Comparative Analysis and Characterization of Ten Complete Chloroplast Genomes of Eremurus Species (Asphodelaceae)

Abstract

Eremurus, a perennial rhizomatous mesophytic ornamental plant and one of the largest genera of the family Asphodelaceae, is distributed mainly in southwestern and central Asia. We sequenced the complete chloroplast genomes of ten species corresponding to all sections of the genus and analyzed their basic structure and evolutionary relationships. The cp genomes showed significant similarities in size, gene sequences, gene classes, and inverted repeat regions (IRs). The complete chloroplast genome of Eremurus has a typical tetrad structure, ranging in length from 153,782 bp (E. lactiflorus) to 155,482 bp (E. aitchisonii). The length of the large single-copy region (LSC) ranges from 84,005 bp (E. lactiflorus) to 84,711 bp (E. robustus), that of the small single-copy region (SSC) ranges from 16,727 bp (E. soogdianus) to 17,824 bp (E. suworowii), and that of the inverted repeat regions (IR) ranges from 26,484 bp (E. lactiflorus) to 26,597 bp (E. inderiensis and E. soogdianus). A total of 131 genes were detected, including 85 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. In addition, we found seven common and eight unique SSRs in ten Eremurus species. Among the protein-coding genes, five highly variable genes (ycf1, rps15, rps16, and rpl36) with high Pi values were detected and showed potential as DNA barcodes for the genus. Three genes (rps19, ycf1, and ndhB) had positive Ka/Ks values. Codon usage patterns were very similar across species: 33 codons had relative synonymous codon usage values of more than one, of which three ended with G, and the remaining codons ended with A and U. Phylogenetic analyses using complete cp genomes and 81 protein-coding genes confirmed previous studies with the genus as well as subgenus Eremurus monophyletic and the subgenus Henningia paraphyletic.