Reference genome sequence of the model plant Setaria
Reference genome sequence of the model plant Setaria
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DOI：
10.1038/nbt.2196
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发表时间：
2012-06-01
影响因子：
46.9
通讯作者：
Devos, Katrien M.
中科院分区：
文献类型：
--
作者：
Bennetzen, Jeffrey L.;Schmutz, Jeremy;Devos, Katrien M.
我们产生了一个高质量的参考基因组序列的谷子（Setaria italica）。类似于400-Mb的组装覆盖了类似于80%的基因组和> 95%的基因空间。将组装体锚定到992个基因座遗传图谱上，并通过与> 130万个表达的序列标签读数进行比较来注释。我们产生了超过5.8亿个RNA-Seq读数，以促进表达分析。我们还对狗尾草（Setaria viridis）进行了测序，狗尾草是狗尾草的祖先野生亲戚。斜体，并确定了差异单核苷酸多态性密度，转座因子，小RNA含量，染色体重排和分离畸变的分布区域。狗尾草属包括天然和栽培物种，表现出广泛的适应能力。这种适应的遗传基础进行了研究，通过比较五个测序草基因组。我们还使用二倍体狗尾草基因组进行评估相关的多倍体，柳枝稷（柳枝稷）的基因组组装。
We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The similar to 400-Mb assembly covers similar to 80% of the genome and > 95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with > 1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).