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Int. J. Mol. Sci. 2017, 18(9), 1942; doi:10.3390/ijms18091942

Genome Survey Sequencing of Luffa Cylindrica L. and Microsatellite High Resolution Melting (SSR-HRM) Analysis for Genetic Relationship of Luffa Genotypes

Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
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Received: 26 July 2017 / Revised: 25 August 2017 / Accepted: 7 September 2017 / Published: 11 September 2017
(This article belongs to the Section Molecular Botany)
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Abstract

Luffa cylindrica (L.) Roem. is an economically important vegetable crop in China. However, the genomic information on this species is currently unknown. In this study, for the first time, a genome survey of L. cylindrica was carried out using next-generation sequencing (NGS) technology. In total, 43.40 Gb sequence data of L. cylindrica, about 54.94× coverage of the estimated genome size of 789.97 Mb, were obtained from HiSeq 2500 sequencing, in which the guanine plus cytosine (GC) content was calculated to be 37.90%. The heterozygosity of genome sequences was only 0.24%. In total, 1,913,731 contigs (>200 bp) with 525 bp N50 length and 1,410,117 scaffolds (>200 bp) with 885.01 Mb total length were obtained. From the initial assembled L. cylindrica genome, 431,234 microsatellites (SSRs) (≥5 repeats) were identified. The motif types of SSR repeats included 62.88% di-nucleotide, 31.03% tri-nucleotide, 4.59% tetra-nucleotide, 0.96% penta-nucleotide and 0.54% hexa-nucleotide. Eighty genomic SSR markers were developed, and 51/80 primers could be used in both “Zheda 23” and “Zheda 83”. Nineteen SSRs were used to investigate the genetic diversity among 32 accessions through SSR-HRM analysis. The unweighted pair group method analysis (UPGMA) dendrogram tree was built by calculating the SSR-HRM raw data. SSR-HRM could be effectively used for genotype relationship analysis of Luffa species. View Full-Text
Keywords: genome survey; genomic SSR markers; SSR-HRM; genetic diversity; Luffa (L. cylindrica) genome survey; genomic SSR markers; SSR-HRM; genetic diversity; Luffa (L. cylindrica)
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

An, J.; Yin, M.; Zhang, Q.; Gong, D.; Jia, X.; Guan, Y.; Hu, J. Genome Survey Sequencing of Luffa Cylindrica L. and Microsatellite High Resolution Melting (SSR-HRM) Analysis for Genetic Relationship of Luffa Genotypes. Int. J. Mol. Sci. 2017, 18, 1942.

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