RNA-Seq improves annotation of protein-coding genes in the cucumber genome
<p>Abstract</p> <p>Background</p> <p>As more and more genomes are sequenced, genome annotation becomes increasingly important in bridging the gap between sequence and biology. Gene prediction, which is at the center of genome annotation, usually integrates various resou...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-11-01
|
| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/12/540 |
| _version_ | 1818583754098081792 |
|---|---|
| author | Fei Zhangjun Yan Pengcheng Huang Sanwen Zhang Zhonghua Li Zhen Lin Kui |
| author_facet | Fei Zhangjun Yan Pengcheng Huang Sanwen Zhang Zhonghua Li Zhen Lin Kui |
| author_sort | Fei Zhangjun |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>As more and more genomes are sequenced, genome annotation becomes increasingly important in bridging the gap between sequence and biology. Gene prediction, which is at the center of genome annotation, usually integrates various resources to compute consensus gene structures. However, many newly sequenced genomes have limited resources for gene predictions. In an effort to create high-quality gene models of the cucumber genome (<it>Cucumis sativus </it>var. <it>sativus</it>), based on the EVidenceModeler gene prediction pipeline, we incorporated the massively parallel complementary DNA sequencing (RNA-Seq) reads of 10 cucumber tissues into EVidenceModeler. We applied the new pipeline to the reassembled cucumber genome and included a comparison between our predicted protein-coding gene sets and a published set.</p> <p>Results</p> <p>The reassembled cucumber genome, annotated with RNA-Seq reads from 10 tissues, has 23, 248 identified protein-coding genes. Compared with the published prediction in 2009, approximately 8, 700 genes reveal structural modifications and 5, 285 genes only appear in the reassembled cucumber genome. All the related results, including genome sequence and annotations, are available at <url>http://cmb.bnu.edu.cn/Cucumis_sativus_v20/</url>.</p> <p>Conclusions</p> <p>We conclude that RNA-Seq greatly improves the accuracy of prediction of protein-coding genes in the reassembled cucumber genome. The comparison between the two gene sets also suggests that it is feasible to use RNA-Seq reads to annotate newly sequenced or less-studied genomes.</p> |
| first_indexed | 2024-12-16T08:10:18Z |
| format | Article |
| id | doaj.art-be7edefc6b364e97927efd423a32efee |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-16T08:10:18Z |
| publishDate | 2011-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-be7edefc6b364e97927efd423a32efee2022-12-21T22:38:22ZengBMCBMC Genomics1471-21642011-11-0112154010.1186/1471-2164-12-540RNA-Seq improves annotation of protein-coding genes in the cucumber genomeFei ZhangjunYan PengchengHuang SanwenZhang ZhonghuaLi ZhenLin Kui<p>Abstract</p> <p>Background</p> <p>As more and more genomes are sequenced, genome annotation becomes increasingly important in bridging the gap between sequence and biology. Gene prediction, which is at the center of genome annotation, usually integrates various resources to compute consensus gene structures. However, many newly sequenced genomes have limited resources for gene predictions. In an effort to create high-quality gene models of the cucumber genome (<it>Cucumis sativus </it>var. <it>sativus</it>), based on the EVidenceModeler gene prediction pipeline, we incorporated the massively parallel complementary DNA sequencing (RNA-Seq) reads of 10 cucumber tissues into EVidenceModeler. We applied the new pipeline to the reassembled cucumber genome and included a comparison between our predicted protein-coding gene sets and a published set.</p> <p>Results</p> <p>The reassembled cucumber genome, annotated with RNA-Seq reads from 10 tissues, has 23, 248 identified protein-coding genes. Compared with the published prediction in 2009, approximately 8, 700 genes reveal structural modifications and 5, 285 genes only appear in the reassembled cucumber genome. All the related results, including genome sequence and annotations, are available at <url>http://cmb.bnu.edu.cn/Cucumis_sativus_v20/</url>.</p> <p>Conclusions</p> <p>We conclude that RNA-Seq greatly improves the accuracy of prediction of protein-coding genes in the reassembled cucumber genome. The comparison between the two gene sets also suggests that it is feasible to use RNA-Seq reads to annotate newly sequenced or less-studied genomes.</p>http://www.biomedcentral.com/1471-2164/12/540 |
| spellingShingle | Fei Zhangjun Yan Pengcheng Huang Sanwen Zhang Zhonghua Li Zhen Lin Kui RNA-Seq improves annotation of protein-coding genes in the cucumber genome BMC Genomics |
| title | RNA-Seq improves annotation of protein-coding genes in the cucumber genome |
| title_full | RNA-Seq improves annotation of protein-coding genes in the cucumber genome |
| title_fullStr | RNA-Seq improves annotation of protein-coding genes in the cucumber genome |
| title_full_unstemmed | RNA-Seq improves annotation of protein-coding genes in the cucumber genome |
| title_short | RNA-Seq improves annotation of protein-coding genes in the cucumber genome |
| title_sort | rna seq improves annotation of protein coding genes in the cucumber genome |
| url | http://www.biomedcentral.com/1471-2164/12/540 |
| work_keys_str_mv | AT feizhangjun rnaseqimprovesannotationofproteincodinggenesinthecucumbergenome AT yanpengcheng rnaseqimprovesannotationofproteincodinggenesinthecucumbergenome AT huangsanwen rnaseqimprovesannotationofproteincodinggenesinthecucumbergenome AT zhangzhonghua rnaseqimprovesannotationofproteincodinggenesinthecucumbergenome AT lizhen rnaseqimprovesannotationofproteincodinggenesinthecucumbergenome AT linkui rnaseqimprovesannotationofproteincodinggenesinthecucumbergenome |