De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis
De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis
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DOI：
10.1093/dnares/dsy048
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发表时间：
2019-06-01
期刊：
影响因子：
4.1
通讯作者：
Isobe, Sachiko N.
中科院分区：
文献类型：
--
作者：
Hirakawa, Hideki;Sumitomo, Katsuhiko;Isobe, Sachiko N.
栽培菊花（chrysanthemum morifolium Ramat.）是世界上最重要的观赏作物之一。它有一个复杂的六倍体基因组（2n = 6x = 54）和大的基因组大小。二倍体菊花（Chrysanthemum seticuspe）常被用作栽培菊花的模型，因为这两个物种是密切相关的。为了扩大我们对栽培菊花的了解，我们在这里使用Illumina测序平台对C. seticuspe进行了从头全基因组组装。XMRS10是一种自亲和菌株AEV2经5代自交而获得的菌株，用于基因组测序。由354,212个支架组成的2.72 Gb的组装序列（CSE_r1.0）覆盖了k-mer分析估计的3.06 Gb的C. seticuspe基因组的89.0%。支架N50长度为44,741 bp。对于蛋白编码基因，推导出71,057个注释基因（cse_r11 .1_cds）。接下来，基于组装好的基因组序列，我们对金菊和栽培菊花进行了连锁图谱构建、基因发现和比较分析。结果显示，在AEV2基因组上存在偏斜区分离。在基因发现分析中，在CSE_r1.1_cds中新发现候选开花相关基因。此外，对C. x morifolium基因组的单核苷酸多态性鉴定和注释表明，C. seticuspe基因组可用于栽培菊花的遗传分析。本文所收集的基因组序列有望为今后的菊花研究做出贡献。此外，我们的方法证明了短读基因组组装的有用性，以及基于后基因组分析的目的选择合适的下一个基因组测序技术的重要性。
Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most economically important ornamental crops grown worldwide. It has a complex hexaploid genome (2n = 6x = 54) and large genome size. The diploid Chrysanthemum seticuspe is often used as a model of cultivated chrysanthemum, since the two species are closely related. To expand our knowledge of the cultivated chrysanthemum, we here performed de novo whole-genome assembly in C. seticuspe using the Illumina sequencing platform. XMRS10, a C. seticuspe accession developed by five generations of self-crossing from a self-compatible strain, AEV2, was used for genome sequencing. The 2.72 Gb of assembled sequences (CSE_r1.0), consisting of 354,212 scaffolds, covered 89.0% of the 3.06 Gb C. seticuspe genome estimated by k-mer analysis. The N50 length of scaffolds was 44,741 bp. For protein-encoding genes, 71,057 annotated genes were deduced (CSE_r1.1_cds). Next, based on the assembled genome sequences, we performed linkage map construction, gene discovery and comparative analyses for C. seticuspe and cultivated chrysanthemum. The generated C. seticuspe linkage map revealed skewed regions in segregation on the AEV2 genome. In gene discovery analysis, candidate flowering-related genes were newly found in CSE_r1.1_cds. Moreover, single nucleotide polymorphism identification and annotation on the C. x morifolium genome showed that the C. seticuspe genome was applicable to genetic analysis in cultivated chrysanthemums. The genome sequences assembled herein are expected to contribute to future chrysanthemum studies. In addition, our approach demonstrated the usefulness of short-read genome assembly and the importance of choosing an appropriate next genome sequencing technology based on the purpose of the post-genome analysis.