論文

査読有り 国際誌
2019年6月1日

De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis.

DNA research : an international journal for rapid publication of reports on genes and genomes
  • Hideki Hirakawa
  • ,
  • Katsuhiko Sumitomo
  • ,
  • Tamotsu Hisamatsu
  • ,
  • Soichiro Nagano
  • ,
  • Kenta Shirasawa
  • ,
  • Yohei Higuchi
  • ,
  • Makoto Kusaba
  • ,
  • Masaji Koshioka
  • ,
  • Yoshihiro Nakano
  • ,
  • Masafumi Yagi
  • ,
  • Hiroyasu Yamaguchi
  • ,
  • Kenji Taniguchi
  • ,
  • Michiharu Nakano
  • ,
  • Sachiko N Isobe

26
3
開始ページ
195
終了ページ
203
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1093/dnares/dsy048

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. × 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.

リンク情報
DOI
https://doi.org/10.1093/dnares/dsy048
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/30689773
PubMed Central
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6589549