Oral microbiome and risk of malignant esophageal lesions in a high-risk area of China:A nested case-control study

Objective:We aimed to prospectively evaluate the association of oral microbiome with malignant esophageal lesions and its predictive potential as a biomarker of risk.Methods:We conducted a case-control study nested within a population-based cohort with up to 8 visits of oral swab collection for each subject over an 11-year period in a high-risk area for esophageal cancer in China.The oral microbiome was evaluated with 16 S ribosomal RNA(rRNA)gene sequencing in 428 pre-diagnostic oral specimens from 84 cases with esophageal lesions of severe squamous dysplasia and above(SDA)and 168 matched healthy controls.DESeq analysis was performed to identify taxa of differential abundance.Differential oral species together with subject characteristics were evaluated for their potential in predicting SDA risk by constructing conditional logistic regression models.Results:A total of 125 taxa including 37 named species showed significantly different abundance between SDA cases and controls(all P<0.05&false discovery rate-adjusted Q<0.10).A multivariate logistic model including 11 SDA lesion-related species and family history of esophageal cancer provided an area under the receiver operating characteristic curve(AUC)of 0.89(95%CI,0.84-0.93).Cross-validation and sensitivity analysis,excluding cases diagnosed within 1 year of collection of the baseline specimen and their matched controls,or restriction to screenendoscopic-detected or clinically diagnosed case-control triads,or using only bacterial data measured at the baseline,yielded AUCs>0.84.Conclusions:The oral microbiome may play an etiological and predictive role in esophageal cancer,and it holds promise as a non-invasive early warning biomarker for risk stratification for esophageal cancer screening programs.

Comparative population genomics dissects the genetic basis of seven domestication traits in jujube

Jujube(Ziziphus jujuba Mill.)is an important perennial fruit tree with a range of interesting horticultural traits.It was domesticated from wild jujube(Ziziphus acidojujuba),but the genomic variation dynamics and genetic changes underlying its horticultural traits during domestication are poorly understood.Here,we report a comprehensive genome variation map based on the resequencing of 350 accessions,including wild,semi-wild and cultivated jujube plants,at a>15×depth.Using the combination of a genome-wide association study(GWAS)and selective sweep analysis,we identified several candidate genes potentially involved in regulating seven domestication traits in jujube.For fruit shape and kernel shape,we integrated the GWAS approach with transcriptome profiling data,expression analysis and the transgenic validation of a candidate gene to identify a causal gene,ZjFS3,which encodes an ethyleneresponsive transcription factor.Similarly,we identified a candidate gene for bearing-shoot length and the number of leaves per bearing shoot and two candidate genes for the seed-setting rate using GWAS.In the selective sweep analysis,we also discovered several putative genes for the presence of prickles on bearing shoots and the postharvest shelf life of fleshy fruits.This study outlines the genetic basis of jujube domestication and evolution and provides a rich genomic resource for mining other horticulturally important genes in jujube.

The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis

Coptis chinensis Franch, a perennial herb, is mainly distributed in southeastern China. The rhizome of C. chinensis hasbeen used as a traditional medicine for more than 2000 years in China and many other Asian countries. Thepharmacological activities of C. chinensis have been validated by research. Here, we present a de novo high-qualitygenome of C. chinensis with a chromosome-level genome of ~958.20 Mb, a contig N50 of 1.58 Mb, and a scaffold N50of 4.53 Mb. We found that the relatively large genome size of C. chinensis was caused by the amplification of longterminal repeat (LTR) retrotransposons. In addition, a whole-genome duplication event in ancestral Ranunculales wasdiscovered. Comparative genomic analysis revealed that the tyrosine decarboxylase (TYDC) and (S)-norcoclaurinesynthase (NCS) genes were expanded and that the aspartate aminotransferase gene (ASP5) was positively selected inthe berberine metabolic pathway. Expression level and HPLC analyses showed that the berberine content was highestin the roots of C. chinensis in the third and fourth years. The chromosome-level reference genome of C. chinensisprovides important genomic data for molecular-assisted breeding and active ingredient biosynthesis.

