Allotetraploidization event of Coptis chinensis shared by all Ranunculales

Coptis chinensis Franch.,also named Chinese goldthread is a member of Ranunculaceae in the order Ranunculales and represents an important lineage of early eudicots with traditional medicinal value.In our study,by using syntenic analysis combined with phylogenomic analysis of C.chinensis and four other representative genomes from basal and core eudicots,we confirmed that the WGD event in C.chinensis was shared by Aquilegia coerulea and Papaver somniferum L.and quickly occurred after Ranunculales diverged from other eudicots,likely a Ranunculales common tetraploidization(RCT).The synonymous nucleotide substitutions at synonymous sites distribution of syntenic blocks across these genomes showed that the evolutionary rate of the P.somniferum genome is faster than that of the C.chinensis genome by approximately 13.7%,possibly due to Papaveraceaes having an additional special tetraploidization event(PST).After Ks correction,the RCT dated to 115—130 million years ago(MYA),which was close to the divergence of Ranunculaceaes and Papaveraceaes approximately115.45—130.51 MYA.Moreover,we identified homologous genes related to polyploidization and speciation and constructed multiple sequence alignments with different reference genomes.Notably,the event-related subgenomes in the basal genomes all showed genomic fractionation bias,suggesting a likely allopolyploid nature of the RCT,PST and T-Alpha and T-Beta events in Tetracentron sinense.In addition,we detected that the sixteen P450 subfamilies were markedly expanded in the genomes of Ranunculales,and most of them were related to the RCT and PST events.We constructed a new platform for Early Eudicot Comparative Genomic Research(http://www.cgrpoee.top/index.html)to store more information.In summary,our findings support the WGD of C.chinensis shared by Ranunculales,which is likely an allotetraploidization event.This present effort offered new insights into the evolution of key polyploidization events and the genes related to secondary metabolites during the diversification of early eudicots.

A likely autotetraploidization event shaped the Chinese mahogany(Toona sinensis)genome

Chinese mahogany(Toona sinensis) is of considerable medical and economic importance, and its genome has been deciphered. However, the process underlying its polyploidy is unclear, and the chromosomal evolutionary trajectory is poorly understood. Here, by reanalysing the T.sinensis genome, we found evidence of a tetraploidization event(T. sinensis special tetraploidization, TST) that occurred approximately 15-17 million years ago(MYA) after the core eudicot-common hexaploidization(ECH or gamma) event. We characterized the synonymous nucleotide substitution rates(Ks values) of collinear genes and found that T. sinensis genes affected by the TST evolve at a slower rate than Acer yangbiense genes. Furthermore, we identified homologous genes related to polyploidization and speciation and constructed multiple alignments with different reference genomes. Notably, the significant balance of gene retention and loss characterized in the two TST-derived subgenomes suggests an autopolyploid nature of the TST. Moreover, we deduced the chromosomal karyotypes of the two subgenomes and identified 7chromosomal fusions that have shaped the T. sinensis genome;more information is available on a newly constructed karyotype platform(http://www.cgrpoee.top/Toona_sinensis/index.html). The T. sinensis genome preserves the ancestral chromosome structure of dicotyledons well and could serve as a good reference for understanding genomic changes in other Meliaceae and Sapindales plants. In addition, we verified that tandem duplication and the ECH have promoted the expansion of terpene synthase(TPS) genes;conversely, the TST seems to have inhibited expansion of these genes. This present effort has clarified the polyploidy events of the T. sinensis genome, filled gaps in the history of karyotype evolution, and laid a solid foundation for further genomic studies in the Meliaceae research community and beyond.

Molecular regulation mechanism of oocyte maturation in beef cattle

Bovine oocytes are one of the indispensable cells in cattle reproduction and have become a research hot spot in cattle reproduction in recent years.The maturation process of oocytes is mainly regulated by enzymes,hormones,cytokines,and other molecules.The factors affecting cattle oocyte maturation have been previously studied to clarify the molecular mechanisms of cattle oocyte maturation.In this review article,phospholipid protein-3-kinase/protein kinase B,mitogen-activated protein kinase/extracellular signal-regulated kinase,Janus kinase/signal transducer and activator of transcription,epidermal growth factor receptor/extracellular signal-regulated kinase,and other signaling pathways related to oocyte maturation are discussed.In addition,the molecular mechanisms of some coding genes(JY-1,FGF-10,CDC20,etc.)and non-coding genes(miRNA,lncRNA,and circRNA)regulating oocyte maturation have been reviewed to provide new ideas for high reproductive performance molecular breeding of high-quality cattle.

Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae

An ancient hexaploidization event in the most but not all Asteraceae plants,may have been responsible for shaping the genomes of many horticultural,ornamental,and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth.However,the duplication process of this hexaploidy,as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization,are still poorly understood.We analyzed 11 genomes from 10 genera in Asteraceae,and redated the Asteraceae common hexaploidization(ACH)event∼70.7–78.6 million years ago(Mya)and the Asteroideae specific tetraploidization(AST)event∼41.6–46.2 Mya.Moreover,we identified the genomic homologies generated from the ACH,AST and speciation events,and constructed a multiple genome alignment framework for Asteraceae.Subsequently,we revealed biased fractionations between the paleopolyploidization produced subgenomes,suggesting the ACH and AST both are allopolyplodization events.Interestingly,the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae.Furthermore,we reconstructed ancestral Asteraceae karyotype(AAK)that has 9 paleochromosomes,and revealed a highly flexible reshuffling of Asteraceae paleogenome.Of specific significance,we explored the genetic diversity of Heat Shock Transcription Factors(Hsfs)associated with recursive whole-genome polyploidizations,gene duplications,and paleogenome reshuffling,and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae.Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae,and is helpful for further communication and exploration of the diversification of plant families and phenotypes.

Coriander Genomics Database:a genomic,transcriptomic,and metabolic database for coriander

Coriander(Coriandrum sativum L.),also known as cilantro,is a globally important vegetable and spice crop.Its genome and that of carrot are models for studying the evolution of the Apiaceae family.Here,we developed the Coriander Genomics Database(CGDB,http://cgdb.bio2db.com/)to collect,store,and integrate the genomic,transcriptomic,metabolic,functional annotation,and repeat sequence data of coriander and carrot to serve as a central online platform for Apiaceae and other related plants.Using these data sets in the CGDB,we intriguingly found that seven transcription factor(TF)families showed significantly greater numbers of members in the coriander genome than in the carrot genome.The highest ratio of the numbers of MADS TFs between coriander and carrot reached 3.15,followed by those for tubby protein(TUB)and heat shock factors.As a demonstration of CGDB applications,we identified 17 TUB family genes and conducted systematic comparative and evolutionary analyses.RNA-seq data deposited in the CGDB also suggest dose compensation effects of gene expression in coriander.CGDB allows bulk downloading,significance searches,genome browser analyses,and BLAST searches for comparisons between coriander and other plants regarding genomics,gene families,gene collinearity,gene expression,and the metabolome.A detailed user manual and contact information are also available to provide support to the scientific research community and address scientific questions.CGDB will be continuously updated,and new data will be integrated for comparative and functional genomic analysis in Apiaceae and other related plants.

DNA methylation and alternative splicing modulate FBXW11 gene expression in Holstein bull testis and are correlated with sperm quality

F-box and WD-40 domain protein 11(FBXW11)is an important component of the E3 ubiquitin-ligase enzyme that plays a key role in the ubiquitin-dependent regulation of spermatogenesis.In our previous research,the mRNA expression of FBXW11 in bull sperm with high motility is significantly higher than that with low motility.In the present study,the protein expression levels of FBXW11 in bull testicular tissues with low-performance sperm quality groups were significantly higher than those in normal performance groups.The immunohistochemistry result demonstrated that FBXW11 protein was located in the periphery of Leydig cells and seminiferous tubules.Three splice variants of the FBXW11 gene,namely,FBXW11-tv1,FBXW11-tv2,and FBXW11-tv3,were identified in testicular tissues.The splicing patterns of the three variants are exon skipping.The transcript FBXW11-tv2 expressions were the highest in each sample.The low-performance groups displayed higher FBXW11-tv1 and FBXW11-tv2 transcript expressions than the normal performance groups.Two CpG islands were located within the 5’UTR and exon 1-2 region of the FBXW11 gene.Bisulfite sequencing PCR results demonstrated that the methylation levels of 11 methylation sites in the CpG island 2 from−99 to−43 in the normal performance groups were significantly lower than those in the low-performance groups.Pearson correlation analysis suggested that the CpG island 2 methylation level was negatively correlated with sperm motility and the transcript FBXW11-tv2 expression level.Our data revealed that alternative splicing and DNA methylation jointly regulated FBXW11 gene expression and were correlated with sperm quality traits during spermatogenesis in Holsteins.

