title: De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species.
abstract: Hemarthria 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 "Yaan" 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.
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University Chengdu, China.
authors.forename: Xiu
authors.initials: X
authors.lastname: Huang
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University Chengdu, China.
authors.forename: Hai-Dong
authors.initials: HD
authors.lastname: Yan
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University Chengdu, China.
authors.forename: Xin-Quan
authors.initials: XQ
authors.lastname: Zhang
authors.affiliation: Herbivorous Livestock Research Institute, Chongqing Academy of Animal Sciences Chongqing, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Horticulture, Virginia Polytechnic Institute and State University Blacksburg, VA, USA.
authors.forename: Taylor P
authors.initials: TP
authors.lastname: Frazier
authors.affiliation: Herbivorous Livestock Research Institute, Chongqing Academy of Animal Sciences Chongqing, China.
authors.forename: De-Jun
authors.initials: DJ
authors.lastname: Huang
authors.affiliation: Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona Cerdanyola del Vallès, Spain.
authors.forename: Lu
authors.initials: L
authors.lastname: Lu
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University Chengdu, China.
authors.forename: Lin-Kai
authors.initials: LK
authors.lastname: Huang
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University Chengdu, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University Chengdu, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Peng
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University Chengdu, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Ma
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University Chengdu, China.
authors.forename: Yan-Hong
authors.initials: YH
authors.lastname: Yan
keywords: Hemarthria R. Br.; RNA-Seq; de novo assembly; marker development; transcriptome