查看更多>>摘要：Sheep(Ovis aries),among the first domesticated species,are now globally widespread and exhibit remarkable adaptability to diverse environments.In this study,we perform whole-genome sequencing of 266 animals from 18 distinct Chinese sheep populations,each displaying unique phenotypes indicative of adaptation to varying environmental conditions.Integrating 131 environmental factors with single nucleotide polymorphism variations,we conduct a comprehensive genetic-environmental association analysis.This analysis identifies 35 key genes likely integral to the environmental adaptation of sheep.The functions of these genes include fat tail formation(HOXA10,HOXA11,JAZF1),wool characteristics(FER,FGF5,MITF,PDE4B),horn phenotypes(RXFP2),reproduction(HIBADH,TRIM71,C6H4orf22),and growth traits(ADGRL3,TRHDE).Notably,we observe a significant correlation between the frequency of missense mutations in the PAPSS2 and RXFP2 genes and variations in altitude.Our study reveals candidate genes for adaptive variation in sheep and demonstrates the diversity in how sheep adapt to their environment.
查看更多>>摘要：Stomata play critical roles in gas exchange and immunity to pathogens.While many genes regulating early stomatal development up to the production of young guard cells(GCs)have been identified in Arabidopsis,much less is known about how young GCs develop into mature functional stomata.Here we perform a maturomics study on stomata,with"maturomics"defined as omics analysis of the maturation process of a tissue or organ.We develop an integrative scheme to analyze three public stomata-related single-cell RNA-seq datasets and identify a list of 586 genes that are specifically up-regulated in all three datasets during stomatal maturation and function formation.The list,termed sc_586,is enriched with known regulators of stomatal maturation and functions.To validate the reliability of the dataset,we selected two candidate G2-like transcription factor genes,MYS1 and MYS2,to investigate their roles in stomata.These two genes redundantly regulate the size and hoop rigidity of mature GCs,and the mys1 mys2 double mutants cause mature GCs with severe defects in regulating their stomatal apertures.Taken together,our results provide a valuable list of genes for studying GC maturation and function formation.
查看更多>>摘要：Nanopore direct RNA sequencing(DRS)provides the direct access to native RNA strands with full-length information,shedding light on rich qualitative and quantitative properties of gene expression profiles.Here with NanoTrans,we present an integrated computational framework that comprehensively covers all major DRS-based application scopes,including isoform clustering and quantification,poly(A)tail length estima-tion,RNA modification profiling,and fusion gene detection.In addition to its merit in providing such a streamlined one-stop solution,NanoTrans also shines in its workflow-orientated modular design,batch processing capability,all-in-one tabular and graphic report output,as well as automatic installation and configuration supports.Finally,by applying NanoTrans to real DRS datasets of yeast,Arabidopsis,as well as human embryonic kidney and cancer cell lines,we further demonstrate its utility,effectiveness,and efficacy across a wide range of DRS-based application settings.
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