Comparative analysis of single nucleotide polymorphisms in the nuclear, chloroplast, and mitochondrial genomes in identification of phylogenetic association among seven melon (Cucumis meloL.) cultivars.
A variety of melons are cultivated worldwide, and their specific biological properties make them an attractive model for molecular studies. This study aimed to investigate the single nucleotide polymorphisms (SNPs) from the mitochondrial, chloroplast, and nuclear genomes of seven melon accessions (Cucumis meloL.) to identify the phylogenetic relationships among melon cultivars with the Illumina HiSeq 2000 platform and bioinformatical analyses. The data showed that there were a total of 658 mitochondrial SNPs (207-295 in each), while there were 0-60 chloroplast SNPs among these seven melon cultivars, compared to the reference genome. Bioinformatical analysis showed that the mitochondrial tree topology was unable to separate the melon features, whereas the maximum parsimony/neighbor joining (MP/NJ) tree of the chloroplast SNPs could define melon features such as seed length, width, thickness, 100-seed weight, and type. SNPs of the nuclear genome were better than the mitochondrial and chloroplast SNPs in the identification of melon features. The data demonstrated the usefulness of mitochondrial, chloroplast, and nuclear SNPs in identification of phylogenetic associations among these seven melon cultivars.
Horticulture College, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang 150030, China.
Qianglong
Q
Zhu
Horticulture College, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang 150030, China.
Peng
P
Gao
Horticulture College, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang 150030, China.
Shi
S
Liu
Horticulture College, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang 150030, China.
Sikandar
S
Amanullah
Horticulture College, Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang 150030, China.
Feishi
F
Luan
SNPs; bioinformatical analysis; chloroplast genome; melon; mitochondrial genome; nuclear genome