(AABB) and a diploid goatgrass Aegilops tauschii(DD). Recent advances in sequencing technology and genome assembly strategies allow the acquisition of multiple wheat genomes, calling for a centralized database to store, manage and query the genomics information in a manner to reflect their evolutionary relationship and to perform effective comparative genome analysis. Here,we built WheatGene, a database that contains five wheat genomes of 318,102 genes and 945,900 transcripts and their expression information in 998 RNA-seq samples that can be searched and compared in an interactive manner. WheatGene was developed with Drupal, a popular content management system and the toolkit Tripal managed the biological information. The database was accessible through a web browser with species, search, gene expression, tools, and literature entries. Tools available were BLAST,synteny viewer, map viewer, JBrowse, data downloads, gene expression heatmap and bar chart, and homologs viewer. Moreover, the map viewer connected genomics data with genetic maps and QTL that can be searched for markers for molecular breeding. WheatGene was developed with open-source modules and libraries. WheatGene is available at http://wheatgene.agrinome.org.展开更多
Magnetotactic bacteria(MTB)display magnetotaxis ability because of biomineralization of intracellular nanometer-sized,membrane-bound organelles termed magnetosomes.Despite having been discovered more than half a centu...Magnetotactic bacteria(MTB)display magnetotaxis ability because of biomineralization of intracellular nanometer-sized,membrane-bound organelles termed magnetosomes.Despite having been discovered more than half a century,only a few representatives of MTB have been isolated and cultured in the laboratory.In this study,we report the genomic characterization of a novel marine magnetotactic spirillum strain SH-1 belonging to the genus Terasakiella that was recently isolated.A gene encoding haloalkane dehalogenase,which is involved in the degradation of chlorocyclohexane,chlorobenzene,chloroalkane,and chloroalkene,was identified.SH-1 genome contained cysCHI and soxBAZYX genes,thus potentially capable of assimilatory sulfate reduction to H_(2)S and using thiosulfate as electron donors and oxidizing it to sulfate.Genome of SH-1 also contained genes encoding periplasmic dissimilatory nitrate reductases(napAB),assimilatory nitrate reductase(nasA)and assimilatory nitrite reductases(nasB),suggesting that it is capable of gaining energy by converting nitrate to ammonia.The pure culture of Terasakiella sp.SH-1 together with its genomic results off ers new opportunities to examine biology,physiology,and biomineralization mechanisms of MTB.展开更多
Objective: To detect genetic alterations in nasopharyngeal carcinoma (NPC) in Cantonese, the population with the highest incidence of NPC, and to correlate the findings with clinical staging. Methods: Comparative geno...Objective: To detect genetic alterations in nasopharyngeal carcinoma (NPC) in Cantonese, the population with the highest incidence of NPC, and to correlate the findings with clinical staging. Methods: Comparative genomic hybridization (CGH) was performed on 35 primary nasopharyngeal carcinomas and a nonparametric χ2 test was used to analyze relationship between chromosome changes and clinical staging. Results: The identified common chromosomal alterations in NPC included gain of chromosomes 12q (21 cases, 60%), 4q (19cases, 43%), 3q (18 cases, 51%), 1q (15 cases, 43%),8q (14 cases, 40%), and 2q (12 cases, 30%). The most frequently detected loss of chromosomal materials involved chromosome 1p (24 cases, 69%), chromosome 3p (21 cases, 60%), 11q (20 cases, 57%), 14q (18 cases, 51%), 16q (14 cases, 40%), 13(12 cases, 34%), and 9p(11 cases, 31%). The high frequency (>50%) 4q gain and 1p loss were novel findings. Compared by nonparametric χ2 test, gains on 12q and 8q were found mainly in stages Ⅲ/Ⅳ and there were significant differences between two clinical stage groups ( stagesⅠ/Ⅱvs stages Ⅲ/Ⅳ). Conclusions: Current analysis has revealed a comprehensive profile of the chromosomal regions showing DNA copy number changes, which may harbor oncogenes or tumor suppressor genes involved in the development of primary NPC.展开更多
基金supported by grants from the Natural Science Foundation of Anhui Province(grant number 2208085MH253)the National Natural Science Foundation(grant number 81702560)the Fundamental Research Funds for the Central Universities(grant number WK9110000110),People's Republic of China.
