Cucurbitaceae genome evolution, gene function, and molecular breeding

Ma, Lili; Wang, Qing; Zheng, Yanyan; Guo, Jing; Yuan, Shuzhi; Fu, Anzhen; Changjun, Bai; Zhao, Xiaoyan; Zheng, Shufang; Wen, Changlong; Guo, Sheng; Gao, Lipu; Grierson, Donald; Zuo, Jinhua; Xu, Yong

doi:10.1093/hr/uhab057

Cited by 44 publications

(43 citation statements)

References 226 publications

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“…Among these species, the most recent speciation events occurred between the species Cucumis hystrix and Cucumis sativus ; they diverged from the common ancestor about 4.81 (3.24–6.48) MYA ( Figure 1 A). The phylogenetic relationship and divergence time are highly consistent with previous studies [ 34 ].…”

Section: Resultssupporting

confidence: 91%

Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species

She

Yang

et al. 2022

IJMS

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Long terminal repeat (LTR)-retrotransposons (LTR-RTs) comprise a major portion of many plant genomes and may exert a profound impact on genome structure, function, and evolution. Although many studies have focused on these elements in an individual species, their dynamics on a family level remains elusive. Here, we investigated the abundance, evolutionary dynamics, and impact on associated genes of LTR-RTs in 16 species in an economically important plant family, Cucurbitaceae. Results showed that full-length LTR-RT numbers and LTR-RT content varied greatly among different species, and they were highly correlated with genome size. Most of the full-length LTR-RTs were amplified after the speciation event, reflecting the ongoing rapid evolution of these genomes. LTR-RTs highly contributed to genome size variation via species-specific distinct proliferations. The Angela and Tekay lineages with a greater evolutionary age were amplified in Trichosanthes anguina, whereas a recent activity burst of Reina and another ancient round of Tekay activity burst were examined in Sechium edule. In addition, Tekay and Retand lineages belonging to the Gypsy superfamily underwent a recent burst in Gynostemma pentaphyllum. Detailed investigation of genes with intronic and promoter LTR-RT insertion showed diverse functions, but the term of metabolism was enriched in most species. Further gene expression analysis in G.pentaphyllum revealed that the LTR-RTs within introns suppress the corresponding gene expression, whereas the LTR-RTs within promoters exert a complex influence on the downstream gene expression, with the main function of promoting gene expression. This study provides novel insights into the organization, evolution, and function of LTR-RTs in Cucurbitaceae genomes.

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Section: Resultssupporting

confidence: 91%

Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species

She

Yang

et al. 2022

IJMS

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“…Species belonging to Benicaseae and Cucurbiteae formed the sister clade. These results were similar with hypothesis of the evolutionary history of the taxa [ 28 ].…”

Section: Resultssupporting

confidence: 92%

Epidermal Patterning Factor 2-like (McEPFL2): A Putative Candidate for the Continuous Ridge (cr) Fruit Skin Locus in Bitter Gourd (Momordica charantia L.)

Yang

Weng

et al. 2022

Genes

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Bitter gourd (Momordica charantia L.) is an economically important vegetable and medicinal crop in many Asian countries. Limited work has been conducted in understanding the genetic basis of horticulturally important traits in bitter gourd. Bitter gourd is consumed primarily for its young, immature fruit, and fruit appearance plays an important role in market acceptability. One such trait is the ridges on the fruit skin. In the present study, molecular mapping of a locus underlying fruit ridge continuity was conducted. Genetic analysis in segregating populations, derived from the crosses between two inbred lines Y1 with continuous ridges (CR) and Z-1-4 with discontinuous ridges (DCR), suggested that CR was controlled by a single recessive gene (cr). High-throughput genome sequencing of CR and DCR bulks combined with high-resolution genetic mapping in an F2 population delimited cr into a 108 kb region with 16 predicted genes. Sequence variation analysis and expression profiling supported the epidermal patterning factor 2-like (McEPFL2) gene as the best candidate of the cr locus. A 1 bp deletion in the first exon of McEPFL2 in Y1 which would result in a truncated McEPFL2 protein may be the causal polymorphism for the phenotypic difference between Y1 and Z-1-4. The association of this 1 bp deletion with CR was further supported by gDNA sequencing of McEPFL2 among 31 bitter gourd accessions. This work provides a foundation for understanding the genetic and molecular control of fruit epidermal pattering and development, which also facilitates marker-assisted selection in bitter melon breeding.

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“…Genome sequences are available to date for 18 different cucurbit species revealing the variation in genome size and organization across the Cucerbitaceae family and reflect the evolution of this highly diverse group (Ma et al ., 2022). Information on intra-specific variation in genome size within this family is, however, still relatively limited.…”

Section: Resultsmentioning

confidence: 99%

Melon pan-genome and multi-parental framework for high-resolution trait dissection

Oren

Dafna

Tzuri

et al. 2022

Preprint

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Linking between genotype and phenotype is a fundamental goal in biology and requires robust data for both layers. The prominent increase in plant genome sequencing and comparisons of multiple related individuals, exposed the abundance of structural genomic variation and suggest that a single reference genome cannot represent the complete sequence diversity of a crop species, leading to the expansion of the pan-genome concept. For high-resolution forward genetics, this unprecedented access to genomic variation should be paralleled by availability and phenotypic characterization of genetic diversity, and effective integration between these layers. Here, we describe a multi-parental framework for trait dissection in melon, leveraging a novel pan-genome constructed for this crop. Melon (Cucumis melo L.) is an important crop from the Cucurbitaceae family, which display extensive phenotypic variation available for breeding. A diverse core set of 25 founder lines (MelonCore25) was sequenced using a combination of short and long-read technologies and their genomes were assembled de novo. The construction of a melon pan-genome exposed substantial variation in genome size and structure, including detection of ~300,000 structural variants and ~9 million SNPs. A half-diallel derived set of 300 F2 populations representing all possible MelonCore25 parental combinations was constructed as framework for trait dissection through integration with the pan-genome. We demonstrate the potential of this unified framework for genetic analysis of various melon traits, including rind color and mottling pattern, fruit sugar content and resistance to fungal diseases. We anticipate that utilization of this integrated resource will enhance genetic dissection of important traits and accelerate melon breeding.Significance statementPan-genomes aim to address the abundance of genome structural variation within species for improved genomic analyses. New pan-genome, constructed from de novo genome assemblies of 25 diverse melon (Cucumis melo L.) accessions is integrated with a half-diallel derived set of 300 F2 populations representing all possible parental combinations. The potential of this unified multi-parental trait dissection framework for melon genetics and breeding is presented.

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Cucurbitaceae genome evolution, gene function, and molecular breeding

Cited by 44 publications

References 226 publications

Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species

Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species

Epidermal Patterning Factor 2-like (McEPFL2): A Putative Candidate for the Continuous Ridge (cr) Fruit Skin Locus in Bitter Gourd (Momordica charantia L.)

Melon pan-genome and multi-parental framework for high-resolution trait dissection

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