The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization
The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization
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DOI：
10.1111/tpj.13781
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发表时间：
2018-01-01
期刊：
影响因子：
7.2
通讯作者：
Mullet, John E.
中科院分区：
文献类型：
--
作者：
McCormick, Ryan F.;Truong, Sandra K.;Mullet, John E.
双色高粱是一种耐旱的C4牧草，用于生产谷物、饲料、糖和木质纤维等生物量，由于其基因组较小(约800Mbp)、二倍体遗传、种质多样性以及与其他C4牧草基因组的共线性，是C4牧草的遗传模式。在这项研究中，使用深度测序、遗传连锁分析和转录组数据来产生和注释高质量的参考基因组序列。改进了参考基因组序列顺序，加入了29.6Mbp的附加序列，注释的基因数量增加了24%，达到34211个，平均基因长度和N50增加，错误频率减少了10倍，每100kbp有1个。在大多数染色体末端都发现了具有微型(TRIM)元件串联重复特征的亚端粒重复序列。核小体占有率预测确定了位于转录起始点下游的核小体，并且在染色体上的密度不同。将来自不同高粱基因型的50多个重新测序的基因组与参考基因组进行比对，发现了大约7.4M个单核苷酸多态(SNPs)和1.9M个Indels。常染色质的大规模变异特征被鉴定出来，周期约为25kbp。从植物主要器官(根、叶、茎、穗和种子)的生长和发育组织(根、叶、茎、穗和种子)的47个RNA-SEQ图谱中，构建了一个基因表达的转录组图谱。对转录组数据的分析表明，组织类型和蛋白激酶表达对转录谱聚类有很大影响。更新的组装、注释和转录组数据代表了C4草研究和作物改良的资源。
Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100kbp. Subtelomeric repeats with characteristics of Tandem Repeats in Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4M single nucleotide polymorphisms (SNPs) and 1.9M indels. Large-scale variant features in euchromatin were identified with periodicities of approximately 25kbp. A transcriptome atlas of gene expression was constructed from 47 RNA-seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.