NGS based complete Cyperus niveus (Cyperaceae) chloroplast genome: A comparative analysis and phylogeny

Abstract

Cyperus niveus, a perennial herb, predominantly thrives along roadsides and within rocky crevices, holds significant traditional and scientific medicinal value. In this study chloroplast genome sequence of C. niveus was determined and compared to other species in genus, and molecular phylogeny was constructed in family Cyperaceae. The chloroplast genome of Cyperus niveus exhibits a quadripartite structure, spanning a length of 185,454 base pairs (bp). Comprising an intricate arrangement, the genome contains a Large Single Copy (LSC) region (99,339 bp), flanked by two Inverted Repeats (IRs) (IRA and IRB: each 38,021 bp), which are separated by a Small Single Copy (SSC) region (10,073 bp). The chloroplast genome of C. niveus was AT rich, with GC content of 33.3%. This GC content varies across the genome's components, with the IR regions exhibiting a notably higher GC content (37.3%) compared to the LSC (30.9%) and SSC (25.5%). Within this genome, a total of 140 unique genes were identified, including 83 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Amino acid frequency analysis unveiled the prevalence of leucine (10.90%) and isoleucine (9.20%), while cysteine occurred with the lowest frequency (1.10%). The application of Perl script MIcroSAtellite identification tools (MISA) revealed the presence of 146 Simple Sequence Repeats (SSR) and 28 compound SSRs within the chloroplast genome of C. niveus. Two types of oligonucleotide repeats were identified, consisting of 28 forward repeats and 21 palindromic repeats. Comparative analysis highlighted greater divergence within the Inverted Repeat (IR) and Small Single Copy (SSC) regions in contrast to the Large Single Copy (LSC) region. Phylogenetic assessment, conducted through Maximum Likelihood tree construction, indicated that species within the Cyperus genus display phylogenetic conservation compared to other genera. Notably, the genus Carex exhibited substantial divergence, indicative of rapid evolutionary changes. In the context of the family tree, Cyperus niveus shared a close resemblance with C. exaltatus. Further positioning Cyperus niveus within the genus, Maximum Likelihood and Neighbor Joining trees were constructed using nine Cyperus species and Bolboschoenus planiculmis as an outgroup. Both approaches reaffirmed the placement of C. niveus, consistent with its position within the family trees. In essence, the chloroplast genome of C. niveus represents a valuable genomic asset that holds significance in species identification, evolutionary investigations, and comparative genomic.