The chloroplast genome of Diplazium polypodioides and its comparison within the family Athyriaceae
Adeel Yunus1, Nighat Sultana1*, Alia Gul2, Abdullah3,4
1Department of Biochemistry, Hazara University, Mansehra, Pakistan
2Department of Botany, Hazara University, Mansehra, Pakistan
3State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
4Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, China
Abstract
The plant family Athyriaceae Alston consists of 3 genera and 650 species dispersed in different regions of the world, including Athyrium Roth, Diplazium Sw., and Deparia Hook. & Grev. The family has diverse morphological characteristics, ranging from creeping rhizomes to ascending or erect scales at apices. In the present study, the chloroplast (cp) genome of Diplazium polypodioides Blume was de novo assembled and compared with twelve other reported genomes of the species of the family Athyriaceae. The cp genome of D. polypodioides was 152,009 bp and showed a quadripartite structure in which a large single copy (82,389 bp) and a small single copy (22,303 bp) were separated by a pair of long inverted repeats (IRa and IRb: 23,659 bp each). We identified 116 genes, including 4 rRNAs, 29 tRNAs, and 84 protein-coding genes, with 15 genes duplicated in inverted repeats. The cp genome sizes of the thirteen analyzed species ranged from 150,797 bp (Diplazium striatum Desv.) to 152,009 bp (D. polypodioides). Despite high variability in SSRs and oligonucleotide repeats, the species showed similarities in GC content, contraction and expansion of inverted repeats, codon usage, amino acid frequency, and substitutions. Transition substitutions were more common than transversion substitutions across all species. Phylogenetic analysis of 84 protein-coding genes revealed monophyletic relationships among the limited species of three genera, namely, Diplazium, Athyrium, and Deparia. In addition, Diplazium was more closely related to Athyrium than to Deparia. Our study provides preliminary insights into the evolutionary dynamics of the cp genome in Athyriaceae and clarifies its phylogenetic relationships.
