Complete Chloroplast Genome of Nepeta griffithii and Comparative Genomics of 10 Nepeta Species

ABSTRACT

Nepeta L. (Lamiaceae) is an ecologically and medicinally important genus, yet complete cp genome resources are available for fewer than 10 of the approximately 300 accepted species, with western Himalayan taxa almost entirely unrepresented. Here, we sequenced, assembled, and annotated the complete cp genome of Nepeta griffithii and compared it with nine previously published Nepeta cp genomes. The 10 cp genomes exhibited a highly conserved quadripartite structure, with genome sizes ranging from 151,254 to 152,348 bp, and contained 113 unique genes (79 protein‐coding, 30 tRNA, 4 rRNA). Gene content, guanine‐cytosine content, intron features, and inverted repeat contraction and expansion were highly conserved. SSR analysis identified 387 repeats across the 10 cp genomes, predominantly mononucleotide A/T motifs in intergenic spacers, yielding candidate cpSSR markers for population‐level studies. Codon usage analysis revealed a strong bias toward A/T‐ending codons, with leucine as the most frequent amino acid. Nucleotide diversity analysis showed intergenic spacers were more variable than both introns and genic regions. Highly polymorphic loci, including ccsA‐ndhD , rpl32‐trnL‐UAG , and ndhG‐ndhI , were identified as candidate markers for phylogenetic and population studies. Maximum likelihood phylogeny based on 79 concatenated protein‐coding genes recovered a well‐resolved topology within Nepeta and placed N. griffithii as sister to N. nuda with maximal bootstrap support of 100%. This study provides the first complete cp genome for N. griffithii , improves plastome sampling within the genus, and offers genomic markers for species identification, systematics, and evolutionary studies.