Copy number variation of B1 controls awn length in wheat

Wheat awns contribute to photosynthesis and grain production.In this study,an F2population and F2:3families from a cross between the awned line 7D12 and the Chinese awnless variety Shiyou 20(SY20)were used to identify loci associated with awn length.Bulked-segregant RNA sequencing and linkage mapping identified a single dominant locus in a 0.3 cM interval on chromosome 5AL.Five genes were in the interval,including the recently cloned awn inhibitor B1.Although a single copy of the B1 gene was detected in 7D12,SY20 carried five copies of the gene.Increased copy number of B1 in SY20enhanced gene expression.Based on sequence variation among the promoter regions of five B1 gene copies in SY20,two dominant markers were developed and found to cosegregate with B1 in a population of 931 wheat accessions.All 77 awnless accessions harbored sequence variations in the B1 promoter regions similar to those of SY20 and thus carried multiple copies of the gene,whereas 15 randomly selected awned wheats carried only one copy.These results suggest that an increase in copy number of the B1 gene is associated with inhibition of awn length.

Genome and transcriptome of Papaver somniferum Chinese landrace CHM indicates that massive genome expansion contributes to high benzylisoquinoline alkaloid biosynthesis

Opium poppy(Papaver somniferum)is a source of morphine,codeine,and semisynthetic derivatives,including oxycodone and naltrexone.Here,we report the de novo assembly and genomic analysis of P.somniferum traditional landrace‘Chinese Herbal Medicine’.Variations between the 2.62 Gb CHM genome and that of the previously sequenced high noscapine 1(HN1)variety were also explored.Among 79,668 protein-coding genes,we functionally annotated 88.9%,compared to 68.8%reported in the HN1 genome.Gene family and 4DTv comparative analyses with three other Papaveraceae species revealed that opium poppy underwent two whole-genome duplication(WGD)events.The first of these,in ancestral Ranunculales,expanded gene families related to characteristic secondary metabolite production and disease resistance.The more recent species-specific WGD mediated by transposable elements resulted in massive genome expansion.Genes carrying structural variations and large-effect variants associated with agronomically different phenotypes between CHM and HN1 that were identified through our transcriptomic comparison of multiple organs and developmental stages can enable the development of new varieties.These genomic and transcriptomic analyses will provide a valuable resource that informs future basic and agricultural studies of the opium poppy.

Draft genome sequence of cauliflower(Brassica oleracea L.var.botrytis)provides new insights into the C genome in Brassica species

Cauliflower is an important variety of Brassica oleracea and is planted worldwide.Here,the high-quality genome sequence of cauliflower was reported.The assembled cauliflower genome was 584.60 Mb in size,with a contig N50 of 2.11 Mb,and contained 47,772 genes;56.65%of the genome was composed of repetitive sequences.Among these sequences,long terminal repeats(LTRs)were the most abundant(32.71%of the genome),followed by transposable elements(TEs)(12.62%).Comparative genomic analysis confirmed that after an ancient paleohexaploidy(γ)event,cauliflower underwent two whole-genome duplication(WGD)events shared with Arabidopsis and an additional whole-genome triplication(WGT)event shared with other Brassica species.The present cultivated cauliflower diverged from the ancestral B.oleracea species~3.0 million years ago(Mya).The speciation of cauliflower(~2.0 Mya)was later than that of B.oleracea L.var.capitata(approximately 2.6 Mya)and other Brassica species(over 2.0 Mya).Chromosome no.03 of cauliflower shared the most syntenic blocks with the A,B,and C genomes of Brassica species and its eight other chromosomes,implying that chromosome no.03 might be the most ancient one in the cauliflower genome,which was consistent with the chromosome being inherited from the common ancestor of Brassica species.In addition,2,718 specific genes,228 expanded genes,2 contracted genes,and 1,065 positively selected genes in cauliflower were identified and functionally annotated.These findings provide new insights into the genomic diversity of Brassica species and serve as a valuable reference for molecular breeding of cauliflower.