文摘Lactobacillus crispatus is a commonly found species in the urogenital tract(UGT)of healthy females and can also colonize other niches,such as the gastrointestinal tract(GIT).Although its potential protective role in cervical cancer has been reported,the anticancer mechanisms involved are still unclear.In this study,we sequenced and characterized the complete genomes of two L.crispatus strains(Lc31 and Lc83)isolated from the UGT of healthy women of reproductive age.Phylogenetic and phylogenomic analyses of these two strains and 15 other L.crispatus strains with complete genome sequences revealed that strains from the UGT and GIT clustered separately.UGT strains had a larger genome size,higher GC contents,and more protein-coding sequences and insertion sequence(Is)elements,indicating the likelihood of active horizontal gene transfer in this niche.We found a universal presence of genes encoding bacteriocins and the absence of virulence factors and antibiotic resistance genes in UGT strains,suggesting the potential of L.crispatus as a urogenital probiotic.Comparative genomic analysis identified an ula gene cluster responsible for L-ascorbate catabolism exclusively in UGT strains,and carbohydrate fermentation experiments confirmed that this substrate supported the growth of L.crispatus Lc31 and Lc83.Our findings improve the understanding of how the genome determines niche adaptation by L.crispatus,providing a foundation for investigating the mechanisms by which urogenital-derived L.crispatus promotes female health.
基金the Science and Technology Project of Changsha City(No.kq2004038)Program for Innovative Leading Talents for Science and Technology of Xianyang City。
文摘Lonicerae Flos(LF)derived from the dried flower buds or opening flowers of four Lonicera plants(Lonicera macranthoides,L.hypoglauca,L.confusa,and L.fulvotnetosa),is a popular traditional Chinese medicine.Because the four origin plants are very similar in morphology,it is difficult to control the quality of LF in actual production.Over the past decade,many reports have pointed out the differences among them,including the botanical characteristics and active ingredients.However,there is still a lack of rapid methods that can be applied to the identification of the four origins.In this study,comparative analysis of the four chloroplast genomes was performed,and they showed low diversity(Pi=0.00267),three variation hotspots regions(rbcL-accD,rps12-ndhF and rps12-trnN-trnG)were identified as potentially molecular marker of highly informative.Meanwhile,the most obvious difference in SSR comparative analysis is reverse and complement repeats were only identified in L.confusa and L.hypoglauca,respectively.Lastly,the phylogenetic tree showed that L.confusa is more closely related to L.fulvotnetosa,while L.macranthoides is closer to L.hypoglauca.This study systematically revealed the differences among the four chloroplast genomes,and it provides valuable genetic information for identifying the origin of LF.
基金Supported by the Science&Technology Basic Resources Investigation Program of China(No.2018FY100205)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA23050302)+2 种基金the National Key R&D Program of China(No.2018YFD0901500)the National Natural Science Foundation of China(No.41776153)the Key R&D Program of Shandong Province(No.2019GSF107012)。
文摘The green seaweeds Ulva linza and U.prolifera are closely related species.They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone.In the Yellow Sea,a genetically unique floating ecotype of U.prolifera even bloomed to cause serious green tides.However,there is still a lack of appropriate molecular markers to distinguish these two species,partially due to limited evaluations on the intraspecific variations in U.prolifera among dif ferent ecotypes.Since organelle genomes could provide rich genetic resources for phylogenetic analysis and development of genetic markers,in this study,the chloroplast genome from one attached population of U.prolifera was completely sequenced,and comparative genomic analyses were performed with other existing chloroplast genomes from U.linza and the floating ecotype of U.prolifera.The results showed that in spite of the high level of collinearity among three genomes,there were plenty of genetic variations especially within the non-coding regions,including introns and gene spacer regions.A strategy was proposed that only those signals of variation,which were identical between two ecotypes of U.prolifera but divergent between U.linza and U.prolifera,were selected to develop the interspecific markers for U.linza and U.prolifera.Two candidate markers,psa B and pet B,were shown to be able to distinguish these two closely related species and were applicable to more attached populations of U.prolifera from a wide range of geographical sources.In addition to the interspecific marker,this study would also provide resources for the development of intraspecific markers for U.prolifera.These markers might contribute to the surveys for Ulva species composition and green tide monitoring especially in the Yellow Sea region.
