Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, India.
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.
序列信息已被证明是作物遗传改良和更好地为人类利用的重要基因组资源。为了对棉花基因组进行大规模的基因组资源开发，我们采用低甲基化的基于限制的基因组富集策略对六个不同基因型进行测序。大约产生了 52 亿个数据（超过 1836 万个读数），经过组装后，代表近 12.7 亿个基因组序列。我们总共预测了 93363 个基因模型（21399 个全长），并鉴定了 35923 个基因模型，这些基因模型与已经测序的植物基因组相对应。总共预测了 1093 个转录因子编码基因、3135 个启动子序列和 78 个 miRNA（包括在棉属中鉴定出的 17 个新 miRNA）。我们鉴定了大量的分子标记，包括 47093 个新的简单重复序列和 66364 个新的单核苷酸多态性。此外，我们开发了 NBRI-综合棉花基因组学数据库，这是一个提供 NBRI 开发的棉花相关基因组资源访问的网络资源。这项研究提供了大量的基因组资源，并表明基因富集测序在孤儿作物基因组资源开发中的潜在作用。
