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

Abstract

<i>Cyperus niveus</i>, a perennial herb, holds significant traditional and scientific medicinal value. In this study, the complete chloroplast genome sequence of <i>C. niveus</i> was assembled and comparisons were conducted among species in the genus Cyperus. Molecular phylogenetic analysis was also conducted in Cyperaceae. The chloroplast genome of <i>C. niveus</i> 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 <i>C. niveus</i> 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 <i>C. niveus</i>, 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 <i>C. niveus</i>. A comparative analysis highlighted greater divergence within the IR and SSC regions. A phylogenetic assessment revealed that species within the genus <i>Cyperus</i> display phylogenetic conservation compared to other genera. Notably, the genus <i>Carex</i> exhibited substantial divergence, indicative of rapid evolutionary changes. <i>C. niveus</i> showed close resemblance with <i>C. iria</i> and <i>C. exaltatus</i>. In essence, this study and of chloroplast genome of <i>C. niveus</i> 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.