The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype

Xie, Dasen; Xu, Yanchao; Wang, Jinpeng; Liu, Wenrui; Zhou, Qian; Luo, Shuhong; Huang, Wu; He, Xiaoming; Li, Qing; Peng, Qingwu; Yang, Xue; Yuan, Jiaqing; Yu, Jigao; Wang, Xiyin; Lucas, William J.; Huang, Sanwen; Jiang, Biao; Zhang, Zhonghua

doi:10.1038/s41467-019-13185-3

Cited by 113 publications

(132 citation statements)

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“…Both protein BUSCO benchmark analysis 32 (ver. 3.0) and an InterProScan search 33 indicated that the Harukei-3 genome annotation represents a highly comprehensive dataset of plant protein-coding genes compared with published cucurbit genomes [26][27][28][34][35][36][37][38][39][40] (complete BUSCO = 1372 [95.3%] and InterPro ID count = 5607; Table 2 and Supplementary Data 1). In addition, we observed that our ONT-based gene prediction method gave accurate insights into exon-intron gene structure, whereas other methods (e.g., AUGUSTUS and Braker2) gave incorrect assessments of structure in some genes ( Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

“…>10 kb) emerged as an alternative approach. Many plant genomes have been assembled and/or re-evaluated using such newer DNA sequencers [22][23][24][25][26][27][28] , including the genome of the Chinese inodorus melon cultivar Payzawat, which was sequenced using a PacBio RSII platform 29 . In addition, such approaches can provide insights into genome structural variation, as was demonstrated in Solanum lycopersicum using ONT ultra-long sequencing technology 22 .…”

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confidence: 99%

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

et al. 2020

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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.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

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

et al. 2020

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“…The sponge gourd genome (656.19 Mb) is substantially larger than that of most other sequenced cucurbitaceous species (269-469 Mb) [13][14][15][16][17][18][19] but smaller than that of wax gourd (913 Mb) 12 . Sponge gourd shows much more obvious TE expansion (62.62%) than other cucurbitaceous species such as watermelon (45.2%) 13 , melon (14.7%) 14 , cucumber (24.4%) 15 , and bitter gourd (15.3%) 19 but similar TE expansion to wax gourd (66.18%) 12 . Accordingly, this expansion may have played a crucial role in the increase in the genome size of sponge gourd.…”

Section: The Evolution and Genome Characteristics Of Sponge Gourdmentioning

confidence: 99%

A high-quality sponge gourd (Luffa cylindrica) genome

Zhao

Gong

et al. 2020

Hortic Res

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Sponge gourd (Luffa cylindrica) is an important cultivated vegetable and medicinal plant in the family Cucurbitaceae. In this study, a draft genome sequence of the sponge gourd inbred line P93075 was analyzed. Using Illumina, PacBio, and 10× Genomics sequencing techniques as well as new assembly techniques such as FALCON and chromatin interaction mapping (Hi-C), a chromosome-scale genome of approximately 656.19 Mb, with an N50 scaffold length of 48.76 Mb, was generated. From this assembly, 25,508 protein-coding gene loci were identified, and 63.81% of the whole-genome consisted of transposable elements, which are major contributors to the expansion of the sponge gourd genome. According to a phylogenetic analysis of conserved genes, the sponge gourd lineage diverged from the bitter gourd lineage approximately 41.6 million years ago. Additionally, many genes that respond to biotic and abiotic stresses were found to be lineage specific or expanded in the sponge gourd genome, as demonstrated by the presence of 462 NBS-LRR genes, a much greater number than are found in the genomes of other cucurbit species; these results are consistent with the high stress resistance of sponge gourd. Collectively, our study provides insights into genome evolution and serves as a valuable reference for the genetic improvement of sponge gourd.

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“…Cogn. (Xie et al, 2019). These advances have made it possible to understand the genetic architecture of seed size variation in cucurbits through QTL studies and genome-wide association analysis.…”

Section: Introductionmentioning

confidence: 99%

Quantitative Trait Loci for Seed Size Variation in Cucurbits – A Review

et al. 2020

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Cucurbits (Cucurbitaceae family) include many economically important fruit vegetable crops such as watermelon, pumpkin/squash, cucumber, and melon. Seed size (SS) is an important trait in cucurbits breeding, which is controlled by quantitative trait loci (QTL). Recent advances have deciphered several signaling pathways underlying seed size variation in model plants such as Arabidopsis and rice, but little is known on the genetic basis of SS variation in cucurbits. Here we conducted literature review on seed size QTL identified in watermelon, pumpkin/squash, cucumber and melon, and inferred 14, 9 and 13 consensus SS QTL based on their physical positions in respective draft genomes. Among them, four from watermelon (ClSS2.2, ClSS6.1, ClSS6.2, and ClSS8.2), two from cucumber (CsSS4.1 and CsSS5.1), and one from melon (CmSS11.1) were majoreffect, stable QTL for seed size and weight. Whole genome sequence alignment revealed that these major-effect QTL were located in syntenic regions across different genomes suggesting possible structural and functional conservation of some important genes for seed size control in cucurbit crops. Annotation of genes in the four watermelon consensus SS QTL regions identified genes that are known to play important roles in seed size control including members of the zinc finger protein and the E3 ubiquitinprotein ligase families. The present work highlights the utility of comparative analysis in understanding the genetic basis of seed size variation, which may help future mapping and cloning of seed size QTL in cucurbits.

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The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype

Cited by 113 publications

References 63 publications

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

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

A high-quality sponge gourd (Luffa cylindrica) genome

Quantitative Trait Loci for Seed Size Variation in Cucurbits – A Review

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