文摘Rice blast caused by <em>Magnaporthe oryzae</em> (<em>M. oryzae</em>) is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To better understand genetic variations among different isolates of <em>M. oryzae</em> in the nature field, we re-sequenced and analyzed the genomes of three field isolates, QJ08-2006, QJ10-10, and QJ10-3001, which showed distinct pathogenicity on Xin-Yin-Zhan, an elite variety in South China. Genome annotation indicated that these three isolates assemblies have similar genome sizes with 38.4 Mb, 38.3 Mb, and 38.4 Mb, respectively. The QJ08-2006 assembly has 2082 contigs with an N50 of 127.4 kb, the QJ10-10 assembly has 2239 contigs with an N50 of 105.13 kb, the QJ10-3001 assembly has 2025 contigs with an N50 of 133.16 kb. A total of 10,432 genes including 1408 putative secreted protein genes were identified from the annotated isolate QJ08-2006 genome, 10,418 genes including 1410 putative secreted protein genes were identified in QJ10-10, and 10,401 genes including 1420 putative secreted protein genes were identified in QJ10-3001. There are as many as 11,076 identical genes in these three isolates and contained only a few unique genes among three isolates, of which 277 unique genes in QJ08-2006 and 264 unique genes in QJ10-10, and 213 unique genes in QJ10-3001. Most of the predicted secreted protein genes had been identified, and the three re-sequenced strains contained 371, 369, and 387 small Indel, respectively. <em>Avr </em>genes were analyzed in several sequenced <em>Magnaporthe</em> strains, the results revealed that <em>Avr-Pi9</em> and <em>Avr-Piz-t </em>were present in all the sequenced isolates. The isolates QJ08-2006 contained <em>AvrPib</em>, QJ10-10, and QJ10-3001 had an insertion of a Pot3 element in the promoter of the <em>AvrPib</em> gene. Our results showed that, the rapid dominancy of virulence mutant isolates via clonal propagation displayed in the field after the release of the elite variety Xin-Yin-Zhan.
基金funded by the National Key Research and Development Program of China[Grant Number 2021YFD2201205]the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD).
文摘Genomics research of Populus deltoides,an important timber species that is widely planted worldwide,is an important part of poplar breeding.Currently,the nuclear and chloroplast genome of P.deltoides have been sequenced,but its mitochondrial genome(mitogenome)has not been reported.To further explore the evolution and phylogeny of P.deltoides,the mitogenome of P.deltoides I-69 was assembled using reads from Nanopore and Illumina sequencing platforms and found to consist of 802,637 bp and three circular chromosomes(336,205,280,841,and 185,591 bp)containing 58 genes(34 protein-coding genes,21 tRNA genes,and 3 rRNA genes).RNA analysis in combination with several species showed signifi cantly fewer RNA editingsites in the mitogenomes of poplar and other angiosperms than in gymnosperms.Sequence transfer analysis showed extensive mitogenome rearrangements in Populus species,and with evolution from lower to higher plants,tRNA transfer from chloroplasts to mitochondria became increasingly frequent.In a phylogenetic analysis,the evolutionary status of P.deltoides was determined,and the section Populus was supported.Our results based on the fi rst report of a multicircular conformation of the Populus mitogenome provide a basis for further study of the evolution and genetics of P.deltoides and other Populus species and for breeding programs.
