Dataset Information

The complete chloroplast genome and phylogenetic analysis of Cyperus malaccensis Lam (Cyperaceae).

ABSTRACT: Cyperus malaccensis Lam is a perennial herbaceous plant that is distributed over a large area along the southern coast of China. Some plants of the Cyperaceae family are highly similar morphologically, which makes them difficult to classify and identify. In this study, the complete chloroplast genome of C. malaccensis was sequenced and assembled. The chloroplast genome is 186,098 bp long with a 33.18% content of GC. The structure of chloroplast genome includes a quadripartite structure that is composed of a pair of inverted repeats (IRs) of 37,434 bp, a small single copy (SSC) region of 10,296 bp, and a large single copy (LSC) region of 100,934 bp. The genome contains 141 genes, including 94 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. A phylogenetic analysis showed that C. malaccensis is the most closely related to the congeneric species C. rotundus. These results enrich the genetic resources of the Cyperaceae and provide a molecular basis for further study on the phylogeny of this family.

SUBMITTER: Pan L

PROVIDER: S-EPMC10810665 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature

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The complete chloroplast genome and phylogenetic analysis of Cyperus malaccensis Lam (Cyperaceae).

Pan Lianghao L Chen Kun K Liao Xin X

Mitochondrial DNA. Part B, Resources 20240121 1

Cyperus malaccensis Lam is a perennial herbaceous plant that is distributed over a large area along the southern coast of China. Some plants of the Cyperaceae family are highly similar morphologically, which makes them difficult to classify and identify. In this study, the complete chloroplast genome of C. malaccensis was sequenced and assembled. The chloroplast genome is 186,098 bp long with a 33.18% content of GC. The structure of chloroplast genome includes a quadripartite struc ...[more]

PMID: 38274852

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Project description:BackgroundCyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes.ResultsWe assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU < 1) tended to end at G or C. The RNA editing sites of the PCGs were relatively few, with only 9 and 23 sites in the mtDNA and cpDNA, respectively. A total of 28 mitochondrial plastid DNAs (MTPTs) in the mtDNA were derived from cpDNA, including three complete trnT-GGU, trnH-GUG, and trnS-GCU. Phylogeny and collinearity indicated that the relationship between C. stoloniferus and C. rotundus are closest. The mitochondrial rns gene exhibited the greatest nucleotide variability, whereas the chloroplast gene with the greatest nucleotide variability was infA. Most PCGs in the organellar genome are negatively selected and highly evolutionarily conserved. Only six mitochondrial genes and two chloroplast genes exhibited Ka/Ks > 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection.ConclusionWe assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.

Dataset Information

The complete chloroplast genome and phylogenetic analysis of Cyperus malaccensis Lam (Cyperaceae).

Publications

The complete chloroplast genome and phylogenetic analysis of <i>Cyperus malaccensis</i> Lam (Cyperaceae).

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