The Genome of Cucurbita argyrosperma (Silver-Seed Gourd) Reveals Faster Rates of Protein-Coding Gene and Long Noncoding RNA Turnover and Neofunctionalization within Cucurbita.

  title={The Genome of Cucurbita argyrosperma (Silver-Seed Gourd) Reveals Faster Rates of Protein-Coding Gene and Long Noncoding RNA Turnover and Neofunctionalization within Cucurbita.},
  author={Josu{\'e} Barrera-Redondo and Enrique Ibarra-Laclette and Alejandra V{\'a}zquez‐Lobo and Yocelyn T. Guti{\'e}rrez-Guerrero and Guillermo S{\'a}nchez de la Vega and Daniel Pi{\~n}ero and S. Montes-Hernandez and Rafael Lira-Saade and Luis E. Eguiarte},
  journal={Molecular plant},
  volume={12 4},

Large-scale gene gains and losses molded the NLR defense arsenal during the Cucurbita evolution

Genome-wide annotation reveals that the gene birth–death process of the Cucurbita R family is associated with a species-specific diversification of TNL and CNL protein classes, which will be useful to discover novel R-genes.

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

The results suggest that retrotransposons contributed to the modification of gene expression during diversification of melon genomes, and may affect fruit ripening-inducible gene expression.

Evolutionary Dynamics of Transferred Sequences Between Organellar Genomes in Cucurbita

Phylogenetic reconstruction and tree selection tests suggest that rpl20 and rbcL mitochondrial paralogs arose before Cucurbita diversification whereas the mitochondrial matK and trnL–trnF paralogS emerged most probably later, in the mesophytic Cucorbita clade.

The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening

The genome sequence reported here serves as a valuable resource for snake gourd genetic research and comparative genomic studies in Cucurbitaceae and other plant species, and fruit transcriptome analysis reveals the candidate genes related to quality traits during snake gOURd fruit development and provides a basis for future research on snake gouredd fruitdevelopment and ripening at the transcript level.

Genome-Wide Identification of YABBY Gene Family in Cucurbitaceae and Expression Analysis in Cucumber (Cucumis sativus L.)

Different YABBY gene numbers in eight cucurbit species indicated that gene loss or duplication events exist in an evolutionary process across Cucurbitaceae, and cis-acting elements analysis implied that the YABbys may be involved in plant development, and phytohormone, stress, and light responses.

Building a cluster of NLR genes conferring resistance to pests and pathogens: the story of the Vat gene cluster in cucurbits

The high putative recognition scale offered in melon is revealed based on a combination of SNPs, number of leucine-rich-repeat domains within each homolog and number of homologs within each cluster that might jointly confer resistance to a large pest and pathogen spectrum.

A wild Cucurbita genome reveals the role of structural variants and introgression in domestication

A monophyletic origin of this domesticated crop in the lowlands of Jalisco is indicated, and candidate domestication genes that are involved in the synthesis and regulation of growth hormones, plant defense mechanisms, flowering time and seed development are uncovered.

Neofunctionalization of a polyploidization-activated cotton long intergenic non-coding RNA DAN1 during drought stress regulation

The role of DAN1 in cotton evolution and drought tolerance regulation suggests that the genomic shock of interspecific hybridization and WGD stimulated neofunctionalization of non-coding genes during the natural evolutionary process.

The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

A monophyletic origin of this domesticated crop in the lowlands of Jalisco is indicated and evidence of gene flow between the domesticated and wild subspecies is found, which likely alleviated the effects of the domestication bottleneck.



De novo assembly of the zucchini genome reveals a whole‐genome duplication associated with the origin of the Cucurbita genus

A high-quality draft of the zucchini genome is presented and three independent evidences support that the C. pepo genome is the result of a Whole Genome Duplication: the topology of the gene family phylogenies, the karyotype organization, and the distribution of 4DTv distances.

The genome of melon (Cucumis melo L.)

The data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber, and a low number of nucleotide-binding site–leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species.

Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae).

The mitochondrial genomes of Citrullus lanatus and Cucurbita pepo are sequenced--the two smallest characterized cucurbit mitochondrial genomes--and their RNA editing content is determined and it is found that Cuculbita has a significantly higher synonymous substitution rate (and presumably mutation rate) than Citrulla but comparable levels of RNA editing.

The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring‐spot virus resistance locus

Insight is provided into the paleohistory of Cucurbitaceae genome evolution, the high-quality genome sequence of bottle gourd provides a useful resource for plant comparative genomics studies and cucurbit improvement, and a cleaved amplified polymorphic sequence (CAPS) marker tightly linked to the Prs locus is developed.

The genome of the cucumber, Cucumis sativus L.

This study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo, and identifies 686 gene clusters related to phloem function.

Chloroplast phylogeny of Cucurbita: Evolution of the domesticated and wild species

The chloroplast evidence provides strong support for a novel grouping of the mesophytic annual C. ficifolia (known only from cultivation) with the xerophytic perennials C. foetidissima and C. pedatifolia, and the first DNA‐based evidence in support of the isozyme‐based hypothesis that C. ovifera was domesticated in the eastern United States.

Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions

  • N. UrasakiH. Takagi H. Matsumura
  • Medicine, Biology
    DNA research : an international journal for rapid publication of reports on genes and genomes
  • 2017
Comparative analysis of genome sequences and predicted genes determined that putative trypsin-inhibitor and ribosome-inactivating genes were distinctive in the bitter gourd genome, which could characterize the bittergourd as a medicinal plant.

Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

Slow rates of nucleotide substitution are accompanied by slow rates of synteny erosion during genome divergence in woody perennials.

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols.

The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits, and provides meaningful insight into the complex pathways required for the synthesis of polyphenols.