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

Authors: YANO, RYOICHI - University Of Tsukuba; ARIIZUMI, TOHRU - University Of Tsukuba; NONAKA, SATOKO - University Of Tsukuba; KAWAZU, YOICHI - National Agriculture And Food Research Organization (NARO), Agricultrual Research Center; ZHONG, SILIN - The Chinese University Of Hong Kong (CUHK); MUELLER, LUKAS - Boyce Thompson Institute; Giovannoni, James; ROSE, JOCELYN - Cornell University; EZURA, HIROSHI - University Of Tsukuba

Submitted to: Communications Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/3/2020
Publication Date: 12/17/2020
Citation: Yano, R., Ariizumi, T., Nonaka, S., Kawazu, Y., Zhong, S., Mueller, L., Giovannoni, J.J., Rose, J., Ezura, H. 2020. Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression. Communications Biology. 3:432. https://doi.org/10.1038/s42003-020-01172-0.
DOI: https://doi.org/10.1038/s42003-020-01172-0

Interpretive Summary: Melon is one of the most economically important fruit crops in the world and is a source of vitamins, minerals, and other health-promoting substances. The melon genome comprises 12 chromosomes, and its genome size was estimated to be ~454'Mb based on the nuclear DNA content. In this current study, we assembled the whole genome sequence of the semi-climacteric Japanese cultivar “Earl’s Favorite Harukei-3” using a variety of short length, paired-end and long read length sequences. This melon shows moderate climacteric ripening behavior, although the rate of ripening is less than that of the well-studied cultivar Charentais. Seven additional genomes were used for comparative analyses. Based on a combination of comparative genomics and comprehensive gene expression analysis, we suggest that retrotransposons played a role in the modification of gene expression as well as evolution of fruit-ripening-inducible gene expression during diversification of melon genomes. This information is valuable in predicting melon gene activity and in selecting genotypes and alleles for breeding toward improved melon varieties.

Technical Abstract: 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.