Large-scale resource development in Gossypium hirsutum L. by 454 sequencing of genic-enriched libraries from six diverse genotypes

Plant Biotechnol J. 2013 Oct;11(8):953-63. doi: 10.1111/pbi.12088. Epub 2013 Jun 19.


The sequence information has been proved to be an essential genomic resource in case of crop plants for their genetic improvement and better utilization by humans. To dissect the Gossypium hirsutum genome for large-scale development of genomic resources, we adopted hypomethylated restriction-based genomic enrichment strategy to sequence six diverse genotypes. Approximately 5.2-Gb data (more than 18.36 million reads) was generated which, after assembly, represents nearly 1.27-Gb genomic sequences. We predicted a total of 93,363 gene models (21,399 full length) and identified 35,923 gene models which were validated against already sequenced plant genomes. A total of 1,093 transcription factor-encoding genes, 3,135 promoter sequences and 78 miRNA (including 17 newly identified in Gossypium) were predicted. We identified significant no. of molecular markers including 47,093 novel simple sequence repeats and 66,364 novel single nucleotide polymorphisms. In addition, we developed NBRI-Comprehensive Cotton Genomics database, a web resource to provide access of cotton-related genomic resources developed at NBRI. This study contributes considerable amount of genomic resources and suggests a potential role of genic-enriched sequencing in genomic resource development for orphan crop plants.

Keywords: Genome; HMPR; SNP; SRA053686; SSR; cotton.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Plant / chemistry
  • Databases, Genetic*
  • Gene Library*
  • Genetic Markers
  • Genotype
  • Gossypium / genetics*
  • Microsatellite Repeats
  • Molecular Sequence Annotation
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA


  • DNA, Plant
  • Genetic Markers