ArticleBMC genomics2011
RNA-Seq improves annotation of protein-coding genes in the cucumber genome.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 108 papers.
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108 citing papers in PubMed.
- The genomic basis of independent marine transitions in turtles: convergent episodic adaptation and demographic shifts.Molecular biology and evolution · 2026Article
- Integrating BSA-Seq, QTL Mapping, and RNA-Seq to Identify Candidate Genes for Hollow Heart in Cucumber Fruits.Plants (Basel, Switzerland) · 2026Article
- Comprehensive analysis of the GeBP gene family in cucumber highlights functional divergence in fruit development and stress tolerance.BMC plant biology · 2026Article
- Multiomics analysis ofHorticulture research · 2026Article
- Cookbook for plant genome sequences.BMC genomics · 2026Review
- A comprehensive analysis of two Chinese cucumber genomes and a mutant population as resources for precision breeding.Horticulture research · 2026Article
- Genome-wide identification of HXK gene families in cucumber and watermelon: CsHXK1 and ClHXK6 play key roles in responding to multiple stresses.BMC plant biology · 2026Article
- Large-scale analysis of MYB genes in Cucurbitaceae identifies a novel gene regulating plant height.Horticulture research · 2025Article
- Evolution and comparison of the expression of TCP genes in the benincaseae and cucurbiteae tribes.Scientific reports · 2025Article
- Genome-Wide Reidentification and Expression Analysis ofInternational journal of molecular sciences · 2025Article
- Research Advances and Perspectives on Early Flowering Traits in Cucumber.Plants (Basel, Switzerland) · 2025Review
- Prediction of transcript isoforms and identification of tissue-specific genes in cucumber.BMC genomics · 2025Article
- Article
- Chromosome-level Haploid Assembly of Cannabis sativa L. cv. Pink Pepper.Scientific data · 2024Article
- Identification of MYC genes in four Cucurbitaceae species and their roles in the response to temperature stress.BMC genomics · 2024Article
- Mining key genes associated with phosphorus deficiency through genome-wide identification and characterization of cucumber SPX family genes.BMC plant biology · 2024Article
- Updated Gene Prediction of the Cucumber (9930) Genome through Manual Annotation.Plants (Basel, Switzerland) · 2024Article
- Comparative Genomic Analysis ofInternational journal of molecular sciences · 2024Article
- Do DEEPER ROOTING 1 Homologs Regulate the Lateral Root Slope Angle in Cucumber (International journal of molecular sciences · 2024Article
- Pan-genome Analysis ofInternational journal of molecular sciences · 2023Article
48 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
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.
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