Comparative Analysis of the Complete Chloroplast Genomes of Six Endangered Cycas Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications

Abstract

Cycas (family Cycadaceae), which spread throughout tropical and subtropical regions, is crucial in conservation biology. Due to subtle morphological variations between species, a solid species-level phylogeny for Cycas is lacking. In the present study, we assembled and analyzed the chloroplast genomes of six Cycas plants, including their genome structure, GC content, and nucleotide diversity. The Cycas chloroplast genome spans from 162,038 to 162,159 bp and contains 131 genes, including 86 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Through a comparative analysis, we found that the chloroplast genome of Cycas was highly conserved, as indicated by the contraction and expansion of the inverted repeat (IR) regions and sequence polymorphisms. In addition, several non-coding sites (psbK-psbI, petN-psbM, trnE-UUC-psbD, ndhC-trnM-CAU, and rpl32-trnP-GGG) showed significant variation. The utilization of phylogenetic analysis relying on protein-coding genes has substantiated the division of Cycas primarily into four groups. The application of these findings will prove valuable in evaluating genetic diversity and the phylogenetic connections among closely related species. Moreover, it will provide essential support for the advancement of wild germplasm resources.

Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Four Ottelia Species

“…Assembly and splicing procedures led to the acquisition of complete circular tetrad-structured cp genomes (Figure 1), including an LSC, an SSC, and two IR regions. The structural composition of the complete cp genomes in the five studied Ottelia samples conforms to the typical configuration observed in most plants, characterized by a single circular quadripartite molecule [24,25].…”

“…Fresh leaves from five Ottelia samples representing four distinct species, namely, O. fengshanensis, O. guanyangensis, O. acuminata var. jingxiensis, O. acuminata, and O. alis- Phylogenomic analyses, leveraging plastomes, have proven successful in unraveling intricate relationships within taxonomically complex plant groups [24,25]. In this study, our phylogenomic analysis not only reaffirmed the monophyly of Ottelia but also offered a comprehensive understanding of the relationships within the genus.…”