Complete Mitochondrial Genome Sequence Structure and Phylogenetic Analysis of Choy Sum (Brassica rapa var. parachinensis)

TL;DR

This study reports the complete mitochondrial genome of choy sum, a Brassica vegetable, and provides insights into its structure, evolution, and potential for breeding.

Contribution

The paper presents the first complete mitochondrial genome of choy sum and identifies key features for evolutionary and breeding studies.

Findings

The choy sum mitochondrial genome is 219,775 bp with 60 annotated genes and 466 RNA editing sites.

The cox2 gene shows the highest nucleotide diversity, suggesting its value as a molecular marker.

Phylogenetic analysis shows choy sum is most closely related to B. rapa var. purpuraria.

Abstract

Choy sum (Brassica rapa var. parachinensis) is an important vegetable crop in Brassicaceae. However, its mitochondrial genome has not been well studied. In this study, Illumina and Nanopore sequencing technologies were combined to assemble the complete mitochondrial genome of choy sum. The mitochondrial genome is a circular molecule of 219,775 bp, with a GC content of 45.23%. A total of 60 genes were annotated, including 33 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and one pseudogene. A total of 466 RNA editing sites were identified in the PCGs. Codon usage analysis revealed that leucine (leu) was the most frequently used amino acid. Twenty-nine codons showed a relative synonymous codon usage (RSCU) value greater than 1. Most of these preferred codons ended with A or U. A total of 308 repetitive sequences were detected, including 136 dispersed repeats, 17 tandem repeats, and 55 simple sequence repeats (SSRs). Evolutionary analysis indicated that most mitochondrial genes are under negative selection. The highest nucleotide diversity detected in the cox2 gene suggests that this gene could serve as a valuable molecular marker for mitochondrial research in the species. Homology analysis found 22 homologous fragments between the mitochondrial and chloroplast genomes of choy sum. These fragments total 13,325 bp, representing 6.06% of the mitochondrial genome. Phylogenetic analysis showed that choy sum is most closely related to B. rapa var. purpuraria. This study offers a genomic resource for genetic improvement and breeding of choy sum. It also provides molecular insights into the evolution of Brassica species.

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