title: RNA-Seq improves annotation of protein-coding genes in the cucumber genome.
abstract: BACKGROUND
  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 (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.
  
  
  RESULTS
  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 http://cmb.bnu.edu.cn/Cucumis_sativus_v20/.
  
  
  CONCLUSIONS
  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.
authors: College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Street, Beijing, 100875, China.
authors: Zhen
authors: Z
authors: Li
authors: Zhonghua
authors: Z
authors: Zhang
authors: Pengcheng
authors: P
authors: Yan
authors: Sanwen
authors: S
authors: Huang
authors: Zhangjun
authors: Z
authors: Fei
authors: Kui
authors: K
authors: Lin
mesh_terms: D002874:Chromosome Mapping; D018553:Cucumis sativus / Q000235:genetics*; D017343:Genes, Plant; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D018749:RNA, Plant