The BioEnergy Science Center and the Department of Genetics, University of Georgia, Athens, Georgia, USA.
Nat Biotechnol. 2012 May 13;30(6):555-61. doi: 10.1038/nbt.2196.
We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼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).
我们生成了一份高质量的狐尾粟（Setaria italica）参考基因组序列。这个约 400Mb 的组装覆盖了基因组的约 80%和 >95%的基因空间。该组装通过与超过 130 万条表达序列标签读数的比较被锚定到一个 992 个基因座的遗传图谱上，并进行了注释。我们生成了超过 5.8 亿条 RNA-Seq 读数，以促进表达分析。我们还对狐尾粟的野生祖先种绿色狐尾粟（Setaria viridis）进行了测序，并鉴定了差异单核苷酸多态性密度、转座元件分布、小 RNA 含量、染色体重排和分离失真的区域。狐尾粟属包括自然和栽培种，它们表现出广泛的适应能力。通过比较五个已测序的草基因组，研究了这种适应的遗传基础。我们还使用二倍体狐尾粟基因组来评估相关多倍体柳枝稷（Panicum virgatum）的正在进行的基因组组装。
