Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass

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dc.contributor.authorHuang, Linkaien
dc.contributor.authorFeng, Guangyanen
dc.contributor.authorYan, Haidongen
dc.contributor.authorZhang, Zhongrenen
dc.contributor.authorBushman, Bradley Shaunen
dc.contributor.authorWang, Jianpingen
dc.contributor.authorBombarely, Aurelianoen
dc.contributor.authorLi, Mingzhouen
dc.contributor.authorYang, Zhongfuen
dc.contributor.authorNie, Gangen
dc.contributor.authorXie, Wengangen
dc.contributor.authorXu, Leien
dc.contributor.authorChen, Peilinen
dc.contributor.authorZhao, Xinxinen
dc.contributor.authorJiang, Wenkaien
dc.contributor.authorZhang, Xinquanen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2020-02-27T13:47:52Zen
dc.date.available2020-02-27T13:47:52Zen
dc.date.issued2020-02en
dc.description.abstractOrchardgrass (Dactylis glomerata L.) is an important forage grass for cultivating livestock worldwide. Here, we report an similar to 1.84-Gb chromosome-scale diploid genome assembly of orchardgrass, with a contig N50 of 0.93 Mb, a scaffold N50 of 6.08 Mb and a super-scaffold N50 of 252.52 Mb, which is the first chromosome-scale assembled genome of a cool-season forage grass. The genome includes 40 088 protein-coding genes, and 69% of the assembled sequences are transposable elements, with long terminal repeats (LTRs) being the most abundant. The LTRretrotransposons may have been activated and expanded in the grass genome in response to environmental changes during the Pleistocene between 0 and 1 million years ago. Phylogenetic analysis reveals that orchardgrass diverged after rice but before three Triticeae species, and evolutionarily conserved chromosomes were detected by analysing ancient chromosome rearrangements in these grass species. We also resequenced the whole genome of 76 orchardgrass accessions and found that germplasm from Northern Europe and East Asia clustered together, likely due to the exchange of plants along the 'Silk Road' or other ancient trade routes connecting the East and West. Last, a combined transcriptome, quantitative genetic and bulk segregant analysis provided insights into the genetic network regulating flowering time in orchardgrass and revealed four main candidate genes controlling this trait. This chromosome-scale genome and the online database of orchardgrass developed here will facilitate the discovery of genes controlling agronomically important traits, stimulate genetic improvement of and functional genetic research on orchardgrass and provide comparative genetic resources for other forage grasses.en
dc.description.adminPublic domain – authored by a U.S. government employeeen
dc.description.notesThis research work was funded by the National Basic Research Program (973 Program) in China (No. 2014CB138705), the National Natural Science Foundation of China (NSFC 31872997), the Earmarked Fund for Modern Agro-industry Technology Research System (No. CARS-34) and the National Project on Sci-Tec Foundation Resources Survey (2017FY100602).en
dc.description.sponsorshipNational Basic Research Program (973 Program) in ChinaNational Basic Research Program of China [2014CB138705]; National Natural Science Foundation of ChinaNational Natural Science Foundation of China [NSFC 31872997]; Earmarked Fund for Modern Agro-industry Technology Research System [CARS-34]; National Project on Sci-Tec Foundation Resources Survey [2017FY100602]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1111/pbi.13205en
dc.identifier.eissn1467-7652en
dc.identifier.issn1467-7644en
dc.identifier.issue2en
dc.identifier.pmid31276273en
dc.identifier.urihttp://hdl.handle.net/10919/97065en
dc.identifier.volume18en
dc.language.isoenen
dc.rightsCC0 1.0 Universalen
dc.rights.urihttp://creativecommons.org/publicdomain/zero/1.0/en
dc.subjectDactylis glomerataen
dc.subjectreference genomeen
dc.subjectlong-read sequencingen
dc.subjecttransposonen
dc.subjectflowering timeen
dc.titleGenome assembly provides insights into the genome evolution and flowering regulation of orchardgrassen
dc.title.serialPlant Biotechnology Journalen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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