Abstract
Main conclusion
The first complete mitochondrial genome of Carex (C. breviculmis) was sequenced and assembled, and its genomic signature was analyzed and the possible conformations of its mitochondrial genome were validated.
Abstract
Carex breviculmis is a very adaptable grass that is highly resistant to environmental stresses such as drought and low light. It is also admired as a landscape plant with high development prospects and scientific research value. In this study, the mitochondrial genome of C. breviculmis was assembled using Pacbio and Illumina sequencing data. We detected 267 pairs of repeats and found that three pairs of repeats could mediate the recombination of its mitochondrial genome and formed four possible conformations, of which we verified the two conformations mediated by the shortest pair of repeats using PCR amplification and Sanger sequencing. The major conformation of the C. breviculmis mitochondrial genome is a 1,414,795 bp long circular molecule with 33 annotated protein-coding genes, 15 tRNA genes, and three rRNA genes. We detected a total of 25 homologous sequences between the chloroplast and mitochondrial genomes, corresponding to 0.40% of the mitochondrial genome. Combined with the low GC content (41.24%), we conclude that the reduction in RNA editing sites in the C. breviculmis mitochondrial genome may be due to an accumulation of point mutations in C-to-T or retroprocessing events within the genome. The relatively low number of RNA editing sites in its mitochondrial genome could serve as important material for subsequent studies on the selection pressure of RNA editing in angiosperms. A maximum likelihood analysis based on 23 conserved mitochondrial genes from 28 species reflects an accurate evolutionary and taxonomic position of C. breviculmis. This research provided us with a comprehensive understanding of the mitochondrial genome of Carex and also provided important information for its molecular breeding.
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Data availability
The datasets generated for this study can be found in the GenBank: ON482180. The raw sequencing data (including Sanger, Illumina and Pacbio sequencing data) were deposited into the GenBank with the accession number PRJNA935946.
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Acknowledgements
We're very grateful to the MitoRun research team for their help with the assembly methods and to Jian He for his help with the analysis of the data and its visualization.
Funding
This study was supported by Beijing Academy of Agriculture and Forestry Sciences (KJCX20220103), Scientific Research Project of Beijing Educational Committee (KZ202110020027), and Postdoctoral Fund of Beijing Academy of Agricultural and Forestry Sciences (2020-ZZ-019). Each of the funding bodies granted the funds based on a research proposal.
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425_2023_4169_MOESM2_ESM.xlsx
Supplementary Figure S1. Illumina remapping results of four sequences obtained by primer PCR amplification. The blue area indicates the sequence coverage, and the number on the left indicates the highest coverage value. Here, 1F1R and 2F2R correspond to the results indicating the read coverage of mitochondrial genome conformation A, and 1F2F and 1R2R indicates the read coverage of mitochondrial genome conformation B (TIF 1854 kb)
Supplementary Table S3. RSCU of individual amino acid pairs in the mitochondrial genome (XLSX 11 kb)
425_2023_4169_MOESM8_ESM.xlsx
Supplementary Table S6. Colinear analysis among Carex breviculmis mitochondrial genome and five related mitochondrial genomes (XLSX 46 kb)
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Xu, S., Teng, K., Zhang, H. et al. The first complete mitochondrial genome of Carex (C. breviculmis): a significantly expanded genome with highly structural variations. Planta 258, 43 (2023). https://doi.org/10.1007/s00425-023-04169-1
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DOI: https://doi.org/10.1007/s00425-023-04169-1