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
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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