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The complete chloroplast genome of Cycas bifida, an extremely small population protected species.

ABSTRACT: Cycas bifida (Dyer) K.D.Hill (2004) is an extremely small population-protected species of China. In this study, we reported the first chloroplast genome sequence of C. bifida. The chloroplast genome of C. bifida included two single-copy regions (large single-copy (LSC) and small single-copy (SSC)) and a pair of inverted repeats (IRs) regions comprising 88,946 bp, 23,107 bp, and 25,053 bp, respectively. The complete chloroplast genome of C. bifida contains 131 genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The overall GC content of the C. bifida chloroplast genome is 39.41%, and the LSC, SSC, and IR regions occupy 38.70%, 36.52%, and 42.02%, respectively. A phylogenetic analysis was performed based on complete chloroplast genomes from 15 species and found that C. bifida was closely related to Cycas szechuanensis W.C.Cheng & L.K.Fu.

SUBMITTER: Zhang D

PROVIDER: S-EPMC8451596 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Mitochondrial genomes of vascular plants are well known for their liability in architecture evolution. However, the evolutionary features of mitogenomes at intra-generic level are seldom studied in vascular plants, especially among gymnosperms. Here we present the complete mitogenome of Cycas debaoensis, an endemic cycad species to the Guangxi region in southern China. In addition to assemblage of draft mitochondrial genome, we test the conservation of gene content and mitogenomic stability by comparing it to the previously published mitogenome of Cycas taitungensis. Furthermore, we explored the factors such as structural rearrangements and nuclear surveillance of double-strand break repair (DSBR) proteins in Cycas in comparison to other vascular plant groups. The C. debaoensis mitogenome is 413,715 bp in size and encodes 69 unique genes, including 40 protein coding genes, 26 tRNAs, and 3 rRNA genes, similar to that of C. taitungensis. Cycas mitogenomes maintained the ancestral intron content of seed plants (26 introns), which is reduced in other lineages of gymnosperms, such as Ginkgo biloba, Taxus cuspidata and Welwitschia mirabilis due to selective pressure or retroprocessing events. C. debaoensis mitogenome holds 1,569 repeated sequences (> 50 bp), which partially account for fairly large intron size (1200 bp in average) of Cycas mitogenome. The comparison of RNA-editing sites revealed 267 shared non-silent editing site among predicted vs. empirically observed editing events. Another 33 silent editing sites from empirical data increase the total number of editing sites in Cycas debaoensis mitochondrial protein coding genes to 300. Our study revealed unexpected conserved evolution between the two Cycas species. Furthermore, we found strict collinearity of the gene order along with the identical set of genomic content in Cycas mt genomes. The stability of Cycas mt genomes is surprising despite the existence of large number of repeats. This structural stability may be related to the relative expansion of three DSBR protein families (i.e., RecA, OSB, and RecG) in Cycas nuclear genome, which inhibit the homologous recombinations, by monitoring the accuracy of mitochondrial chromosome repair.

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The complete chloroplast genome of Cycas bifida, an extremely small population protected species.

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