Chloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species
Autor: | Zhaochao Liu, Xuye Du, Hongcheng Wang, Zuomin Gao, Chenchen Gan, Lijuan Hu, Fang Qian, Bin Zhu |
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Jazyk: | angličtina |
Rok vydání: | 2021 |
Předmět: |
0106 biological sciences
Evolutionary Genetics Inverted repeat Raphanus Sequence assembly Plant Science Plant Genetics 01 natural sciences Genome Biochemistry Plant Genomics Photosynthesis Genome Evolution Phylogeny Data Management Genetics 0303 health sciences Multidisciplinary biology Phylogenetic tree Plant Biochemistry Eukaryota Chromosome Mapping Phylogenetic Analysis Genomics Plants Phylogenetics C3 Photosynthesis Medicine Engineering and Technology C4 Photosynthesis Research Article Biotechnology Genome evolution Computer and Information Sciences Science Bioengineering Brassica Molecular Evolution 03 medical and health sciences Open Reading Frames Species Specificity Evolutionary Systematics Codon Genome Chloroplast Gene 030304 developmental biology Taxonomy Evolutionary Biology Organisms Biology and Life Sciences Computational Biology biology.organism_classification Carbon Amino Acid Substitution Genetic Loci Brassicaceae Plant Biotechnology 010606 plant biology & botany Microsatellite Repeats |
Zdroj: | PLoS ONE PLoS ONE, Vol 16, Iss 7, p e0254109 (2021) |
ISSN: | 1932-6203 |
Popis: | Moricandia arvensis, a plant species originating from the Mediterranean, has been classified as a rare C3-C4 intermediate species, and it is a possible bridge during the evolutionary process from C3 to C4 plant photosynthesis in the family Brassicaceae. Understanding the genomic structure, gene order, and gene content of chloroplasts (cp) of such species can provide a glimpse into the evolution of photosynthesis. In the present study, we obtained a well-annotated cp genome of M. arvensis using long PacBio and short Illumina reads with a de novo assembly strategy. The M. arvensis cp genome was a quadripartite circular molecule with the length of 153,312 bp, including two inverted repeats (IR) regions of 26,196 bp, divided by a small single copy (SSC) region of 17,786 bp and a large single copy (LSC) region of 83,134 bp. We detected 112 unigenes in this genome, comprising 79 protein-coding genes, 29 tRNAs, and four rRNAs. Forty-nine long repeat sequences and 51 simple sequence repeat (SSR) loci of 15 repeat types were identified. The analysis of Ks (synonymous) and Ka (non-synonymous) substitution rates indicated that the genes associated with “subunits of ATP synthase” (atpB), “subunits of NADH-dehydrogenase” (ndhG and ndhE), and “self-replication” (rps12 and rpl16) showed relatively higher Ka/Ks values than those of the other genes. The gene content, gene order, and LSC/IR/SSC boundaries and adjacent genes of the M. arvensis cp genome were highly conserved compared to those in related C3 species. Our phylogenetic analysis demonstrated that M. arvensis was clustered into a subclade with cultivated Brassica species and Raphanus sativus, indicating that M. arvensis was not involved in an independent evolutionary origin event. These results will open the way for further studies on the evolutionary process from C3 to C4 photosynthesis and hopefully provide guidance for utilizing M. arvensis as a resource for improvinng photosynthesis efficiency in cultivated Brassica species. |
Databáze: | OpenAIRE |
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