基金supported by the Open Fund of State Key Laboratory of Tree Genetics and Breeding (Chinese Academy of Forestry)(Grant No.TGB2021004)National Natural Science Foundation of China (Grant Nos.31770225,31570594)Program of Guangzhou Municipal Science and Technology Bureau(Grant No.202102021257)。
文摘Weeping forsythia (Forsythia suspensa,Oleaceae) is a deciduous broad-leaved tree species distributed in the warm temperate zone of China.However,the species still lacks a chromosome-level genome.In this study,the former draft genome (Accession No.WIPI00000000) of weeping forsythia was assembled into 14 chromosomes with a 712.9 Mb genome size.Weeping forsythia underwent a and b whole-genome duplication events.After the divergence between weeping forsythia and Olea europaea,1 453 gene families had a significant expansion,and 1 146 gene families had a significant contraction.The enrichment pathways and ontologies of expanded genes suggested that the tillering,photosynthesis and growth capacity of weeping forsythia were enhanced after the divergence of weeping forsythia and O.europaea.The contracted genes suggested that the resistance of weeping forsythia to cold and drought was weakened.The last glacial period led to a significant decline in the effective population size of weeping forsythia.Forty-six candidate genes were identified for the synthesis of the forsythin and forsythoside A by genomic and transcriptomic data.In this study,we improved the previous draft genome of weeping forsythia.Our genome will provide genomic resources for the subsequent evolution and breeding research of weeping forsythia.
文摘The Triticum-Aegilops complex provides ideal models for the study of polyploidization,and mitochondrial genomes(mtDNA)can be used to trace cytoplasmic inheritance and energy production following polyploidization.In this study,gapless mitochondrial genomes for 19 accessions of five Triticum or Aegilops species were assembled.Comparative genomics confirmed that the BB-genome progenitor donated mtDNA to tetraploid T.turgidum(genome formula AABB),and that this mtDNA was then passed on to the hexaploid T.aestivum(AABBDD).T urartu(AA)was the paternal parent of T.timopheevii(AAGG),and an earlier Ae.tauschii(DD)was the maternal parent of Ae.cylindrica(CCDD).Genic sequences were highly conserved within species,but frequent rearrangements and nuclear or chloroplast DNA insertions occurred during speciation.Four highly variable mitochondrial genes(atp6,cob,nad6,and nad9)were established as marker genes for Triticum and Aegilops species identification.The BB/GG-specific atp6 and cob genes,which were imported from the nuclear genome,could facilitate identification of their diploid progenitors.Genic haplotypes and repeat-sequence patterns indicated that BB was much closer to GG than to Ae.speltoides(SS).These findings provide novel insights into the polyploid evolution of the Triticum/Aegilops complex from the perspective of mtDNA,advancing understanding of energy supply and adaptation in wheat species。
基金supported by the Natural Science Foundation of Jiangsu Province(BK20200084)the National Natural Science Foundation of China(31871773 and 31820103010)+1 种基金the Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province and Key Talents Project of“Strengthening Health through Science and Education”of Wuxi Health and Family Planning Commission(ZDRC039)Top Talents Project of“Six-one Project”for High-level Health Talents in Jiangsu Province(LGY2018016)。
文摘The high intraspecies heterogeneity of Baciillus coagulans leads to significant phenotypic differences among different strains.Thus,6 B.coagulans strains were tested in the present study using an irritable bowel syndrome(IBS)animal model to determine whether the IBS-alleviating effects of B.coagulans strains are strain-specific.The results of this study showed that the ingestion of B.coagulans GBI-30,6086,and B.coagulans CCFM1041 significantly alleviated IBS symptoms in mice.In contrast,other B.coagulans strains showed no or limited alleviating effects on IBS symptoms.According to our experimental results,the two main common features of these strains were as follows:1)The resistance of vegetative cells to bile salts,and 2)ability to synthesize specific lipids and secondary metabolites.Screening strains based on these two indicators may greatly reduce costs and provide a basis for mining new functional B.coagulans strains.Our results also suggest that administration of B.coagulans could significantly regulate microbiota dysbiosis in animal models.Moreover,the close relationships between the gut microbiota,gut microbiota metabolites,and IBS were further confirmed in this study.
