Identification and characterization of genome-wide resistance gene analogs (RGAs) of durian (Durio zibethinus L.)

Cortaga, Cris Q.; Latina, Romnick A.; Habunal, Rosteo R; Lantican, Darlon V.

doi:10.1186/s43141-022-00313-8

Cited by 18 publications

(13 citation statements)

References 57 publications

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“…The reanalysis of this genome showed a hexaploidization event in the durian genome about 19–21 million years ago (Mya) ( Wang et al., 2019 ). Another analysis of the same genome sequence revealed a catalog of 2,586 resistance gene analogs in this durian cultivar ( Cortaga et al., 2022 ). This genome sequence has proven itself to be an important resource for understanding the agronomic characteristics and evolution of durian.…”

Section: Introductionmentioning

confidence: 99%

Resequencing of durian genomes reveals large genetic variations among different cultivars

Nawae

Naktang²,

Charoensri³

et al. 2023

Front. Plant Sci.

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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.

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Section: Introductionmentioning

confidence: 99%

Resequencing of durian genomes reveals large genetic variations among different cultivars

Nawae

Naktang²,

Charoensri³

et al. 2023

Front. Plant Sci.

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“…Both varieties are of the same species (M. indica) and are important varieties in the mango international trade. With the availability of WGS data, in-depth genome analysis can be performed to unravel gene networks, reveal intron-exon boundaries, detect transposable elements, discover novel biological processes, develop molecular markers tagging economically important traits for breeding (e.g., insect pest and disease resistance), and identify genome-wide variants such as single-nucleotide polymorphisms (SNPs) and insertionsdeletions (InDels) [10][11][12][13][14]. SNPs and InDels are differences and variations in the genome which can have a huge impact on the biological and physical traits of an organism.…”

Section: Introductionmentioning

confidence: 99%

“…. Majority of the SNPs observed were in the intergenic(14,016,127; 76.52%) and intronic (3,305,720; 18.05%) regions, and 9,020,409 (49.25%) and 8,384,036 (45.77%) SNPs were positioned in the upstream and downstream regions from the genes set, respectively. Meanwhile, 569,575 (3.11%) SNPs were missense variants.…”

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confidence: 96%

Genome-wide SNP and InDel analysis of three Philippine mango species inferred from whole-genome sequencing

Cortaga

Lachica

Lantican

et al. 2022

Journal of Genetic Engineering and Biotechnology

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Background The Philippines is among the top 10 major exporters of mango worldwide. However, genomic studies of Philippine mangoes remain largely unexplored and lacking. Here, we sequenced the whole genome of the three Philippine mango species, namely, Mangifera odorata (Huani), Mangifera altissima (Paho), and Mangifera indica “Carabao” variety using Illumina HiSeq 2500, to identify and analyze their genome-wide variants (SNPs and InDels). Results The high confidence variants were identified by successfully mapping 93–95% of the quality-filtered reads to the Alphonso and Tommy Atkins mango reference genomes. Using these two currently available mango genomes, most variants were observed in M. odorata (4,353,063 and 4,277,287), followed by M. altissima (3,392,763 and 3,449,917), and lastly, M. indica Carabao (2,755,267 and 2,852,480). Approximately 50, 46, and 38% of the variants were unique in the three Philippine mango genomes. The analysis of variant effects and functional annotation across the three mango species revealed 56,982 variants with high-impact effects mapped onto 37,746 genes, of which 25% were found to be novel. The affected mango genes include those with potential economic importance such as 6945 genes for defense/resistance/immune response, 323 genes for fruit development, and 338 genes for anthocyanin production. Conclusions To date, this is the first sequencing effort to comprehensively analyze genome-wide variants essential for the development of genome-wide markers specific to these mango species native to the Philippines. This study provides an important genomic resource that can be used for the genetic improvement of mangoes.

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“…We suggest extending research into the genomics of durian, for example, to identify resistance‐related genes, to species beyond commonly cultivated cultivars such as ‘Musang King’, which are the focus of most recent studies (see, e.g. Cortaga et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

The king of fruits

Thorogood

Ghazalli

Siti‐Munirah

et al. 2022

Plants People Planet

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The durian (genus Durio) has aroused curiosity among botanists for centuries, and influenced local culture across Southeast Asia for millennia. Of the 30 described species of Durio, about a third produce edible fruits, yet just one (Durio zibethinus) is grown on a commercial scale. Several new species have been described recently, which may be a reservoir of important genetic resources. Meanwhile, unregulated durian cultivation triggered by rapidly growing demand and a high return on investment may pose a threat to natural forests. Here we review recent findings in the genus with a focus on Malaysia and Indonesia. We suggest that further research into obscure wild relatives and local cultivars, will be important in the context of growing international demand for durian, coupled with an increasing reliance on commercial cultivars of this economically and culturally important fruit. Finally we suggest greater attention should be given to the potential threat to biodiversity posed by illegal durian plantations in one of the most biodiverse regions of the planet.

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Identification and characterization of genome-wide resistance gene analogs (RGAs) of durian (Durio zibethinus L.)

Cited by 18 publications

References 57 publications

Resequencing of durian genomes reveals large genetic variations among different cultivars

Resequencing of durian genomes reveals large genetic variations among different cultivars

Genome-wide SNP and InDel analysis of three Philippine mango species inferred from whole-genome sequencing

The king of fruits

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