Dataset Information

The complete chloroplast genome sequence of the Cucurbita pepo L. (Cucurbitaceae).

ABSTRACT: Cucurbita pepo is an important economic plant cultivated widely in the world. The complete chloroplast genome sequence of C. pepo is reported here. The genome is 157,343?bp in length and exhibits a typical quadripartite structure of the large (LSC, 87,970?bp) and small (SSC, 18,167?bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,603?bp). A total of 131 genes were predicted including 85 protein-coding genes, eight rRNA genes and 38 tRNA genes. Further, phylogenetic analysis showed that C. pepo were closely related to other species in the family Cucurbitaceae. The complete chloroplast genome of C. pepo would be taken as a useful molecular tool for species discrimination, taxonomy, and phylogenetic relationships in the family Cucurbitaceae.

SUBMITTER: Zhang C

PROVIDER: S-EPMC7799668 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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The complete chloroplast genome sequence of the Cucurbita pepo L. (Cucurbitaceae).

Zhang Chen C Zhu Qianglong Q Liu Shi S Gao Peng P Zhu Zicheng Z Wang Xuezheng X Luan Feishi F

Mitochondrial DNA. Part B, Resources 20180629 2

Cucurbita pepo is an important economic plant cultivated widely in the world. The complete chloroplast genome sequence of C. pepo is reported here. The genome is 157,343 bp in length and exhibits a typical quadripartite structure of the large (LSC, 87,970 bp) and small (SSC, 18,167 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,603 bp). A total of 131 genes were predicted including 85 protein-coding genes, eight rRNA genes and 38 tRNA genes. Further, phyl ...[more]

PMID: 33474295

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Project description:BACKGROUND: Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat and vitamins. A broad range of genomic tools are today available for other cucurbits that have become models for the study of different metabolic processes. However, these tools are still lacking in the Cucurbita genus, thus limiting gene discovery and the process of breeding. RESULTS: We report the generation of a total of 512,751 C. pepo EST sequences, using 454 GS FLX Titanium technology. ESTs were obtained from normalized cDNA libraries (root, leaves, and flower tissue) prepared using two varieties with contrasting phenotypes for plant, flowering and fruit traits, representing the two C. pepo subspecies: subsp. pepo cv. Zucchini and subsp. ovifera cv Scallop. De novo assembling was performed to generate a collection of 49,610 Cucurbita unigenes (average length of 626 bp) that represent the first transcriptome of the species. Over 60% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The distributions of Cucurbita unigenes followed similar tendencies than that reported for Arabidopsis or melon, suggesting that the dataset may represent the whole Cucurbita transcriptome. About 34% unigenes were detected to have known orthologs of Arabidopsis or melon, including genes potentially involved in disease resistance, flowering and fruit quality. Furthermore, a set of 1,882 unigenes with SSR motifs and 9,043 high confidence SNPs between Zucchini and Scallop were identified, of which 3,538 SNPs met criteria for use with high throughput genotyping platforms, and 144 could be detected as CAPS. A set of markers were validated, being 80% of them polymorphic in a set of variable C. pepo and C. moschata accessions. CONCLUSION: We present the first broad survey of gene sequences and allelic variation in C. pepo, where limited prior genomic information existed. The transcriptome provides an invaluable new tool for biological research. The developed molecular markers are the basis for future genetic linkage and quantitative trait loci analysis, and will be essential to speed up the process of breeding new and better adapted squash varieties.

Dataset Information

The complete chloroplast genome sequence of the Cucurbita pepo L. (Cucurbitaceae).

Publications

The complete chloroplast genome sequence of the <i>Cucurbita pepo</i> L. (Cucurbitaceae).

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