Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships

English version

Autoři: Yu Ge ^aff001; Xiangshu Dong ^aff002; Bin Wu ^aff001; Nan Wang ^aff001; Di Chen ^aff001; Haihong Chen ^aff003; Minghong Zou ^aff004; Zining Xu ^aff001; Lin Tan ^aff001; Rulin Zhan ^aff001
Působiště autorů: Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China ^aff001; College of Agriculture, Yunnan University, Yunnan, China ^aff002; College of Agriculture, Guangxi Vocational and Technical College, Nanning, China ^aff003; South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China ^aff004
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0221827

Souhrn

Chloroplasts significantly influence species phylogenies because of their maternal inheritance and the moderate evolutionary rate of their genomes. Avocado, which is a member of the family Lauraceae, has received considerable attention from botanists, likely because of its position as a basal angiosperm. However, there is relatively little avocado genomic information currently available. In this study, six complete avocado chloroplast genomes from three ecological races were assembled to examine the sequence diversity among the three avocado ecological races. A comparative genomic analysis revealed that 515 simple sequence repeat loci and 176 repeats belonging to four other types were polymorphic across the six chloroplast genomes. Three highly variable regions (trnC-GCA-petN, petN-psbM, and petA-psbJ) were identified as highly informative markers. A phylogenetic analysis based on 79 common protein-coding genes indicated that the six examined avocado accessions from three ecological races form a monophyletic clade. The other three genera belonging to the Persea group clustered to form a sister clade with a high bootstrap value. These chloroplast genomes provide important genetic information for future attempts at identifying avocado races and for the related biological research.

Klíčová slova:

Biology and life sciences – Genetics – Genomics – Plant genomics – Plant genomes – Chloroplast genome – Genome complexity – Pseudogenes – Comparative genomics – Plant genetics – Gene types – Bioengineering – Biotechnology – Plant biotechnology – Plant science – Evolutionary biology – Evolutionary systematics – Phylogenetics – Phylogenetic analysis – Taxonomy – Organisms – Eukaryota – Plants – Flowering plants – Fruits – Computational biology – Engineering and technology – Computer and information sciences – Data management – People and places – Population groupings – Ethnicities – Latin American people – Mexican people

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Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships

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