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The complete chloroplast genome of a distylous-homostylous species, Primula homogama (Primulaceae).

ABSTRACT: Primula homogama F. H. Chen & C. M. Hu (Primulaceae) is endemic to the Emei Mountain of China. In this study, we characterized the complete chloroplast genome of P. homogama based on next-generation sequencing (NGS). The complete chloroplast genome of P. homogama was 154,677 bp in size with a typical quadripartite structure, containing a large single-copy (LSC) region of 85,299 bp and a small single-copy (SSC) region of 17,816 bp. These two regions were separated by a pair of inverted repeat regions (IRs), each of 25,781 bp. A total of 130 functional genes were encoded, consisted of 86 protein-coding genes (PCG), 36 tRNA genes, and eight ribosomal RNA (rRNA) genes.

SUBMITTER: Sun HY

PROVIDER: S-EPMC7872557 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The genus Primula (Primulaceae) comprises more than 500 species, with 300 species distributed in China. The contradictory results between systematic analyses and morphology-based taxonomy make taxonomy studies difficult. Furthermore, frequent introgression between closely related species of Primula can result in non-monophyletic species. In this study, the complete chloroplast genome of sixteen Primula obconica subsp. obconica individuals were assembled and compared with 84 accessions of 74 species from 21 sections of the 24 sections of the genus in China. The plastome sizes of P. obconica subsp. obconica range from 153,584 bp to 154,028 bp. Genome-wide variations were detected, and 1915 high-quality SNPs and 346 InDels were found. Most SNPs were detected in downstream and upstream gene regions (45.549% and 41.91%). Two cultivated accessions, ZP1 and ZP2, were abundant with SSRs. Moreover, 12 SSRs shared by 9 accessions showed variations that may be used as molecular markers for population genetic studies. The phylogenetic tree showed that P. obconica subsp. obconica cluster into two independent clades. Two subspecies have highly recognizable morphological characteristics, isolated geographical distribution areas, and distinct phylogenetic relationships compared with P. obconica subsp. obconica. We elevate the two subspecies of P. obconica to separate species. Our phylogenetic tree is largely inconsistent with morphology-based taxonomy. Twenty-one sections of Primula were mainly divided into three clades. The monophyly of Sect. Auganthus, Sect. Minutissimae, Sect. Sikkimensis, Sect. Petiolares, and Sect. Ranunculoides are well supported in the phylogenetic tree. The Sect. Obconicolisteri, Sect. Monocarpicae, Sect. Carolinella, Sect. Cortusoides, Sect. Aleuritia, Sect. Denticulata, Sect. Proliferae Pax, and Sect. Crystallophlomis are not a monophyletic group. The possible explanations for non-monophyly may be hybridization, polyploidization, recent introgression, incorrect taxonomy, or chloroplast capture. Multiple genomic data and population genetic studies are therefore needed to reveal the evolutionary history of Primula. Our results provided valuable information for intraspecific variation and phylogenetic relationships within Primula.

Dataset Information

The complete chloroplast genome of a distylous-homostylous species, Primula homogama (Primulaceae).

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