The First Complete Chloroplast Genome of Cordia monoica: Structure and Comparative Analysis

Abstract

Cordia monoica is a member of the Boraginaceae family. This plant is widely distributed in tropical regions and has a great deal of medical value as well as economic importance. In the current study, the complete chloroplast (cp) genome of C. monoica was sequenced, assembled, annotated, and reported. This circular chloroplast genome had a size of 148,711 bp, with a quadripartite structure alternating between a pair of repeated inverted regions (26,897–26,901 bp) and a single copy region (77,893 bp). Among the 134 genes encoded by the cp genome, there were 89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 1387 tandem repeats were detected, with the hexanucleotides class making up 28 percent of the repeats. Cordia monoica has 26,303 codons in its protein-coding regions, and leucine amino acid was the most frequently encoded amino acid in contrast to cysteine. In addition, 12 of the 89 protein-coding genes were found to be under positive selection. The phyloplastomic taxonomical clustering of the Boraginaceae species provides further evidence that chloroplast genome data are reliable not only at family level but also in deciphering the phylogeny at genus level (e.g., Cordia).

Genome Assembly of Cordia subcordata, a Coastal Protection Species in Tropical Coral Islands

“…Our phylogenetic analysis indicated that C. subcordata was sister to Coffee eugenioides, when none of the other Boraginaceae species were included. This result was consistent with the results of Alshegaihi et al [21]. In their study, they assembled the complete cpDNA genome of C. monoica.…”

“…Gene duplications in C. subcordata were examined by Doubletrouble v0.99.1 [91]. These duplications were classified into WGD, tandem duplications (TD), proximal duplications (PD), transposed duplications (TRD), and dispersed duplications (DD) [21]. In the doubletrouble analysis, Coffea eugenioides was used as the outgroup species.…”

Comparative Chloroplast Genomics Reveals a Unique Gene Inversion in Two Cordia Trees (Cordiaceae)

“…Inversion events in the genome are possibly caused by tRNA activity or intragenomic recombination in GC-rich regions [31][32][33][34]. After all analyses had been conducted, we became aware of a published paper that covered one species (C. monoica) that was analyzed in our paper [61], but the findings were different from those reported here, especially the absence of inversions that were found in the trnM-rbcL region of the C. monoica plastome. The difference in chloroplast genome sequences of individuals from the same species has been reported in some plant taxa [62][63][64].…”