Sex dimorphism and gene expression were studied in developing catkins in 159 F 2 individuals from the bioenergy crop Salix purpurea,and potential mechanisms and pathways for regulating sex development were explored.Di...Sex dimorphism and gene expression were studied in developing catkins in 159 F 2 individuals from the bioenergy crop Salix purpurea,and potential mechanisms and pathways for regulating sex development were explored.Differential expression,eQTL,bisulfite sequencing,and network analysis were used to characterize sex dimorphism,detect candidate master regulator genes,and identify pathways through which the sex determination region(SDR)may mediate sex dimorphism.Eleven genes are presented as candidates for master regulators of sex,supported by gene expression and network analyses.These include genes putatively involved in hormone signaling,epigenetic modification,and regulation of transcription.eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region.Furthermore,data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways.These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus.This further demonstrates the dynamic nature of SDRs in plants,which involves a multitude of mechanisms of sex determination and a high rate of turnover.展开更多
Early efforts to classify Mortierellaceae were based on macro-and micromorphology,but sequencing and phylogenetic studies with ribosomal DNA(rDNA)markers have demonstrated conflicting taxonomic groupings and polyphyle...Early efforts to classify Mortierellaceae were based on macro-and micromorphology,but sequencing and phylogenetic studies with ribosomal DNA(rDNA)markers have demonstrated conflicting taxonomic groupings and polyphyletic genera.Although some taxonomic confusion in the family has been clarified,rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae.In this study,we applied two parallel approaches to resolve the Mortierel-laceae phylogeny:low coverage genome(LCG)sequencing and high-throughput,multiplexed targeted amplicon sequenc-ing to generate sequence data for multi-gene phylogenetics.We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset.Resolving the Mortierellaceae phylogeny into monophyletic genera resulted in 13 genera,7 of which are newly proposed.Low-coverage genome sequencing proved to be a relatively cost-effective means of generating a high-confidence phylogeny.The multi-gene phylogenetics approach enabled much greater sampling depth and breadth than the LCG approach,but has limitations too.We present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity and evolution.展开更多
基金Support for this research was provided by grants(DEB-1542486,DEB-1542599)from the National Science Foundationfrom the USDA National Institute for Food and Agriculture(2015-67009-23957)。
文摘Sex dimorphism and gene expression were studied in developing catkins in 159 F 2 individuals from the bioenergy crop Salix purpurea,and potential mechanisms and pathways for regulating sex development were explored.Differential expression,eQTL,bisulfite sequencing,and network analysis were used to characterize sex dimorphism,detect candidate master regulator genes,and identify pathways through which the sex determination region(SDR)may mediate sex dimorphism.Eleven genes are presented as candidates for master regulators of sex,supported by gene expression and network analyses.These include genes putatively involved in hormone signaling,epigenetic modification,and regulation of transcription.eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region.Furthermore,data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways.These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus.This further demonstrates the dynamic nature of SDRs in plants,which involves a multitude of mechanisms of sex determination and a high rate of turnover.
基金US National Science Foundation(NSF)DEB 1737898(GB and NVP),Michigan State University AgBioResearch NIFA project MICL02416(GB),NSF STC BEACON Cooperative Agreement DBI-093954(GB&NVP)US National Science Foundation(The Zygomycetes Genealogy of Life)DEB1354802 and DEB1441677(JS)+1 种基金JGI-the work conducted by the U.S.Department of Energy Joint Genome Institute,a DOE Office of Science User Facility,is supported by the Office of Science of the U.S.Department of Energy under Contract No.DE-AC02-05CH11231Data analyses were performed on the High-Performance Computing Cluster at the University of California-Riverside in the Institute of Integrative Genome Biology supported by NSF DBI-1429826 and NIH S10-OD016290(JS).
文摘Early efforts to classify Mortierellaceae were based on macro-and micromorphology,but sequencing and phylogenetic studies with ribosomal DNA(rDNA)markers have demonstrated conflicting taxonomic groupings and polyphyletic genera.Although some taxonomic confusion in the family has been clarified,rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae.In this study,we applied two parallel approaches to resolve the Mortierel-laceae phylogeny:low coverage genome(LCG)sequencing and high-throughput,multiplexed targeted amplicon sequenc-ing to generate sequence data for multi-gene phylogenetics.We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset.Resolving the Mortierellaceae phylogeny into monophyletic genera resulted in 13 genera,7 of which are newly proposed.Low-coverage genome sequencing proved to be a relatively cost-effective means of generating a high-confidence phylogeny.The multi-gene phylogenetics approach enabled much greater sampling depth and breadth than the LCG approach,but has limitations too.We present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity and evolution.
