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

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.

Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype

“…For instance, in Payzawat genome only 22,924 genes were identified ( Zhang et al., 2019 ). In contrast, in Harukei-3 and DHL92 genomes, 33,829 and 29,980 genes were identified respectively ( Yano et al., 2020 ; Castanera et al., 2020 ). These differences are likely due to the methods used to automatically annotate the sequenced genomes and genome divergence between the botanical groups.…”

“…For instance, two high-quality melon genomes have been recently assembled from the inodorus and reticulatus horticultural groups of C. melo ssp. melo ( Yano et al., 2020 ; Zhang et al., 2019 ). Two high quality melon genomes were also assembled for C. melo ssp .…”

A cryptic variation in a member of the Ovate Family Proteins is underlying the melon fruit shape QTL fsqs8.1

“…Domínguez et al ( 2020) found associations of transposon element insertion polymorphisms with major agronomic traits and secondary metabolites in cultivated tomato. Similarly, evidence of the role of retrotransposons on the evolution of the genome and modification of gene expression has also been reported in melon (Demirci et al 2021;Sanseverino et al 2015;Yano et al 2020). Thus, fsqs8.1 is perhaps another case of gene expression changes due to structural variation mediated by transposon activity.…”

Comprehensive analysis of both long and short read transcriptomes of a clonal and a seed-propagated model plant species reveal the prerequisites for transcriptional activation of autonomous and non-autonomous transposons in plants

“…These elements have long been considered unavoidable deleterious components of host genomes, being described variously as parasitic or junk DNA. However, there has been a recent resurgence in interest in the roles of TEs, in particular those associated with genome and organism evolution [2,4,[9][10][11][12], as well as environmental adaptation [3,[13][14][15].…”