The chromosome-based lavender genome provides new in sights into Lamiaceae evolution and terpenoid biosynthesis

The aromatic shrub Lavandula angustifolia produces various volatile terpenoids that serve as resources for essential oils and function in plant-insect communication.To better understand the genetic basis of the terpenoid diversity in lavender,we present a high-quality reference genome for the Chinese lavender cultivar‘Jingxun 2'using PacBio and Hi-C technologies to anchor the 894.50 Mb genome assembly into 27 pseudochromosomes.In addition to the y triplication event,lavender underwent two rounds of whole-genome duplication(WGD)during the Eocene-Oligocene(29.6 MYA)and Miocene-Pliocene(6.9 MYA)transitions.As a result of tandem duplications and lineage-specific WGDs,gene families related to terpenoid biosynthesis in lavender are substantially expanded compared to those of five other species in Lamiaceae.Many terpenoid biosynthesis transcripts are abundant in glandular trichomes.We further integrated the contents of ecologically functional terpenoids and coexpressed terpenoid biosynthetic genes to construct terpenoid-gene networks.Typical gene clusters,including TPS-TPS,TPS-CYP450,and TPS-BAHD,linked with compounds that primarily function as attractants or repellents,were identified by their similar patterns of change during flower development or in response to methyl jasmonate.Comprehensive analysis of the genetic basis of the production of volatiles in lavender could serve as a foundation for future research into lavender evolution,phytochemistry,and ecology.

Genomic footprints of wheat evolution in China reflected by a Wheat660K SNP array

Common wheat(Triticum aestiuum L.)is one of the most important crops because it provides about 20%of the total calories for humans.T.aestiuum is an excellent modern species for studying concerted evolution of sub-genomes in polyploid species,because of its large chromosome size and three well-known genome donors.Establishment of common wheat genome reference sequence and development of high-density SNP chips provide an excellent foundation to answer questions of wheat evolution and breeding at the genomic level.By genotyping more than 600 accessions of common wheat and their diploid and tetraploid ancestors using a Wheat660 K SNP array,we found dramatic genome changes due to tetraploidization and hexaploidization,in contrast to weaker influences of domestication and breeding on them.Further,since common wheat was introduced in China in 1500 BCE,Chinese landraces formed two subgroups(T.aestiuum-L1 and T.aestiuum-L2)with considerably diverse geographic distributions and agronomic traits.T.aestiuum-L2,mainly distributed in central and east China is found to have more but smaller oval grains with early maturity characteristics.We found that variation and selection in intergenic regions of the A and B sub-genomes dominated this differentiation,in which chromosomes 7 A and 3 B took the leading roles due to the existence of putative genes related to defense responses and environmental adaption in the highly differentiated regions.Large haplotype blocks were detected on 3 B(232.6-398.3 Mb)and 7 A(211.7-272.9 Mb)in the landraces,forming two distinct haplotypes,respectively.We discovered that artificial crosses in breeding promoted recombination in the whole genome,however,this recombination and differentiation was highly asymmetric among the three sub-genomes in homoeologous regions.In addition,we found that the wide use of European and northern American cultivars in breeding at early era,led dramatic changes in Chinese wheat genome,whereas,the recent breeding functioned to optimize it.This study will provide the insight for reconsideration of wheat evolution and breeding,and a new strategy for parent selection in breeding.

