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Background Herb genomics is a rapidly developing field of medicinal plant research and development. Plant genomic studies demonstrate the unique advantage of employing plants in medicinal therapy. The genus Lepidium falls under the Brassicaceae family and it includes crucial medicinal plants. Herein, we sequenced the complete chloroplast (cp) genomes of Lepidium apetalum (LA) and Lepidium perfoliatum (LP) and assessed their genetic profiles against the reported profiles of Lepidium sativum (LS), Lepidium meyenii (LM), and Lepidium virginicum (LV). Results In particular, we examined genomic arrangement, gene number, type, and repeat sequences. Based on our annotation data, both LA and LP possessed 130 distinct genes that included 85 protein-coding, 37 transfer RNA (tRNA), and 8 ribosomal RNA (rRNA) genes. Our repeat analyses revealed that LA harbored 20 forward repeats, 16 palindrome repeats, 30 tandem repeats, and 87 simple sequence repeats, whereas LP had 15 forward repeats, 20 palindrome repeats,4 reverse repeats, 21 tandem repeats, and 98 simple sequence repeats. Using syntenic analysis, we also revealed a high degree of sequence similarity within the coding regions of Lepidium cp genomes and a remarkably high degree of divergence among the intergenic spacers. Pairwise alignment and single-nucleotide polymorphism (SNP) examinations further revealed certain Lepidium-specific gene fragments, particularly in the intergenic regions of the trnK-atpA, trnC-psbC, trnT-rbcL, ndhF-ndhH, ycf1-trnR, accD, ccsA, matK, ndhF, rpoB, rpoC2, and ycf1 genes. Moreover, following codon usage analysis, we observed that codon 14 was the most frequently used codon in the Lepidium CDS. In addition, correlation investigations revealed that the ENC (the effective number of codon) content was strongly associated with GC3, GC3s, and N. Conclusion Based on these data, LA and LP originate from very similar genetic backgrounds. Furthermore, neutrality, ENC, and PR2-plots analyses demonstrated that the CUB (the codon usage bias) of Lepidium cp genome was strongly influenced by mutation and natural selection. Our analysis of the cp genomic sequences of LA and LP will likely enhance breeding, species recognition, phylogenetic evolution, and cp genetic engineering of the Lepidium medicinal plants. |