基金funded by Natural Science Foundation of Zhejiang(LQ14C010006)National Natural Science Foundation of China(81501363)Planned Science and Technology Project of Zhejiang(2014C33261)
文摘在现在的学习,完全的染色体四普通(4/EV71/Wenzhou/CHN/2014, 15/EV71/Wenzhou/CHN/2014, 116/EV71/Wenzhou/CHN/2014,和 120/EV71/Wenzhou/CHN/2014 ) 并且二剧毒(11/EV71/Wenzhou/CHN/2014 和 109/EV71/Wenzhou/CHN/2014 ) enterovirus (EV71 ) 71 孤立被定序并且描述。他们是在长度的 7405 bp 并且属于 EV71 亚遗传型 C4 (C4a 簇) 。核苷酸顺序排列揭示了六个核苷酸变化( G <sup > P151 </sup > T <sup > P151 </sup>, G <sup > P199 </sup > <sup > P199 </sup>, G <sup > P261 </sup > T <sup > P261 </sup>, A <sup > P328 </sup > C <sup > P328 </sup>, G <sup > P422 </sup > <sup > P422 </sup>,和 G <sup > P437 </sup > T <sup > P437 </sup>)在二剧毒在 IRES 元素的 5UTR 以内孤立。怒火和 FCE 的 RNA 第二等的结构预言显示普通孤立分享的类似的结构,它与那些不同剧毒孤立。而且, G <sup > P114 </sup > C <sup > P114 </sup> 和 G <sup > P151 </sup > T <sup > P151 </sup> 变化在剧毒孤立在 SL II 贡献了唯一的 RNA 第二等的结构的形成。而且, EV71 孤立的 82 的 nucleotide/amino 酸顺序排列显示了那六个地点(T <sup > P488 </sup> 和 C <sup > 在 5UTR 的 P577 </sup> ;Asn <sup > 在 2A 的 P57 </sup> ;Ile <sup > 在 3C 的 P56 </sup> ;C <sup > P10 </sup> 和 A <sup > 在 3UTR 的 P47 </sup>) 潜在地与 EV71 的 neurovirulence 被联系。最后, 2A 的 3D 结构是类似的,而 VP1 和 3C 的结构是可变的。
基金Supported by the National Natural Science Foundation of China(Nos.41006082,31372517)
文摘Cobetia marina is a model proteobacteria in researches on marine biofouling. Its taxonomic nomenclature has been revised many times over the past few decades. ~To better understand the role of the surface-associated lifestyle of C. marina and the phylogeny of the family Halomonadaceae, we sequenced the entire genome of C. marina JCM 21022 ~T using single molecule real-time sequencing technology(SMR^T) and performed comparative genomics and phylogenomics analyses. ~The circular chromosome was 4 176 300 bp with an average GC content of 62.44% and contained 3 611 predicted coding sequences, 72 t RNA genes, and 21 r RNA genes. ~The C. marina JCM 21022 ~T genome contained a set of crucial genes involved in surface colonization processes. ~The comparative genome analysis indicated the significant diff erences between C. marina JCM 21022 ~T and Cobetia amphilecti KMM 296(formerly named C. marina KMM 296) resulted from sequence insertions or deletions and chromosomal recombination. Despite these diff erences, pan and core genome analysis showed similar gene functions between the two strains. ~The phylogenomic study of the family Halomonadaceae is reported here for the first time. We found that the relationships were well resolved among every genera tested, including Chromohalobacter, Halomonas, Cobetia, Kushneria, Zymobacter, and Halotalea.
基金supported by the National Natural Science Foundation of China(31820103010,31530056,and 31871773)National Key Research and Development Project(2018YFC1604206)+3 种基金Projects of Innovation and Development Pillar Program for Key Industries in Southern Xinjiang of Xinjiang Production and Construction Corps(2018DB002)National FirstClass Discipline Program of Food Science and Technology(JUFSTR20180102)BBSRC Newton Fund Joint Centre Award(BB/J004529/1)Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province。
文摘Emerging evidence shows that some Lactobacillus fermentum(L.fermentum)strains can contribute to the prevention and treatment of ulcerative colitis(UC).In this study,105 isolates of L.fermentum strains were separated from fecal samples of populations in different regions in China and their draft genomes were sequenced.Pan-genomic and phylogenetic characterizations of these strains and four model strains(L.fermentum 3872,CECT5716,IF03956,and VRI003)were performed.Phylogenetic analysis ind icated that there was no significant adaptive evolution between the genomes of L.fermentum strains and the geographical location,sex,ethnicity,and age of the hosts.Three L.fermentum strains(FWXBH115,FGDLZR121,and FXJCJ61)from different branches of the phylogenetic tree and strain type L.fermentum CECT5716 were selected and their anti-inflammatory and immune modulatory activities in a dextran sulphate sodium(DSS)-induced colitis mouse model were further investigated.Both L.fermentum FXJCJ61 and CECT5716 significantly alleviated UC by reducing all colitis-associated histological indices,maintaining mucosal integrity,and stimulating replenishment of short-chain fatty acids(SCFAs),while the other two strains failed to offer similar protection.The anti-inflammato ry mechanisms of L.fermentum FXJCJ61 and CECT5716 were related to the inhibition of nuclear factor kappa-B(NF-κB)signaling pathway activation and enhancement of interleukin 10(IL-10)production.Comparative genomic analysis of these strains identified candidate genes that may contribute to the anti-inflammatory effects of specific L.fermentum strains.
