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Research paper

Comparative Cyto-molecular Analysis of Repetitive DNA Provides Insights into the Differential Genome Structure and Evolution of Five Cucumis Species

Shuqiong Yanga,b, Chunyan Chenga, Xiaodong Qina, Xiaqing Yua, Qunfeng Loua, Ji Lia, Chuntao Qiana, Jinfeng Chena( )
State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, School of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, China

Peer review under responsibility of Chinese Society for Horticultural Science (CSHS) and Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS)

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Abstract

The genus Cucumis, includes the cucumber (2n = 14), melon (2n = 24), and other wild species, which is a good model for studying genome organization and evolution due to their variation in genome size and basic chromosome number. In this study, five Cucumis species with different geographical origins and basic chromosome numbers (i.e., C. sativus, C. hystrix, C. melo, C. anguria, and C. metuliferus) were used to identify and characterize the repetitive DNA in detail using a phylogenetic method. Comparative cyto-molecular genetic analysis of repetitive DNA was carried out using a graph-based clustering method, construction of Neighbor-Joining tree and fluorescence in situ hybridization (FISH). The results revealed that the five Cucumis species had differences in the repeat content of their genome, as well as in the composition of repetitive DNA and their genomic proportions. Three species from subgenus Melo showed a decreased tendency in both repeat types and genomic proportions, while two species from subgenus Cucumis also showed a decreased tendency in repeat types, but an increased tendency in genomic proportions. Phylogenic analysis of Cucumis Ty1/Copia, Ty3/Gypsy, and 45S rDNA ITS regions revealed that C. sativus, C. hystrix, and C. melo were closely related species, which C. sativus and C. hystrix were closer, while C. anguria and C. metuliferus were closer to each other and further from the other three species. Differential accumulation and elimination of different repeat types divergently shaped the genomic architecture of these five Cucumis species, contributing to the genome's evolution and diversification. Overall, these results enhance our understanding of the genomes of these five Cucumis species, and contribute to a more holistic view of genome evolution and phylogenetics of this genus.

Keywords

comparative genomicsFISHCucumisrepetitive sequencephylogenetic evolution

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Horticultural Plant Journal
Volume 5 Issue 5,
September 2019
Pages 192-204
DOI: 10.1016/j.hpj.2019.07.002
Cite this article:
Yang S, Cheng C, Qin X, et al. Comparative Cyto-molecular Analysis of Repetitive DNA Provides Insights into the Differential Genome Structure and Evolution of Five Cucumis Species. Horticultural Plant Journal, 2019, 5(5): 192-204. https://doi.org/10.1016/j.hpj.2019.07.002

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Received: 21 March 2019
Revised: 20 May 2019
Accepted: 16 June 2019
Published: 15 July 2019
© 2019 Chinese Society for Horticultural Science (CSHS) and Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS).

This is an open access article under the CC BY-NC-ND license. (http://creativecommons.org/licenses/by-nc-nd/4.0/)
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