Dataset Information

Evolutionary and phylogenetic aspects of the chloroplast genome of Chaenomeles species.

ABSTRACT: Chaenomeles (family Rosaceae) is a genus of five diploid species of deciduous spiny shrubs that are native to Central Asia and Japan. It is an important horticultural crop (commonly known as flowering quinces) in Europe and Asia for its high yield in fruits that are rich in juice, aroma, and dietary fiber. Therefore, the development of effective genetic markers of Chaenomeles species is advantageous for crop improvement through breeding and selection. In this study, we successfully assembled and analyzed the chloroplast genome of five Chaenomeles species. The chloroplast genomes of the five Chaenomeles species were very similar with no structural or content rearrangements among them. The chloroplast genomes ranged from 159,436 to 160,040 bp in length and contained a total of 112 unique genes, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Three highly variable regions, including trnR-atpA, trnL-F, and rpl32-ccsA, were identified. Phylogenetic analysis based on the complete chloroplast genome showed that Chaenomeles forms a monophyletic clade and had a close relationship with the genera Docynia and Malus. Analyses for phylogenetic relationships and the development of available genetic markers in future could provide valuable information regarding genetics and breeding mechanisms of the Chaenomeles species.

SUBMITTER: Sun J

PROVIDER: S-EPMC7351712 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Evolutionary and phylogenetic aspects of the chloroplast genome of Chaenomeles species.

Sun Jiahui J Wang Yiheng Y Liu Yanlei Y Xu Chao C Yuan Qingjun Q Guo Lanping L Huang Luqi L

Scientific reports 20200710 1

Chaenomeles (family Rosaceae) is a genus of five diploid species of deciduous spiny shrubs that are native to Central Asia and Japan. It is an important horticultural crop (commonly known as flowering quinces) in Europe and Asia for its high yield in fruits that are rich in juice, aroma, and dietary fiber. Therefore, the development of effective genetic markers of Chaenomeles species is advantageous for crop improvement through breeding and selection. In this study, we successfully assembled and ...[more]

PMID: 32651417

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Project description:BackgroundThe large genus Ficus comprises approximately 800 species, most of which possess high ornamental and ecological values. However, its evolutionary history remains largely unknown. Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveiling evolutionary relationships between species, genus and other rank groups. In this work we present the plastomes of ten Ficus species.ResultsThe complete chloroplast (CP) genomes of eleven Ficus specimens belonging to ten species were determined and analysed. The full length of the Ficus plastome was nearly 160 kbp with a similar overall GC content, ranging from 35.88 to 36.02%. A total of 114 unique genes, distributed in 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, were annotated in each of the Ficus CP genome. In addition, these CP genomes showed variation in their inverted repeat regions (IR). Tandem repeats and mononucleotide simple sequence repeat (SSR) are widely distributed across the Ficus CP genome. Comparative genome analysis showed low sequence variability. In addition, eight variable regions to be used as potential molecular markers were proposed for future Ficus species identification. According to the phylogenetic analysis, these ten Ficus species were clustered together and further divided into three clades based on different subgenera. Simultaneously, it also showed the relatedness between Ficus and Morus.ConclusionThe chloroplast genome structure of 10 Ficus species was similar to that of other angiosperms, with a typical four-part structure. Chloroplast genome sizes vary slightly due to expansion and contraction of the IR region. And the variation of noncoding regions of the chloroplast genome is larger than that of coding regions. Phylogenetic analysis showed that these eleven sampled CP genomes were divided into three clades, clustered with species from subgenus Urostigma, Sycomorus, and Ficus, respectively. These results support the Berg classification system, in which the subgenus Ficus was further decomposed into the subgenus Sycomorus. In general, the sequencing and analysis of Ficus plastomes, especially the ones of species with no or limited sequences available yet, contribute to the study of genetic diversity and species evolution of Ficus, while providing useful information for taxonomic and phylogenetic studies of Ficus.

Project description:BackgroundPodocarpus lambertii (Podocarpaceae) is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp) genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii.Methodology/principal findingsThe P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR). It contains 118 unique genes and one duplicated tRNA (trnN-GUU), which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi) and Araucariaceae (Agathis dammara). Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency.ConclusionThe complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of this genus.

Dataset Information

Evolutionary and phylogenetic aspects of the chloroplast genome of Chaenomeles species.

Publications

Evolutionary and phylogenetic aspects of the chloroplast genome of Chaenomeles species.

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