文摘Objective To investigate the relationship between genomic DNA imbalance in oligodendroglial tumors and its different classification. Methods 16 oligodendrogliomas and 17 anaplastic oligodendrogliomas were investigated by comparative genomic hybridization on Paraffin-Embedded tissue samples,and the chromosomal genomic DNA imbalances were analyzed. Results Chromosome DNA imbalance rates in oligodendrogliomas
基金supported by the National Key Research and Development Program of China[2021YFC2301000]the Project for Novel Detection Techniques of Bacterial Pathogens[32073]+1 种基金Enhancement of Comprehensive Monitoring,Prevention,and Control Capabilities for Traditional Infectious Diseases Such as Plague,Cholera,and Brucellosis[102393230020020000002]Prevention and Intervention of Bacterial and Fungal Infectious Diseases[102393220020020000031]。
文摘Objective Campylobacter jejuni NCTC11168 is commonly used as a standard strain for flagellar biosynthesis research.In this report,two distinguished phenotypic isolates(CJ1Z,flhA mutant strain,lawn;CJ2S,flhA complemented strain,normal colony)appeared during laboratory passages for NCTC11168.Methods Phenotypic assessments,including motility plates,transmission electron microscopy,biofilm formation assay,autoagglutination assay,and genome re-sequencing for these two isolates(CJ1Z,flhA mutant strain;CJ2S,flhA complemented strain)were carried out in this study.Results Transmission electron microscopy revealed that the flagellum was lost in CJ1Z.Phenotypic assessments and genome sequencing of the two isolates were performed in this study.The capacity for biofilm formation,colony auto-agglutination,and isolate motility was reduced in the mutant CJ1Z.Comparative genomic analysis indicated a unique native nucleotide insertion in flhA(nt,2154)that caused the I719Y and I720Y mutations and early truncation in flhA.Conclusion FlhA has been found to influence the expression of flagella in C.jejuni.To the best of our knowledge,this is the first study to describe the function of the C-terminal of this protein.
基金supported by the Natural Science Foundation of Jiangsu Province (BK20200084)The National Natural Science Foundation of China (32021005 and 31871773)Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province。
文摘Akkermansia muciniphila, one of the most promising next-generation probiotics, was reported to exhibit beneficial modulatory effects on the gut barrier. However, the strain-specific and underlying regulatory mechanisms of this species on gut barrier function were not well studied. Therefore, this study evaluated the protective effect of A. muciniphila strains on the intestinal barrier and investigated the mode of action and material basis of this modulatory effect. We first confirmed the strain-specific effects of A. muciniphila on intestinal barrier regulation and found that this phenomenon may be explained by the different abilities of strains to affect tight junction protein expression in enterocytes. Comparative genomic analysis proved that the ability of A. muciniphila to regulate the intestinal barrier was exerted in part by the functional genes(such as COG0438, COG0463, and COG2244)related to the synthesis of cellular surface proteins. The role of these surface proteins in intestinal barrier regulation was further verified by strain-comparative experiments in animal and cell models and surface protein removal trials. This study confirmed the different effects of A. muciniphila strains on gut barrier modulation and provided molecular and genetic targets for the screening of A. muciniphila strains with superior protection against gut barrier dysfunction.
