Abstract
Primula helodoxa Balf.f. is a species endemic to southeastern China distributed in Tengchong county of Yunnan Province. Here is the first time to report the complete chloroplast genome sequence of P. helodoxa. The complete chloroplast genome was 151,909 bp in length, containing a large single-copy (LSC) region of 83192 bp, a small single-copy (SSC) region of 17,797 bp, and a pair of inverted repeats (IRs) regions of 25,460 bp. There are 137 genes in total, 91 protein-coding genes, eight rRNA genes, and 38 transfer RNA genes. The phylogenetic tree showed relative relationship of P. helodoxa and P. chrysochlora.
Keywords: Complete chloroplast genome, Primula helodoxa, endemic species
Primula helodoxa Balf.f. is a species endemic to southeastern China distributed in Tengchong county of Yunnan Province (Hu and Kelso 1996). This species was published in 1916 as a new species in the Sect. Proliferae of family Primulaceae, then be treated as a member of group Primula prolifera Wallich (Richards 1993, 2003). In recent 20 years, P. helodoxa has been found again in Tengchong County since first discovery in 1910s and treated as an independent taxon in Flora of China (Hu and Kelso 1996). Because P. helodoxa has bright golden yellow corolla, it is a valuable parent to hybridize with relative candelabrum species. Here, we first report the complete chloroplast genome sequence of P. helodoxa for understanding its systematics and provide scientific basis for the breeding hybrid in the garden.
The fresh leaves of P. helodoxa were collected from Tengchong, Yunan Province. The voucher specimen was deposit in the Herbarium of Yunnan Normal University (accession no: WZK140621). Total genomic DNA was extracted from the isolated chloroplasts using a modified CTAB method. According to the criterion, we fragmented the DNA and used Illumina Hiseq X Ten sequencer to construct the genomic library for Illumina paired-end (PE) sequencing. Then, NOVOplasty v2.7.2 (Dierckxsens et al. 2017) has been used to assemble the complete chloroplast genome of P. helodoxa. We also used Geneious v 8.0.2 software to annotate the chloroplast genome assembled (Kearse et al. 2012).
The annotated complete chloroplast genome of P. helodoxa was 151,909 bp in length with an overall GC content 37.0% (GenBank number MN504640). The assembled genome contained a large single-copy (LSC) region of 83,192 bp, a small single-copy (SSC) region of 17,797 bp, and a pair of inverted repeats (IRs) regions of 25,460 bp. In total, the chloroplast genome sample consisted of 137 gene, 91 protein-coding genes, eight rRNA genes, and 38 transfer RNA genes, including 115 unique genes, 81 unique CDSs, 30 unique tRNAs, and four unique rRNAs.
The phylogenetic relationship between P. helodoxa and relative species of Primula was inferred base on the relative 11 species with complete chloroplast genomes downloaded from GenBank. All the sequences were aligned by the MAFFT version 7 software (Katoh et al. 2002). The maximum-likelihood (ML) tree was constructed using IQ-TREE v1.6.10 (Nguyen et al. 2015) and performed base on TVM + F+R2 model according to Bayesian information criterion using ModelFinder (Kalyaanamoorthy et al. 2017); ultrafast bootstrap (UFBoot) was used to test branch supports (Hoang et al. 2018) and SH-like approximate likelihood ratio (Figure 1). The phylogenetic tree showed that P. helodoxa and P. chrysochlora formed a monophyletic clade with 100% bootstrap value, being consistent with former taxonomic studies of the genus Primula (Yan et al. 2015). The complete chloroplast genome of P. helodoxa also provided a reference chloroplast genome for the breeding in garden as well as the phylogentic studies of Primulaceae.
Figure 1.
ML phylogenetic tree of Primula helodoxa and 10 Primulaceae species based on chloroplast complete genome, branch supports values were reported as SH-aLRT/UFBoot, green solid dot denotes supports values of 100/100.
Funding Statement
The research was supported by NSFC, grant No. [31960050, 31560062], the Science and Technology planning project of Yunnan Province, grant No. [2016BC013], the Major Project on Biodiversity Conservation of Ministry of Ecology and Environment.
Disclosure statement
No potential conflict of interest was reported by the authors.
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