Resequencing of durian genomes reveals large genetic variations among different cultivars

Abstract

Durian (Durio zibethinus), which yields the fruit known as the “King of Fruits,” is an important economic crop in Southeast Asia. Several durian cultivars have been developed in this region. In this study, we resequenced the genomes of three popular durian cultivars in Thailand, including Kradumthong (KD), Monthong (MT), and Puangmanee (PM) to investigate genetic diversities of cultivated durians. KD, MT, and PM genome assemblies were 832.7, 762.6, and 821.6 Mb, and their annotations covered 95.7, 92.4, and 92.7% of the embryophyta core proteins, respectively. We constructed the draft durian pangenome and analyzed comparative genomes with related species in Malvales. Long terminal repeat (LTR) sequences and protein families in durian genomes had slower evolution rates than that in cotton genomes. However, protein families with transcriptional regulation function and protein phosphorylation function involved in abiotic and biotic stress responses appeared to evolve faster in durians. The analyses of phylogenetic relationships, copy number variations (CNVs), and presence/absence variations (PAVs) suggested that the genome evolution of Thai durians was different from that of the Malaysian durian, Musang King (MK). Among the three newly sequenced genomes, the PAV and CNV profiles of disease resistance genes and the expressions of methylesterase inhibitor domain containing genes involved in flowering and fruit maturation in MT were different from those in KD and PM. These genome assemblies and their analyses provide valuable resources to gain a better understanding of the genetic diversity of cultivated durians, which may be useful for the future development of new durian cultivars.

Durian (Durio zibethinus L.): Nutritional Composition, Pharmacological Implications, Value-Added Products, and Omics-Based Investigations

“…This research provides valuable insights into the molecular regulation of the key gene (MGL) responsible for the production of VSCs during the ripening process. Beyond investigations into molecular mechanisms during fruit post-harvest ripening, a few studies undertook a reanalysis of durian genomic data [115][116][117].…”

“…Without extensive genomic variation data spanning a diverse spectrum of durian varieties, including wild species, the identification of novel genes contributing to pivotal domestication traits on a global scale remains elusive. Noteworthy case studies in the existing literature have delved into genome resequencing in grapevine [122] and durian [117]. The latter study encompassed the whole-genome resequencing of three popular durian cultivars, unveiling genetic variations among them.…”