文摘BACKGROUND Chromosomal Xq28 region duplication encompassing methyl-CpG-binding protein 2(MECP2)results in an identifiable phenotype and global developmental delay known as MECP2 duplication syndrome(MDS).This syndrome has a wide range of clinical manifestations,including abnormalities in appearance,neurodevelopment,and gastrointestinal motility;recurrent infections;and spasticity.Here,we report a case of confirmed MDS at our institution.CASE SUMMARY A 12-year-old Chinese boy presented with intellectual disability(poor intellectual[reasoning,judgment,abstract thinking,and learning]and adaptive[lack of communication and absent social skills,apraxia,and ataxia]functioning)and dysmorphism.He had no history of recurrent infections,seizures,or bowel dysfunction,which is different from that in reported cases.Microarray comparative genomic hybridization confirmed MECP2 duplication in the patient and his mother who is a carrier.The duplication size was the same in the patient and his mother.No prophylactic antibiotic or anti-seizure therapy was offered to the patient or his mother before or after the consultation.CONCLUSION MDS is rare and has various clinical presentations.Clinical suspicion is critical in patients presenting with developmental delays.
文摘Diaphorina citri is a global citrus pest.As a vector insect,it can transmit the causative agents of citrus huanglongbing,causing irreversible losses to the citrus industry.The acquisition of genomic information can provide a molecular genetic basis for effective control of D.citri.Here,the DNBSEQ™,Oxford Nanopore Technologies,and Hi-C technologies are applied to generate a high-quality chromosome-level genome of D.citri.The genome size of D.citri was 523.78 Mb with a scaffold N50 of 47.05 Mb distributed on 13 chromosomes.A total of 250.64 Mb(47.85%)repeat sequences and 24048 protein-coding genes were predicted.Genome resequencing of female and male individuals indicated that the sex chromosome system of D.citri is XO.Phylogenetic analysis demonstrated that D.citri and Pachypsylla venusta,which separated from their most recent common ancestor about 336.62 million years ago,were the most closely related.Additionally,we identified genes potentially involved in detoxification metabolism,pathogen transmission,and honeydew secretion for further investigation.The high-quality genome provides an important reference for developing effective management strategies of D.citri.
基金The National Center for Biotechnology Information(NCBI)BioProject and BioSample accession numbers of Perdix hodgsoniae are PRJNA760267 and SAMN21212221,respectivelyThe raw reads have been deposited in the NCBI SRA database with the accession numbers SRR15900414(Illumina),SRR15900412,and SRR15900413(PacBio).
文摘The Tibetan Partridge(Perdix hodgsoniae)is an endemic species distributed in high-altitude areas of 3600–5600 m on the Qinghai–Tibet Plateau.To explore how the species is adapted to the high elevation environment,we as-sembled a draft genome based on both the Illumina and PacBio sequencing platforms with its population genetics and genomics analysis.In total,134.74 Gb short reads and 30.81 Gb long reads raw data were generated.The 1.05-Gb assembled genome had a contig N50 of 4.56 Mb,with 91.94%complete BUSCOs.The 17457 genes were annotated,and 11.35%of the genome was composed of repeat sequences.The phylogenetic tree showed that P.hodgsoniae was located at the basal position of the clade,including Golden Pheasant(Chrysolophus pictus),Common Pheasant(Phasianus colchicus),and Mikado Pheasant(Syrmaticus mikado).We found that 1014,2595,and 2732 of the 6641 one-to-one orthologous genes were under positive selection in P.hodgsoniae,detected using PAML,BUSTED,and aBSREL programs,respectively,of which 965 genes were common under positive selec-tion with 3 different programs.Several positively selected genes and immunity pathways relevant to high-altitude adaptation were detected.Gene family evolution showed that 99 gene families experienced significant expansion events,while 6 gene families were under contraction.The total number of olfactory receptor genes was relatively low in P.hodgsoniae.Genomic data provide an important resource for a further study on the evolutionary history of P.hodgsoniae,which provides a new insight into its high-altitude adaptation mechanisms.