A high-quality chromosome-scale assembly of the centipedegrass[Eremochloa ophiuroides(Munro)Hack.]genome provides in sights into chromosomal structural evolution and prostrate growth habit

Centipedegrass[Eremochloa ophiuroides(Munro)Hack.],a member of the Panicoideae subfamily,is one of the most important warm-season turfgrasses originating from China.This grass has an extremely developed prostrate growth habit and has been widely used in transitional and warm climatic regions.To better understand the genetic basis of important biological characteristics,such as prostrate growth and seed yield,in warm-season turfgrasses,we present a high-quality reference genome for centipedegrass and use PacBio,BioNano,and Hi-C technologies to anchor the 867.43 Mb genome assembly into nine pseudochromosomes,with a scaffold N50 of 86.05 Mb and 36,572 annotated genes.Centipedegrass was most closely related to sorghum and diverged from their common ancestor~16.8 Mya.We detected a novel chromosome reshuf fling event in centipedegrass,namely,the nest chromosome fusion event in which fusion of chromosomes 8 and 10 of sorghum into chromosome 3 of centipedegrass likely occurred after the divergence of centipedegrass from sorghum.The typical prostrate growth trait in centipedegrass may be linked to the expansion of candidate PROSTRATE GROWTH 1(PROG1)genes on chromosome 2.Two orthologous genes of OsPROGl,EoPROGl,and EoPROG2,were con firmed to increase the stem number and decrease the stem angle in Arabidopsis.Collectively,our assembled reference genome of centipedegrass offers new knowledge and resources to dissect the genome evolution of Panicoideae and accelerate genome-assisted breeding and improvement of plant architecture in turf plants.

The genome of Medicago polymorpha provides insights into its edibility and nutritional value as a vegetable and forage legume

Medicago polymorpha is a nutritious and palatable forage and vegetable plant that also fixes nitrogen.Here,we reveal the chromosome-scale genome sequence of M.polymorpha using an integrated approach including Illumina,PacBio and Hi-C technologies.We combined PacBio full-length RNA-seq,metabolomic analysis,structural anatomy analysis and related physiological indexes to elucidate the important agronomic traits of M.polymorpha for forage and vegetable usage.The assembled M.polymorpha genome consisted of 457.53Mb with a long scaffold N50 of 57.72Mb,and 92.92%(441.83Mb)of the assembly was assigned to seven pseudochromosomes.Comparative genomic analysis revealed that expansion and contraction of the photosynthesis and lignin biosynthetic gene families,respectively,led to enhancement of nutritious compounds and reduced lignin biosynthesis in M.polymorpha.In addition,we found that several positively selected nitrogen metabolism-related genes were responsible for crude protein biosynthesis.Notably,the metabolomic results revealed that a large number of flavonoids,vitamins,alkaloids,and terpenoids were enriched in M.polymorpha.These results imply that the decreased lignin content but relatively high nutrient content of M.polymorpha enhance its edibility and nutritional value as a forage and vegetable.Our genomic data provide a genetic basis that will accelerate functional genomic and breeding research on M.polymorpha as well as other Medicago and legume plants.

Whole-genome sequencing reveals rare off-target mutations in CRISPR/Cas9-edited grapevine

The CRISPR(clustered regularly interspaced short palindromic repeats)-associated protein 9(Cas9)system is a powerful tool for targeted genome editing,with applications that include plant biotechnology and functional genomics research.However,the specificity of Cas9 targeting is poorly investigated in many plant species,including fruit trees.To assess the off-target mutation rate in grapevine(Vitis vinifera),we performed whole-genome sequencing(WGS)of seven Cas9-edited grapevine plants in which one of two genes was targeted by CRISPR/Cas9 and three wild-type(WT)plants.In total,we identified between 202,008 and 272,397 single nucleotide polymorphisms(SNPs)and between 26,391 and 55,414 insertions/deletions(indels)in the seven Cas9-edited grapevine plants compared with the three WT plants.Subsequently,3272 potential off-target sites were selected for further analysis.Only one off-target indel mutation was identified from the WGS data and validated by Sanger sequencing.In addition,we found 243 newly generated off-target sites caused by genetic variants between the Thompson Seedless cultivar and the grape reference genome(PN40024)but no true off-target mutations.In conclusion,we observed high specificity of CRISPR/Cas9 for genome editing of grapevine.

