Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance

Abstract

Background: Cyperus 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.

Results: We 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.

Conclusion: We 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.

Keywords: Cyperus stoloniferus; Comparative analysis; Systematic evolution; cpDNA; mtDNA.

Fig. 1

Contig assembly and PCR amplification detection of C. stoloniferus mtDNA. A The mtDNA consists of two independent circular DNAs, including mt1 and mt2. B mt2 consists of four contigs, among which contig2 is a 15,034bp reverse repeating direction. The counterclockwise arrow indicates a forward repeating sequence, while the clockwise arrow indicates a reverse repeating sequence. C Agarose gel electrophoresis of PCR amplification products of four overlapping regions (P1, P2, P3 and P4). 1 and 2 represent PCR amplification products of different DNA templates

Fig. 2

Circular DNA map of the organelle genome in C. stoloniferus. Different functional groups of genes are represented by different colors

Fig. 3

The repetitive sequence of the organelle genome in C. stoloniferus. A The short lines in the outer, middle, and inner circles represent the positions of SSRs, tandem repeats, and dispersed repeats in the organelle genome, respectively. B The types and quantities of SSRs. C The types and quantities of tandem repeats and dispersed repeats

Fig. 4

Relative synonymous codon usage (RSCU) of the organelle genome in C. stoloniferus. A RSCU analysis of cpDNA. B RSCU analysis of mtDNA. The color of the histogram is the same as the codon’s color

Fig. 5

Prediction and validation of RNA editing sites in the organelle genome PCGs of C. stoloniferus. A RNA editing site prediction. B PCR amplification product electrophoresis detection. C Comparison of gDNA and cDNA editing sites. The RNA editing site is named "gene name", and "-" connects the position of RNA editing nucleotides in the coding region

Fig. 6

Transfer events of plastid DNA to the mitochondrial genome in C. stoloniferus. The outer arc represents mt1, mt2, and cpDNA, while the inner arc represents the corresponding transfer MTPTs

Fig. 7

The phylogenetic relationship between C. stoloniferus and 10 other species. A and (B) are phylogenetic trees constructed based on genes shared by 27 mitochondria (Table S19) and 68 chloroplasts (Table S20), respectively. Colors represent plants of the same family

Fig. 8

The collinear blocks between the organelle genomes of four species in Cyperaceae. A and (B) are collinear blocks of mtDNA and cpDNA, respectively. The bar chart represents the organelle genome, and the arc represents the homologous sequence of adjacent species. The red highlighted area represents homologous segments with lengths greater than 500 bp and an E values of 0, while the gray area represents homologous fragments with lengths less than 500 bp and an E values greater than 0

Fig. 9

Nucleotide diversity of genes in organelle genomes of 9 closely related species. A The Pi value of mitochondrial genes. B and (C) indicate the Pi values of chloroplast genes

Fig. 10

Ka/Ks analysis of PCGs in the organelle genomes of 9 closely related species. A The Ka/Ks of mitochondrial PCGs. B and (C) indicate the Ka/Ks of chloroplast PCGs. The black solid lines on the box plot represents the average value, and the dashed lines represents the middle value