基金financially supported by National Key Research and Development Program of China (2016YFD0101004)Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciencessupported by the Chinese Government Scholarship。
文摘Common wheat(Triticum aestivum) is a hexaploid plant(AABBDD) derived from genetically related tetraploid wheat T. turgidum(AABB) and a diploid goatgrass Aegilops tauschii(DD). Recent advances in sequencing technology and genome assembly strategies allow the acquisition of multiple wheat genomes, calling for a centralized database to store, manage and query the genomics information in a manner to reflect their evolutionary relationship and to perform effective comparative genome analysis. Here,we built WheatGene, a database that contains five wheat genomes of 318,102 genes and 945,900 transcripts and their expression information in 998 RNA-seq samples that can be searched and compared in an interactive manner. WheatGene was developed with Drupal, a popular content management system and the toolkit Tripal managed the biological information. The database was accessible through a web browser with species, search, gene expression, tools, and literature entries. Tools available were BLAST,synteny viewer, map viewer, JBrowse, data downloads, gene expression heatmap and bar chart, and homologs viewer. Moreover, the map viewer connected genomics data with genetic maps and QTL that can be searched for markers for molecular breeding. WheatGene was developed with open-source modules and libraries. WheatGene is available at http://wheatgene.agrinome.org.
基金Supported by the National Natural Science Foundation of China-Shandong Joint Fund(No.U1706208)the National Natural Science Foundation of China(Nos.41776131,41776130)。
文摘Magnetotactic bacteria(MTB)display magnetotaxis ability because of biomineralization of intracellular nanometer-sized,membrane-bound organelles termed magnetosomes.Despite having been discovered more than half a century,only a few representatives of MTB have been isolated and cultured in the laboratory.In this study,we report the genomic characterization of a novel marine magnetotactic spirillum strain SH-1 belonging to the genus Terasakiella that was recently isolated.A gene encoding haloalkane dehalogenase,which is involved in the degradation of chlorocyclohexane,chlorobenzene,chloroalkane,and chloroalkene,was identified.SH-1 genome contained cysCHI and soxBAZYX genes,thus potentially capable of assimilatory sulfate reduction to H_(2)S and using thiosulfate as electron donors and oxidizing it to sulfate.Genome of SH-1 also contained genes encoding periplasmic dissimilatory nitrate reductases(napAB),assimilatory nitrate reductase(nasA)and assimilatory nitrite reductases(nasB),suggesting that it is capable of gaining energy by converting nitrate to ammonia.The pure culture of Terasakiella sp.SH-1 together with its genomic results off ers new opportunities to examine biology,physiology,and biomineralization mechanisms of MTB.
基金supported by the"973"National Key Basic Research Program of China(No.G1998051202)the National Scientific Research Foundation for Excellent Young Scientist of China(type B)(No.39825511).
文摘Objective: To detect genetic alterations in nasopharyngeal carcinoma (NPC) in Cantonese, the population with the highest incidence of NPC, and to correlate the findings with clinical staging. Methods: Comparative genomic hybridization (CGH) was performed on 35 primary nasopharyngeal carcinomas and a nonparametric χ2 test was used to analyze relationship between chromosome changes and clinical staging. Results: The identified common chromosomal alterations in NPC included gain of chromosomes 12q (21 cases, 60%), 4q (19cases, 43%), 3q (18 cases, 51%), 1q (15 cases, 43%),8q (14 cases, 40%), and 2q (12 cases, 30%). The most frequently detected loss of chromosomal materials involved chromosome 1p (24 cases, 69%), chromosome 3p (21 cases, 60%), 11q (20 cases, 57%), 14q (18 cases, 51%), 16q (14 cases, 40%), 13(12 cases, 34%), and 9p(11 cases, 31%). The high frequency (>50%) 4q gain and 1p loss were novel findings. Compared by nonparametric χ2 test, gains on 12q and 8q were found mainly in stages Ⅲ/Ⅳ and there were significant differences between two clinical stage groups ( stagesⅠ/Ⅱvs stages Ⅲ/Ⅳ). Conclusions: Current analysis has revealed a comprehensive profile of the chromosomal regions showing DNA copy number changes, which may harbor oncogenes or tumor suppressor genes involved in the development of primary NPC.