期刊
COMMUNICATIONS BIOLOGY
卷 3, 期 1, 页码 -出版社
NATURE PORTFOLIO
DOI: 10.1038/s42003-020-01172-0
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资金
- JSPS KAKENHI [16K18633]
- JST PRESTO [JPMJPR17Q7]
- Cross-ministerial Strategic Innovation Promotion Program (SIP)
- Grants-in-Aid for Scientific Research [16K18633] Funding Source: KAKEN
Ryoichi Yano et al. report a Nanopore-based reference genome assembly of muskmelon-a fruit known for its many cultivated varieties, including cantaloupe and honeydew-using the Japanese Harukei-3 cultivar. They identify structural genetic variation by comparing the reference to several melon genome assemblies and investigate tissue-wide gene expression patterns by RNA sequencing. 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.
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