De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species

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dc.contributor.authorHuang, Xiuen
dc.contributor.authorYan, Haidongen
dc.contributor.authorZhang, Xinquanen
dc.contributor.authorZhang, Jianen
dc.contributor.authorFrazier, Taylor P.en
dc.contributor.authorHuang, Dejunen
dc.contributor.authorLu, Luen
dc.contributor.authorHuang, Linkaien
dc.contributor.authorLiu, Weien
dc.contributor.authorPeng, Yanen
dc.contributor.authorMa, Xiaoen
dc.contributor.authorYan, Yan-Hongen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2019-04-29T13:01:15Zen
dc.date.available2019-04-29T13:01:15Zen
dc.date.issued2016-04-18en
dc.description.abstractHemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa "Yaan" and H. altissima "1110." Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for "Yaan" and "1110," respectively. In addition, a total of 86,731 "Yawn" and 48,645 "1110" unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11-87.04%) of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus.en
dc.description.notesThis work was supported by National Basic Research Program of China (973 Program) (2014CB138705), Strategic Planning and Management Innovation of Science and Technology Support Demonstration Project of Chongqing Modern Cattle and Sheep Industry (cstc2014zktjccxbx0021), Modern Agro-industry Technology Research System (CARS-35-05), and the Sichuan Agricultural University Excellent Master's Degree Papers Breeding (YS2014003).en
dc.description.sponsorshipNational Basic Research Program of China (973 Program) [2014CB138705]en
dc.description.sponsorshipStrategic Planning and Management Innovation of Science and Technology Support Demonstration Project of Chongqing Modern Cattle and Sheep Industry [cstc2014zktjccxbx0021]en
dc.description.sponsorshipModern Agro-industry Technology Research System [CARS-35-05]en
dc.description.sponsorshipSichuan Agricultural University Excellent Master's Degree Papers Breeding [YS2014003]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.3389/fpls.2016.00496en
dc.identifier.eissn1664-462Xen
dc.identifier.other496en
dc.identifier.pmid27148320en
dc.identifier.urihttp://hdl.handle.net/10919/89250en
dc.identifier.volume7en
dc.language.isoenen
dc.publisherFrontiersen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectde novo assemblyen
dc.subjectmarker developmenten
dc.subjectHemarthria R. Br.en
dc.subjectRNA-Seqen
dc.subjecttranscriptomeen
dc.titleDe novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Speciesen
dc.title.serialFrontiers In Plant Scienceen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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