First complete chloroplast genome of Cyanotis nyctitropa Deflers and its phylogenetic relationships within the tribe cyanotinae (Commelinaceae)

Abstract

Cyanotis nyctitropa Deflers is an herb native to the southern Arabian Peninsula. Little is known about this species, and no genomic sequences are available in the public databases. This is the first report on the cpDNA data for the endemic species C. nyctitropa and includes a comparative assessment with relatives in the Cyanotinae subtribe. The C. nyctitropa plastome has 157,472 base pairs (bp) and exhibits a typical quadripartite structure, comprising a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRa and IRb). The lengths of the LSC and SSC regions are 88,395 bp and 17,693 bp, respectively, whereas the lengths of the IRa and IRb segments are 25,692 bp each. A significant reduction in the length of the IR region was observed in C. nyctitropa, as well as the variation in the positional distribution of genes at the boundaries. The overall number of simple sequence repeats (SSRs) identified within the Cyanotinae species ranged from 396 to 466. Nucleotide diversity analysis revealed that trnQ-UUG, trnT-UGU, atpB, rpI33, psbB, petB, ycf1, and ndhD sites with the highest Pi values. The construction of DNA markers on the basis of these high-nucleotide-diversity sites is recommended. Bayesian phylogenetic analysis of Cyanotinae chloroplast yielded a monophyletic clade. These results highlight the usefulness of plastome sequence data as a resource for determining the relationships among Commelinaceae taxa.

Bangladesh J. Plant Taxon. 33(1): 53-63, 2026 (June)