A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis

Pitaya(Hylocereus)is the most economically important fleshy-fruited tree of the Cactaceae family that is grown worldwide,and it has attracted significant attention because of its betalain-abundant fruits.Nonetheless,the lack of a pitaya reference genome significantly hinders studies focused on its evolution,as well as the potential for genetic improvement of this crop.Herein,we employed various sequencing approaches,namely,PacBio-SMRT,Illumina HiSeq paired-end,10×Genomics,and Hi-C(high-throughput chromosome conformation capture)to provide a chromosome-level genomic assembly of‘GHB’pitaya(H.undatus,2n=2x=22 chromosomes).The size of the assembled pitaya genome was 1.41 Gb,with a scaffold N50 of~127.15 Mb.In total,27,753 protein-coding genes and 896.31Mb of repetitive sequences in the H.undatus genome were annotated.Pitaya has undergone a WGT(whole-genome triplication),and a recent WGD(whole-genome duplication)occurred after the gamma event,which is common to the other species in Cactaceae.A total of 29,328 intact LTR-RTs(~696.45Mb)were obtained in H.undatus,of which two significantly expanded lineages,Ty1/copia and Ty3/gypsy,were the main drivers of the expanded genome.A high-density genetic map of F1 hybrid populations of‘GHB’בDahong’pitayas(H.monacanthus)and their parents were constructed,and a total of 20,872 bin markers were identified(56,380 SNPs)for 11 linkage groups.More importantly,through transcriptomic and WGCNA(weighted gene coexpression network analysis),a global view of the gene regulatory network,including structural genes and the transcription factors involved in pitaya fruit betalain biosynthesis,was presented.Our data present a valuable resource for facilitating molecular breeding programs of pitaya and shed novel light on its genomic evolution,as well as the modulation of betalain biosynthesis in edible fruits.

Chromosome-scale genome assembly of brownspotted flathead Platycephalus sp.1 provides insights into demersal adaptation in flathead fish

Flatheads are valuable commercial fish species endemic to the Indo-West Pacific.Due to their economic value and unique biological traits,such as metamorphosis and camouflage,they serve as ideal marine organisms for studies on demersal adaptation and evolution.The brown-spotted flathead(Platycephalus sp.1)is the most widely distributed in the northwestern Pacific.Despite the lack of a valid scientific name,it has been long recognized and exploited in the marine fisheries of China,Japan,and Korea.In the current study。

The first chromosome-level Fallopia multiflora genome assembly provides insights into stilbene biosynthesis

Fallopia multiflora(Thunb.)Harald,a vine belonging to the Polygonaceae family,is used in traditional medicine.The stilbenes contained in it have significant pharmacological activities in anti-oxidation and anti-aging.This study describes the assembly of the F.multiflora genome and presents its chromosome-level genome sequence containing 1.46 gigabases of data(with a contig N50 of 1.97 megabases),1.44 gigabases of which was assigned to 11 pseudochromosomes.Comparative genomics confirmed that F.multiflora shared a whole-genome duplication event with Tartary buckwheat and then underwent different transposon evolution after separation.Combining genomics,transcriptomics,and metabolomics data to map a network of associated genes and metabolites,we identified two FmRS genes responsible for the catalysis of one molecule of p-coumaroyl-CoA and three molecules of malonyl-CoA to resveratrol in F.multiflora.These findings not only serve as the basis for revealing the stilbene biosynthetic pathway but will also contribute to the development of tools for increasing the production of bioactive stilbenes through molecular breeding in plants or metabolic engineering in microbes.Moreover,the reference genome of F.multiflora is a useful addition to the genomes of the Polygonaceae family.

QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean

Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects. Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height. Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping. This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines(RILs) and their bi-parents, Zhonghuang 13(ZH) and Zhongpin 03-5373(ZP). The total genetic distance of this bin map was 3 139.15 cM,with an average interval of 0.78 cM between adjacent bin markers. Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome. Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci(qPH-b_11, qPH-b_17 and qPH-b_18). Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56-32.7% of the phenotypic variance. They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively. Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.

