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.…”

Unveiling unknown transcripts and exons: Insights into durian var. D24 (Durio zibethinus Murr.) fruit development and ripening

“…Several scientific studies have suggested that deep sequencing can detect differential expression of genes, novel genes, transcripts, differentially expressed isoforms and splice variation unique for each condition (Jakhesara et al 2013). Transcriptome data of Malaysia and Thailand durian (Teh et al 2017;Husin et al 2022;Nawae et al 2023) and associated annotation data may fill in some gaps in durian molecular biology, often focused on phytochemical compositions and nutritional properties. The reference assembly of the durian genome (MK) used in this study consisted of chromosome-scale pseudomolecules with a length of 30 pseudomolecules larger than 10 Mb and comprising 95 % of the 712-Mb assembly (the pseudomolecules are hereafter referred to as chromosomes, numbered by scale).…”

“…The study reveals that a large portion of the Kradumthong (KD), Monthong (MT), and Puangmanee (PM) assemblies align closely with the Musang King (MK) assembly, surpassing 50 % identity. However, certain regions, particularly within repeat sections of the MK assembly, show lower identity percentages (Nawae et al 2023). Unknown transcripts (UTs) can include both coding and non-coding RNA sequences.…”

“…Therefore, while some UTs may be non-coding RNAs (ncRNAs), others may represent novel protein-coding genes or alternative isoforms of known genes (Zhao et al 2022). While the genomes and transcriptomes of durian of the Malaysian MK variety (Teh et al 2017), Malaysian D24 variety (Husin et al 2022), and three Thailand durian cultivars (Nawae et al 2023) have been extensively studied, little attention has been given to the identification of unknown genes or transcripts expressed in the durian transcriptome. Novel transcripts from durian transcriptome data are pieces of RNA sequences found during a transcriptome analysis but whose origin or functions still need to be discovered.…”