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Transcriptome Characterization and Functional Marker Development in Sorghum Sudanense
Sudangrass, Sorghum sudanense, is an important forage in warm regions. But little is known about its genome. In this study, the transcriptomes of sudangrass S722 and sorghum Tx623B were sequenced by Illumina sequencing. More than 4Gb bases were sequenced for each library. For Tx623B and S722, 88.79%...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2016
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4859472/ https://www.ncbi.nlm.nih.gov/pubmed/27152648 http://dx.doi.org/10.1371/journal.pone.0154947 |
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author | Li, Jieqin Wang, Lihua Zhan, Qiuwen Liu, Yanlong Yang, Xiaocui |
author_facet | Li, Jieqin Wang, Lihua Zhan, Qiuwen Liu, Yanlong Yang, Xiaocui |
author_sort | Li, Jieqin |
collection | PubMed |
description | Sudangrass, Sorghum sudanense, is an important forage in warm regions. But little is known about its genome. In this study, the transcriptomes of sudangrass S722 and sorghum Tx623B were sequenced by Illumina sequencing. More than 4Gb bases were sequenced for each library. For Tx623B and S722, 88.79% and 83.88% reads, respectively were matched to the Sorghum bicolor genome. A total of 2,397 differentially expressed genes (DEGs) were detected by RNA-Seq between the two libraries, including 849 up-regulated genes and 1,548 down-regulated genes. These DEGs could be divided into three groups by annotation analysis. A total of 44,495 single nucleotide polymorphisms (SNPs) were discovered by aligning S722 reads to the sorghum reference genome. Of these SNPs, 61.37% were transition, and this value did not differ much between different chromosomes. In addition, 16,928 insertion and deletion (indel) loci were identified between the two genomes. A total of 5,344 indel markers were designed, 15 of which were selected to construct the genetic map derived from the cross of Tx623A and Sa. It was indicated that the indel markers were useful and versatile between sorghum and sudangrass. Comparison of synonymous base substitutions (Ks) and non-synonymous base substitutions (Ka) between the two libraries showed that 95% orthologous pairs exhibited Ka/Ks<1.0, indicating that these genes were influenced by purifying selection. The results from this study provide important information for molecular genetic research and a rich resource for marker development in sudangrass and other Sorghum species. |
format | Online Article Text |
id | pubmed-4859472 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-48594722016-05-13 Transcriptome Characterization and Functional Marker Development in Sorghum Sudanense Li, Jieqin Wang, Lihua Zhan, Qiuwen Liu, Yanlong Yang, Xiaocui PLoS One Research Article Sudangrass, Sorghum sudanense, is an important forage in warm regions. But little is known about its genome. In this study, the transcriptomes of sudangrass S722 and sorghum Tx623B were sequenced by Illumina sequencing. More than 4Gb bases were sequenced for each library. For Tx623B and S722, 88.79% and 83.88% reads, respectively were matched to the Sorghum bicolor genome. A total of 2,397 differentially expressed genes (DEGs) were detected by RNA-Seq between the two libraries, including 849 up-regulated genes and 1,548 down-regulated genes. These DEGs could be divided into three groups by annotation analysis. A total of 44,495 single nucleotide polymorphisms (SNPs) were discovered by aligning S722 reads to the sorghum reference genome. Of these SNPs, 61.37% were transition, and this value did not differ much between different chromosomes. In addition, 16,928 insertion and deletion (indel) loci were identified between the two genomes. A total of 5,344 indel markers were designed, 15 of which were selected to construct the genetic map derived from the cross of Tx623A and Sa. It was indicated that the indel markers were useful and versatile between sorghum and sudangrass. Comparison of synonymous base substitutions (Ks) and non-synonymous base substitutions (Ka) between the two libraries showed that 95% orthologous pairs exhibited Ka/Ks<1.0, indicating that these genes were influenced by purifying selection. The results from this study provide important information for molecular genetic research and a rich resource for marker development in sudangrass and other Sorghum species. Public Library of Science 2016-05-06 /pmc/articles/PMC4859472/ /pubmed/27152648 http://dx.doi.org/10.1371/journal.pone.0154947 Text en © 2016 Li et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Li, Jieqin Wang, Lihua Zhan, Qiuwen Liu, Yanlong Yang, Xiaocui Transcriptome Characterization and Functional Marker Development in Sorghum Sudanense |
title | Transcriptome Characterization and Functional Marker Development in Sorghum Sudanense |
title_full | Transcriptome Characterization and Functional Marker Development in Sorghum Sudanense |
title_fullStr | Transcriptome Characterization and Functional Marker Development in Sorghum Sudanense |
title_full_unstemmed | Transcriptome Characterization and Functional Marker Development in Sorghum Sudanense |
title_short | Transcriptome Characterization and Functional Marker Development in Sorghum Sudanense |
title_sort | transcriptome characterization and functional marker development in sorghum sudanense |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4859472/ https://www.ncbi.nlm.nih.gov/pubmed/27152648 http://dx.doi.org/10.1371/journal.pone.0154947 |
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