延长蛋鸡群产蛋期的管理措施

为了发挥蛋鸡群的遗传潜力,必须对管理、营养、生物安全和疾病预防等参数进行密切监控。本文从后备母鸡质量、蛋品质管理和蛋鸡状态对上述不同参数进行了密切监控,以延长蛋鸡群的产蛋期。

孵化管理的重要工具:出雏期

出雏期对1日龄雏鸡质量和后续饲养至关重要,因此必须对其进行监控。本文介绍了出雏期的评估流程、对雏鸡的影响和影响出雏期的因素,旨在为孵化场缩短出雏期提供借鉴。

Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution

The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb.Each chromosome is represented by a single contig and the genomic sequences of all chromosomes are gapless.Quality evaluation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice genomes.Further comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements(TEs)and segmental duplications(SDs),the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/neo-functionalization.The insertion of TEs can also affect the expression of duplicated genes,which may drive the evolution of these genes.Furthermore,we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly,suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental processes.Collectively,our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution.

Population genome of the newly discovered Jinchuan yak to understand its adaptive evolution in extreme environments and generation mechanism of the multirib trait

The adaptation and diversity of animals to the extreme environments of the Qinghai–Tibet Plateau(QTP)are typical materials to study adaptive evolution.The recently discovered Jinchuan yak population has many individuals with multiple ribs.However,little is known about this yak’s origin,evolution,and the genetic mechanisms that formed its unique multirib trait.Here,we report a valuable population genome resource of the Jinchuan yak by resequencing the whole genome of 150 individuals.Population genetic polymorphism and structure analysis reveal that Jinchuan yak can be differentiated as a unique and original yak population among the domestic yak.Combined with geological change,the Jinchuan yak’s evolutionary origin is speculated to be about 6290 years ago,which may be related to the unique geographical environment of the eastern edge of the QTP during this period.Compared with other domestic yaks,this new population has 280 positively selected genes.The genes related to skeletal function hold a considerable and remarkable proportion,suggesting that the specific skeletal characteristics have been enhanced in the adaptive evolution of Jinchuan yak in the extreme plateau environment.The genome-wide association study has revealed that TUBA8 and TUBA4A,the genes that regulate the cytoskeleton,are potential genes associated with the multirib trait.Our findings provide a basis to further understand the generation mechanism of the adaptive evolution of this new population in high-altitude extreme environments and the multivertebrate trait of domestic animals.

The Genome of Medicinal Plant Macleaya cordata Provides New Insights into Benzylisoquinoline Alkaloids Metabolism

The overuse of antibiotics in animal agriculture and medicine has caused a series of potential threats to public health. Macleaya cordata is a medicinal plant species from the Papaveraceae family, providing a safe resource for the manufacture of antimicrobial feed additive for livestock. The active constituents from M. cordata are known to include benzylisoquinoline alkaloids （BIAs） such as sanguinarine （SAN） and chelerythrine （CHE）, but their metabolic pathways have yet to be studied in this non-model plant. The active biosynthesis of SAN and CHE in M. cordata was first examined and confirmed by feeding ^13C-labeled tyrosine. To gain further insights, we de novo sequenced the whole genome of M. cordata, the first to be sequenced from the Papaveraceae family. The M. cordata genome covering 378 Mb encodes 22,328 predicted protein-coding genes with 43.5% being transposable elements. As a member of basal eudicot, M. cordata genome lacks the paleohexaploidy event that occurred in almost all eudicots. From the genomics data, a complete set of 16 metabolic genes for SAN and CHE biosynthesis was retrieved, and 14 of their biochemical activities were validated. These genomics and metabolic data show the conserved BIA metabolic pathways in M. cordata and provide the knowledge foundation for future productions of SAN and CHE by crop improvement or microbial pathway reconstruction.