Sorghum bicolor strain:Keller, E-Tian, Ji2731 Genome sequencing and assembly

Sorghum (Sorghum bicolor) is globally produced as a source of food, feed, fibre and fuel. Grain and sweet sorghums differ in a number of important traits including stem sugar and juice accumulation, plant height and production of grain and biomass. The first whole genome sequence of a grain sorghum is available, but additional genome sequences are required to study genome-wide and intraspecies variation for dissecting the genetic basis of these important traits and for tailor-designed breeding of this important C4 crop. We resequenced two sweet and one grain sorghum inbred lines, and identified a set of nearly 1,500 genes differentiating sweet and grain sorghum. In addition, we uncovered 1,057,018 SNPs, 99,948 indels of 1-10bp in length and 16,487 presence/absence variations. In addition, 17,111 CNVs were detected. This is a first report on the identification of genome-wide patterns of genetic variation in sorghum. Because some genes might exist in sorghum but are missed in the currently assembled BTx623 sorghum genome. We assembled unmapped reads with SOAPdenovo and obtained contigs with a total length of 7.2 Mb of sequences. Annotation of these contigs showed 73 putative absent genes with an average length of 409bp (only coding regions were considered). A BLAST search against Arabidopsis, rice and maize genome databases revealed that 33 of these genes showed homology with known proteins (E value < 1e-617 ).

高粱（Sorghum bicolor）作为粮食、饲料、纤维与能源作物在全球范围内广泛种植。粒用高粱与甜高粱在多个重要性状上存在显著差异，包括茎秆糖分与汁液积累量、株高以及籽粒与生物量产量。目前已公布首个粒用高粱的全基因组序列，但为解析这一重要C4作物上述关键性状的遗传基础，并开展定制化育种，仍需获取更多基因组序列以开展全基因组范围及种内变异研究。本研究对2份甜高粱自交系与1份粒用高粱自交系进行了重测序，鉴定得到近1500个可区分甜、粒用高粱的基因集。此外，本研究共发现1,057,018个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）、99,948个长度为1-10bp的插入缺失变异（Insertion-Deletion, indels）以及16,487个存在/缺失变异，同时检测到17,111个拷贝数变异（Copy Number Variation, CNVs）。本研究首次报道了高粱全基因组水平的遗传变异模式。由于部分基因可能天然存在于高粱基因组中，但在当前已组装的BTx623高粱参考基因组中未被捕获组装，我们使用SOAPdenovo对未比对到参考基因组的reads进行从头组装，得到总长度为7.2 Mb的重叠群（contigs）序列。对这些重叠群的注释结果显示，共获得73个推定的缺失基因，平均长度为409bp（仅考虑编码区域）。通过针对拟南芥、水稻和玉米基因组数据库进行BLAST比对搜索，其中33个基因与已知蛋白具有同源性（E值<1e-617）。

搜集汇总

背景与挑战

背景概述

该数据集包含高粱（Sorghum bicolor）的基因组测序和组装数据，特别关注甜高粱和粒用高粱之间的遗传变异。研究识别了近1,500个区分两者的基因，以及超过100万个SNPs和其他类型的遗传变异，为高粱的遗传研究和育种提供了重要资源。