論文

2020年8月

Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression

Communications biology
  • Yano, Ryoichi
  • ,
  • Ariizumi, Tohru
  • ,
  • Nonaka, Satoko
  • ,
  • Kawazu, Yoichi
  • ,
  • Zhong, Silin
  • ,
  • Mueller, Lukas
  • ,
  • Giovannoni, James J
  • ,
  • Rose, Jocelyn K C
  • ,
  • Ezura, Hiroshi

3
1
開始ページ
432
終了ページ
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1038/s42003-020-01172-0
出版者・発行元
NATURE PUBLISHING GROUP

Melon exhibits substantial natural variation especially in fruit ripening physiology, including both climacteric (ethylene-producing) and non-climacteric types. However, genomic mechanisms underlying such variation are not yet fully understood. Here, we report an Oxford Nanopore-based high-grade genome reference in the semi-climacteric cultivar Harukei-3 (378 Mb + 33,829 protein-coding genes), with an update of tissue-wide RNA-seq atlas in the Melonet-DB database. Comparison between Harukei-3 and DHL92, the first published melon genome, enabled identification of 24,758 one-to-one orthologue gene pairs, whereas others were candidates of copy number variation or presence/absence polymorphisms (PAPs). Further comparison based on 10 melon genome assemblies identified genome-wide PAPs of 415 retrotransposon Gag-like sequences. Of these, 160 showed fruit ripening-inducible expression, with 59.4% of the neighboring genes showing similar expression patterns (r > 0.8). Our results suggest that retrotransposons contributed to the modification of gene expression during diversification of melon genomes, and may affect fruit ripening-inducible gene expression.

リンク情報
DOI
https://doi.org/10.1038/s42003-020-01172-0

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