Aging Characteristics of XLPE Insulation of 110 kV Cables in the Initial Stage of Operation

The aging characteristics of the XLPE insulation of 110 kV power cables in the initial stage of operation are studied in this paper.The XLPE insulation from cables with different running time was tested by using electrical and physicochemical methods,from which the degradation state of XLPE under multiple stresses during operation was derived.The broadband dielectric spectrum test taken from 10–1 to 10^(6) Hz showed that the dielectric constant and dielectric loss of the XLPE insulation first decrease and then increase with the increase of cable running time,which show obvious variation until 10 years of operation.The AC breakdown strengths of the XLPE insulation of operated cables with the service year no longer than 10 years were higher than that of new cables.The mechanical properties of the XLPE insulation showed no dependence with the cable running time.The crystallinity and perfection of the crystallization area were found to be enhanced during operation and the polar functional groups inside the XLPE insulation were found to be determined not only by the cross-linking by-products but also by the oxidation process during cable operation.The experimental results in this paper are important for improving the operation reliability and reducing the maintenance costs of the cables.

Bio-assembled smart nanocapsules for targeted delivery of KRAS shRNA and cancer cell bioimage

The five-year survival rate for pancreatic cancer is less than 5%. However, the current clinical multimodal therapy combined with first-line chemotherapy drugs only increases the patient’s median survival from 5.0 months to 7.2 months. Consequently, a new strategy of cancer treatments is urgently needed to overcome this high-fatality disease. Through a series of biometric analyses, we found that KRAS is highly expressed in the tumor of pancreatic cancer patients, and this high expression is closely related to the poor prognosis of patients. It shows that inhibiting the expression of KRAS has great potential in gene therapy for pancreatic cancer. Given those above, we have exploited the possibility of targeted delivery of KRAS shRNA with the intelligent and bio-responsive nanomedicine to detect the special oxidative stress microenvironment of cancer cells and realize efficient cancer theranostics. Our observations demonstrate that by designing the smart self-assembled nanocapsules of melanin with fluorescent nanoclusters we can readily achieve the bio-recognition and bioimaging of cancer cells in biological solution or serum.The self-assembled nanocapsules can make a significant bio-response to the oxidative stress microenvironment of cancer cells and generate fluorescent zinc oxide Nanoclusters in situ for targeted cell bioimaging. Moreover, it can also readily facilitate cancer cell suppression through the targeted delivery of KRAS shRNA and low-temperature hyperthermia. This raises the possibility to provide a promising theranostics platform and self-assembled nanomedicine for targeted cancer diagnostics and treatments through special oxidative stress-responsive effects of cancer cells.

Targeting UBE2C for degradation by bioPROTACs based on bacterial E3 ligase

UBE2C(Ubiquitin conjugating enzyme E2 C), a key regulator of cell cycle progression, is a promising target for discovery of antitumor agents. However, it is challenging to develop inhibitors of UBE2C owing to its lack of “druggable” pockets. Bio PROTACs(biological proteolysis targeting chimeras) are a kind of protein-based degraders by fusing an adaptor to a subunit of E3 ligase for ubiquitination and subsequent proteasome-dependent degradation of target protein. We report herein the design and biological evaluation of a UBE2C-targeting bio PROTAC based on the NEL(novel E3 ligase) domain of bacterial E3 ligase Ipa H9.8 and the UBE2C-binding WHB(winged-helix B) domain of APC_(2)(anaphase promoting complex subunit 2). The in vitro ubiquitination test and Mass Spectrometry analysis showed that the bio PROTAC could transfer ubiquitin to surface exposed lysines on UBE2C and catalyzed the formation of polyubiquitin chains. In addition, the transient co-expression experiment showed that the bio PROTAC could promote proteasomal degradation of heterologous UBE2C and rescue its downstream substrates in mammalian cells.

A likely paleo-autotetraploidization event shaped the high conservation of Nyssaceae genome

Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global climate.To investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families.The genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic analysis.We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor genome.D.involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families.Combing both its high retention of paleochromosomes and its low mutation rate,D.involucrata provides the best case in conservation of the core eudicot paleogenome.

Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement

Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut.

Paleo-polyploidization in Lycophytes

Lycophytes and seed plants constitute the typical vascular plants.Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants.Here,genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events,with one occurring approximately 13–15 million years ago(MYA)and another about 125–142 MYA,during the evolution of the genome of Selaginella moellendorffii,a model lycophyte.In addition,comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleopolyploidization events than seed plants.Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages—lycophytes and seed plants—of vascular plants.

Inadequate Nutrition and Associated Factors in Children Aged 6 to 24 Months-4 Counties,Liangshan Yi Autonomous Prefecture,China,2018

Summary What is already known about this topic?Symptoms of malnutrition including anemia,stunting,wasting,and being underweight among children remained one of the major public health problems in poorer areas in China.More research is needed to guide interventions to improve nutrition and health among children in low-income regions.