Resequencing of durian genomes reveals large genetic variations among different cultivars

Frontiers in Plant Science

Plant Science

Orwintinee Chusri¹  Wirulda Pootakham²  Chaiwat Naktang²  Salisa Charoensri²  Sithichoke Tangphatsornruang²  Sonicha U-thoomporn²  Wanapinun Nawae²  Nattapol Narong² 

[1] Chantaburi Horticulture Research Center, Horticulture Research Institute, Department of Agriculture, Chantaburi, Thailand;National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand;

关键词: durian;    genome assembly;    pangenome;    comparative genomics;    genomic structural variation;   

DOI  :  10.3389/fpls.2023.1137077

 received in 2023-01-04, accepted in 2023-02-06,  发布年份 2023

来源: Frontiers

【 摘 要 】

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.

【 授权许可】

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Copyright © 2023 Nawae, Naktang, Charoensri, U-thoomporn, Narong, Chusri, Tangphatsornruang and Pootakham