Complete Chloroplast Genome of Cardamine microzyga and Phylogenetic Analysis

Cardamine microzyga (Brassicaceae) is a perennial herbaceous species native to mountainous regions of southwestern China, yet its genomic resources remain poorly characterized. In this study, we assembled and annotated the complete chloroplast (cp) genome of C. microzyga based on Illumina HiSeq 4000 sequencing data, and conducted comprehensive analyses of its genomic structure, repeat sequences, codon usage, nucleotide diversity, and phylogenetic relationships. The cp genome is 154,661 bp in length, exhibiting a typical quadripartite structure comprising a large single-copy (LSC) region (84,261 bp), a small single-copy (SSC) region (17,774 bp), and a pair of inverted repeat (IR) regions (26,313 bp each). A total of 129 genes were annotated, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Fifty-seven mononucleotide and four dinucleotide simple sequence repeats (SSRs) were identified, all of which exhibited a pronounced A/T bias, together with nine complex compound SSRs. Comparative analysis of the IR/LSC and IR/SSC boundaries among 11 Brassicaceae species revealed high structural conservation, with only minor variations. Codon usage analysis indicated that 30 codons had relative synonymous codon usage (RSCU) values > 1, with a strong preference for A/T-ending codons. Nucleotide diversity (Pi) analysis across 106 protein-coding genes identified nine hypervariable regions (Pi > 0.0156), among which trnS-GCU (Pi = 0.03736), rrn4.5S (0.03280), and ycf1 (0.03224) represented promising candidates for DNA barcoding and phylogenetic marker development. Phylogenetic reconstruction based on 45 complete cp genomes using maximum likelihood (ML) method placed C. microzyga within a well-supported clade (bootstrap = 100) comprising C. lyrata, C . fallax , and C. amariformis, with Rorippa as the sister group. This study provides the first complete cp genome of C. microzyga, which not only fills a key genomic gap in an alpine-endemic species but also offers insights into the adaptive evolution of high-altitude plants. These resources will facilitate future taxonomic, evolutionary, and conservation genetics studies in the genus Cardamine and the family Brassicaceae.