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The complete mitochondrial genome of an endangered mangrove plant: Scyphiphora hydrophyllacea.

ABSTRACT: The complete mitochondrial genome of an endangered mangrove plant: Scyphiphora hydrophyllacea was analyzed in this paper, which is the first for the genus within the family Rubiaceae. The mitogenome sequence is 354,155 bp in length containing 3 ribosomal RNA genes, 16 transfer RNA genes, and 37 protein-coding genes. Gene ccmFc, ccmFn, rps3, rps13, rps10, rpl12, nad3 and cox1 contain one intron, gene cox2 and atp9 contain three introns and gene nad1, nad4 and nad7 contain four introns. Furthermore, Gene nad2 and nad5 have five introns. Gene nad1, nad2, nad5, nad7and Cox2 are trans-splicing genes. Phylogenetic analysis using the maximum likelihood method positioned S. hydrophyllacea closely with Asclepias syriaca in Gentianales.

SUBMITTER: Chen Y

PROVIDER: S-EPMC7782974 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundFritillaria ussuriensis is an endangered medicinal plant known for its notable therapeutic properties. Unfortunately, its population has drastically declined due to the destruction of forest habitats. Thus, effectively protecting F. ussuriensis from extinction poses a significant challenge. A profound understanding of its genetic foundation is crucial. To date, research on the complete mitochondrial genome of F. ussuriensis has not yet been reported.ResultsThe complete mitochondrial genome of F. ussuriensis was sequenced and assembled by integrating PacBio and Illumina sequencing technologies, revealing 13 circular chromosomes totaling 737,569 bp with an average GC content of 45.41%. A total of 55 genes were annotated in this mitogenome, including 2 rRNA genes, 12 tRNA genes, and 41 PCGs. The mitochondrial genome of F. ussuriensis contained 192 SSRs and 4,027 dispersed repeats. In the PCGs of F. ussuriensis mitogenome, 90.00% of the RSCU values exceeding 1 exhibited a preference for A-ended or U-ended codons. In addition, 505 RNA editing sites were predicted across these PCGs. Selective pressure analysis suggested negative selection on most PCGs to preserve mitochondrial functionality, as the notable exception of the gene nad3 showed positive selection. Comparison between the mitochondrial and chloroplast genomes of F. ussuriensis revealed 20 homologous fragments totaling 8,954 bp. Nucleotide diversity analysis revealed the variation among genes, and gene atp9 was the most notable. Despite the conservation of GC content, mitogenome sizes varied significantly among six closely related species, and colinear analysis confirmed the lack of conservation in their genomic structures. Phylogenetic analysis indicated a close relationship between F. ussuriensis and Lilium tsingtauense.ConclusionsIn this study, we sequenced and annotated the mitogenome of F. ussuriensis and compared it with the mitogenomes of other closely related species. In addition to genomic features and evolutionary position, this study also provides valuable genomic resources to further understand and utilize this medicinal plant.

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The complete mitochondrial genome of an endangered mangrove plant: Scyphiphora hydrophyllacea.

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