Tsai Kevin J, Lu Mei-Yeh Jade, Yang Kai-Jung, Li Mengyun, Teng Yuchuan, Chen Shihmay, Ku Maurice S B, Li Wen-Hsiung
Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 11574 Taiwan.
Institute of Biomedical Informatics, National Yang-Ming University, Taipei, 11221 Taiwan.
Sci Rep. 2016 Oct 13;6:35076. doi: 10.1038/srep35076.
The diploid C plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp. The assembly anchors over 98% of the predicted genes to the nine assembled nuclear chromosomes and contains more functional annotation gene models than previous assemblies. Our annotation has identified a large number of unique gene ontology terms related to metabolic activities, a region of chromosome 9 with several growth factor proteins, and regions syntenic with pearl millet or maize genomic regions that have been previously shown to affect growth. The new assembly and annotation for this important species can be used for detailed investigation and future innovations in growth for millet and other grains.
二倍体C4植物谷子（Setaria italica L. Beauv.）在非洲和亚洲的许多地区都是重要作物，因其谷物消费量巨大且能在恶劣环境中生长，但在完整基因组结构方面仍未得到充分研究。迄今为止，仅有两次基因组组装和注释工作，且两个组装都未达到估计基因组大小的86%。我们将从头组装与针对一种流行谷子品种的定制参考引导改进相结合，获得了一个长度为477 Mbp的基因组组装，占估计的490 Mbp的97%以上。该组装将超过98%的预测基因定位到九条组装好的核染色体上，并且比以前的组装包含更多的功能注释基因模型。我们的注释鉴定出了大量与代谢活动相关的独特基因本体术语、一个含有几种生长因子蛋白的9号染色体区域，以及与先前已证明影响生长的珍珠粟或玉米基因组区域同线的区域。这个重要物种的新组装和注释可用于谷子及其他谷物生长的详细研究和未来创新。
