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De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species
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 comprehensiv...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2016
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834353/ https://www.ncbi.nlm.nih.gov/pubmed/27148320 http://dx.doi.org/10.3389/fpls.2016.00496 |
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author | Huang, Xiu Yan, Hai-Dong Zhang, Xin-Quan Zhang, Jian Frazier, Taylor P. Huang, De-Jun Lu, Lu Huang, Lin-Kai Liu, Wei Peng, Yan Ma, Xiao Yan, Yan-Hong |
author_facet | Huang, Xiu Yan, Hai-Dong Zhang, Xin-Quan Zhang, Jian Frazier, Taylor P. Huang, De-Jun Lu, Lu Huang, Lin-Kai Liu, Wei Peng, Yan Ma, Xiao Yan, Yan-Hong |
author_sort | Huang, Xiu |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4834353 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-48343532016-05-04 De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species Huang, Xiu Yan, Hai-Dong Zhang, Xin-Quan Zhang, Jian Frazier, Taylor P. Huang, De-Jun Lu, Lu Huang, Lin-Kai Liu, Wei Peng, Yan Ma, Xiao Yan, Yan-Hong Front Plant Sci Plant Science 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. Frontiers Media S.A. 2016-04-18 /pmc/articles/PMC4834353/ /pubmed/27148320 http://dx.doi.org/10.3389/fpls.2016.00496 Text en Copyright © 2016 Huang, Yan, Zhang, Zhang, Frazier, Huang, Lu, Huang, Liu, Peng, Ma and Yan. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Huang, Xiu Yan, Hai-Dong Zhang, Xin-Quan Zhang, Jian Frazier, Taylor P. Huang, De-Jun Lu, Lu Huang, Lin-Kai Liu, Wei Peng, Yan Ma, Xiao Yan, Yan-Hong De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species |
title | De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species |
title_full | De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species |
title_fullStr | De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species |
title_full_unstemmed | De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species |
title_short | De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species |
title_sort | de novo transcriptome analysis and molecular marker development of two hemarthria species |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834353/ https://www.ncbi.nlm.nih.gov/pubmed/27148320 http://dx.doi.org/10.3389/fpls.2016.00496 |
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