Characterization of the mitochondrial genome of Cucumis hystrix and comparison with other cucurbit crops

Lei Xia; Chunyan Cheng; Xiaokun Zhao; Xiaolu He; Xiaqing Yu; Ji Li; Yuhui Wang; Jinfeng Chen

doi:10.1016/j.gene.2022.146342

Characterization of the mitochondrial genome of Cucumis hystrix and comparison with other cucurbit crops

Gene. 2022 May 20:823:146342. doi: 10.1016/j.gene.2022.146342. Epub 2022 Feb 24.

Authors

Lei Xia¹, Chunyan Cheng², Xiaokun Zhao³, Xiaolu He⁴, Xiaqing Yu⁵, Ji Li⁶, Yuhui Wang⁷, Jinfeng Chen⁸

Affiliations

¹ State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: 2019204026@njau.edu.cn.
² State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: chunyancheng@njau.edu.cn.
³ State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: 2020204022@stu.njau.edu.cn.
⁴ State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: 2019104045@njau.edu.cn.
⁵ State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: xqyu@njau.edu.cn.
⁶ State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: liji1981@njau.edu.cn.
⁷ State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: yuhui_wang@njau.edu.cn.
⁸ State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: jfchen@njau.edu.cn.

PMID: 35219813
DOI: 10.1016/j.gene.2022.146342

Abstract

The mitochondria ofCucumis genus contain several intriguing features such as paternal inheritance and three-ring genome structure. However, the evolutionary relationships of mitochondria inCucumisremain elusive. Here, we assembled the mitochondrial genome ofC. hystrixand performed a comparative genomic analysis with other crops inthe Cucurbitaceae. The mitochondrial genome ofC. hystrixhas three circular-mapping chromosomes of lengths 1,113,461 bp, 110,683 bp, and 92,288 bp, which contain 73 genes including 38 protein-coding genes, 31tRNAgenes, and 4rRNAgenes. Repeat sequences, RNA editing, and horizontal gene transfer events were identified. The results of phylogenetic analyses, collinearity and gene clusters revealed thatC. hystrixis closer toC. sativus than to C. melo. Meanwhile, wedemonstrated mitochondrial paternal inheritance inC. hystrixbymolecular markers. In comparison with other cucurbitcrops, wefound amarker foridentification of germplasm resources ofCucumis. Collectively, our findings provide a tool to help clarify the paternal lineage within that genus in the evolution of Cucumis.

Keywords: Cucumis hystrix; Mitochondrial genome; Molecular markers; Phylogeny.

Publication types

Comparative Study

MeSH terms

Crops, Agricultural / genetics
Cucumis / genetics*
Cucurbitaceae / classification
Cucurbitaceae / genetics*
Evolution, Molecular
Gene Transfer, Horizontal
Genome Size
Genome, Mitochondrial*
Genomics
High-Throughput Nucleotide Sequencing
Mitochondria / genetics*
Phylogeny
Sequence Analysis, DNA / methods*