Affordable Access

Access to the full text

RNA-Seq improves annotation of protein-coding genes in the cucumber genome

Authors
  • Li, Zhen1
  • Zhang, Zhonghua2
  • Yan, Pengcheng1
  • Huang, Sanwen2
  • Fei, Zhangjun3
  • Lin, Kui1
  • 1 Beijing Normal University, College of Life Sciences, 19 Xinjiekouwai Street, Beijing, 100875, China , Beijing (China)
  • 2 Chinese Academy of Agricultural Sciences, Key Laboratory of Horticultural Crops Genetic Improvement of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics Technology, Institute of Vegetables and Flowers, 12 Zhongguancunnan Street, Beijing, 100081, China , Beijing (China)
  • 3 Cornell University, Boyce Thompson Institute and USDA Robert W. Holley Center for Agriculture and Health, Tower Road Ithaca, New York, 14853-1801, USA , New York (United States)
Type
Published Article
Journal
BMC Genomics
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Nov 02, 2011
Volume
12
Issue
1
Identifiers
DOI: 10.1186/1471-2164-12-540
Source
Springer Nature
Keywords
License
Yellow

Abstract

BackgroundAs 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 (Cucumis sativus var. sativus), 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.ResultsThe 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 http://cmb.bnu.edu.cn/Cucumis_sativus_v20/.ConclusionsWe 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.

Report this publication

Statistics

Seen <100 times