Next-generation sequencing based Cyperus niveus (Cyperaceae) complete chloroplast genome: A comparative analysis and phylogeny

Abstract

Cyperus niveus, a perennial herb, holds significant traditional and scientific medicinal value. In this study, the complete chloroplast genome sequence of C. niveus was assembled and comparisons were conducted among species in the genus Cyperus. Molecular phylogenetic analysis was also conducted in Cyperaceae. The chloroplast genome of C. niveus exhibits a quadripartite structure, spanning a length of 185,454 base pairs (bp). The genome contains a large single-copy region (99,339 bp), flanked by two inverted repeats (IRs) (IRA and IRB: each 38,021 bp) separated by a small single-copy (SSC) region (10,073 bp). The chloroplast genome of C. niveus was rich in adenine-thymine (AT) at 66.7% and guanine-cytosine (GC) at 33.3%. A total of 140 unique genes were identified in the chloroplast genome of C. niveus, including 83 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. An amino acid frequency analysis uncovered the prevalence of leucine (10.90%) and isoleucine (9.20%). One hundred and forty-six simple sequence repeats and 49 oligonucleotide repeats were found in the chloroplast genome of C. niveus. A comparative analysis highlighted greater divergence within the IR and SSC regions. A phylogenetic assessment revealed that species within the genus Cyperus display phylogenetic conservation compared to other genera. Notably, the genus Carex exhibited substantial divergence, indicative of rapid evolutionary changes. C. niveus showed close resemblance with C. iria and C. exaltatus. In essence, this study and of chloroplast genome of C. niveus represents a valuable genomic asset that holds significance in species identification and comparative genomic research, presenting the first evolutionary relationship in Cyperaceae on the basis of chloroplast genome.