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The complete chloroplast genomes of two species from Capparaceae.

ABSTRACT: Capparis spinosa L. and Capparis decidua Forsk. belong to the Capparaceae family. The two species are important medicinal plants uses in treatment of various ailments. In this study, we present the complete chloroplast genomes of the two species. The complete plastome genomes of the two species have a circular structure and a length of 157,728 bp in Capparis spinosa and 157,573 bp in Capparis decidua and GC content of 35.91, 35.96% respectively. The chloroplast genome of C. spinosa and C. decidua is divided into four regions: LSC of 86,732 and 85,950 bp respectively, SSC from 18,322 to 18,621 bp and a pair of inverted repeats 26,337 and 26,501 bp each. Both of the chloroplast genomes contained 115 different genes, including 80 protein coding genes, 31 tRNA genes and four rRNA genes. A phylogenetic analysis demonstrated that C. spinosa is sister to Capparis urophylla. The two species are sister to C. decidua.

SUBMITTER: Alzahrani D

PROVIDER: S-EPMC7901692 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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The complete chloroplast genomes of two species from Capparaceae.

Alzahrani Dhafer D Albokhari Enas E Yaradua Samaila S Abba Abidina A

Mitochondrial DNA. Part B, Resources 20210220 2

Capparis spinosa L. and Capparis decidua Forsk. belong to the Capparaceae family. The two species are important medicinal plants uses in treatment of various ailments. In this study, we present the complete chloroplast genomes of the two species. The complete plastome genomes of the two species have a circular structure and a length of 157,728 bp in Capparis spinosa and 157,573 bp in Capparis decidua and GC content of 35.91, 35.96% respectively. The chloroplast genome ...[more]

PMID: 33681464

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Project description:BackgroundThe suamc genus Rhus (sensu stricto) includes two subgenera, Lobadium (ca. 25 spp.) and Rhus (ca. 10 spp.). Their members, R. glabra and R. typhina (Rosanae: Sapindales: Anacardiaceae), are two economic important species. Chloroplast genome information is of great significance for the study of plant phylogeny and taxonomy.ResultsThe three complete chloroplast genomes from two Rhus glabra and one R. typhina accessions were obtained with a total of each about 159k bp in length including a large single-copy region (LSC, about 88k bp), a small single-copy regions (SSC, about 19k bp) and a pair of inverted repeats regions (IRa/IRb, about 26k bp), to form a canonical quadripartite structure. Each genome contained 88 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes and two pseudogenes. The overall GC content of the three genomes all were same (37.8%), and RSCU values showed that they all had the same codon prefers, i.e., to use codon ended with A/U (93%) except termination codon. Three variable hotspots, i.e., ycf4-cemA, ndhF-rpl32-trnL and ccsA-ndhD, and a total of 152-156 simple sequence repeats (SSR) were identified. The nonsynonymous (Ka)/synonymous (Ks) ratio was calculated, and cemA and ycf2 genes are important indicators of gene evolution. The phylogenetic analyses of the family Anacardiaceae showed that the eight genera were grouped into three clusters, and supported the monophyly of the subfamilies and all the genera. The accessions of five Rhus species formed four clusters, while, one individual of R. typhina grouped with the R. glabra accessions instead of clustering into the two other individuals of R. typhina in the subgenus Rhus, which showed a paraphyletic relationship.ConclusionsComparing the complete chloroplast genomes of the Rhus species, it was found that most SSRs were A/T rich and located in the intergenic spacer, and the nucleotide divergence exhibited higher levels in the non-coding region than in the coding region. The Ka/Ks ratio of cemA gene was > 1 for species collected in America, while it was < 1 for other species in China, which dedicated that the Rhus species from North America and East Asia have different evolutionary pressure. The phylogenetic analysis of the complete chloroplast genome clarified the Rhus placement and relationship. The results obtained in this study are expected to provide valuable genetic resources to perform species identification, molecular breeding, and intraspecific diversity of the Rhus species.

Project description:In this study, we assembled and annotated the chloroplast (cp) genomes of four Ligustrum species, L. sinense, L. obtusifolium, L. vicaryi, and L. ovalifolium 'Aureum'. Including six other published Ligustrum species, we compared various characteristics such as gene structure, sequence alignment, codon preference, and nucleic acid diversity, and performed positive-selection genes screening and phylogenetic analysis. The results showed that the cp genome of Ligustrum was 162,185-166,800 bp in length, with a circular tetrad structure, including a large single-copy region (86,885-90,106 bp), a small single-copy region (11,446-11,499 bp), and a pair of IRa and IRb sequences with the same coding but in opposite directions (31,608-32,624 bp). This structure is similar to the cp genomes of most angiosperms. We found 132-137 genes in the cp genome of Ligustrum, including 89-90 protein-coding genes, 35-39 tRNAs, and 8 rRNAs. The GC content was 37.93-38.06% and varied among regions, with the IR region having the highest content. The single-nucleotide (A/T)n was dominant in simple-sequence repeats of the Ligustrum cp genome, with an obvious A/T preference. Six hotspot regions were identified from multiple sequence alignment of Ligustrum; the ycf1 gene region and the clpP1 exon region can be used as potential DNA barcodes for the identification and phylogeny of the genus Ligustrum. Branch-site model and Bayes empirical Bayes (BEB) analysis showed that four protein-coding genes (accD, clpP, ycf1, and ycf2) were positively selected, and BEB analysis showed that accD and rpl20 had positively selected sites. A phylogenetic tree of Oleaceae species was constructed based on the whole cp genomes, and the results were consistent with the traditional taxonomic results. The phylogenetic results showed that genus Ligustrum is most closely related to genus Syringa. Our study provides important genetic information to support further investigations of the phylogenetic development and adaptive evolution of Ligustrum species.

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The complete chloroplast genomes of two species from Capparaceae.

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The complete chloroplast genomes of two species from Capparaceae.

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