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. 2020 Jan 14;5(1):581–582. doi: 10.1080/23802359.2019.1710589

The complete chloroplast genome sequence of Prunus sibirica

Shengjun Dong a, Xin Zhang a,b, Yongqiang Sun a, Hao Xu a, Haokai Zhang a, Jianhua Chen a, Mingguo Liu a,✉
PMCID: PMC7748795  PMID: 33366656

Abstract

In this study, the chloroplast genome sequence of Prunus sibirica was obtained from the whole genome sequencing data of Prunus sibirica. Its length is 158,248 bp, which consists of 86,331 bp large single-copy region (LSC), 26,408 bp two reverse repeat regions (IR) and 19,101 bp small single-copy region (SSC). GC content of the whole chloroplast genome is 36.71%. Those of LSC region, SSC region, and IR region were 35, 30, and 43%, respectively. There are 131 unique genes in the chloroplast genome, including 90 protein-coding genes, 33 tRNA genes, and 8 rRNA genes. A maximum-likelihood phylogenetic tree was generated from the chloroplast genomes of 10 species of Rosaceae and 11 peripheral plants. The results showed that Prunus sibirica belongs to Rosaceae and is sister to Prunus salicina.

Keywords: Prunus sibirica, chloroplast genome, phylogenetic tree

Siberian apricot is a joint name of wild apricot. Nine apricot species have been identified in China, among which Prunus sibirica, P. mandshurica, and P. vulgaris are the most generous. Siberian apricots are significant ecological and economic trees, which are light loving, cold resistant and barren resistant. It is the preferred trees for afforestation in arid and semi-arid areas. Its economic product is mainly bitter apricot and found to be in short supply. However, the low and unstable output has become the main bottleneck restricting the industry, which needs thorough research at a population level to provide high and stable yield varieties for the industry (Li et al. 2013, 2018).

The Prunus sibirica leaves samples were collected in Zhalantun (Inner Mongolia, China; 47°54′N, 120°48′E) and stored in the Herbarium of Shenyang Agricultural University as a voucher specimen (AS2019061-1), and fresh leaves total DNA was isolated by modified CTAB method (Doyle and Doyle 1987) in the herbarium. The Illumina library was constructed and sequenced on Hiseq 2000 (Illumina, San Diego, CA, USA).

For generated 199,953,290 reads, the genome was assembled by Velvet (Zerbino and Birney 2008), NOVOPlasty (Dierckxsens et al. 2016), and SSPACE (Boetzer et al. 2011). GapFiller (1000 Genomes Project Consortium 2012) was used to complement gaps in the scaffold sequence. The chloroplast was annotated by GeSeq, tRNAscan-SE (Lowe and Chan 2016), and ARAGORN (Laslett and Canback 2004). After the chloroplast genome assembly was qualified, it was submitted to GenBank (ID: MN708049).

The length of Prunus sibirica chloroplast genome is 158,248 bp, consists of 86,331 bp large single copy (LSC), 26,408 bp two reverse repeats (IR) and 19,101 bp small single copy (SSC). GC content of them were 35, 43, and 30%, respectively. The coding sequences (CDS) accounted for 50.36%. There are 131 unique genes, including 90 protein, 33 tRNA and 8 rRNA. Ten genes contain introns, ycf3 and clpP were found with two introns. The 5′ end exon, 3′ end exon and intron of rps12 are located in the LSC and IR region, respectively. A total of 19 genes were found in IR region, including 9 tRNAs (tmH-GUG, trnM-CAU, trnL-CAA, trnV-GAC, trnI-GAU, trnA-UGC, trnL-CAA, trnN-GUU, and trnR-ACG), 8 protein genes (rps7, rpl2, rpl23, rps12, rps19, ndhB, ycf1, and ycf2) and 2 rRNAs (16S and 23S RNA). At the same time, pseudogenes were formed in the part of ycf1 and rps19 in the IR.

A phylogenetic tree (with 1000 replicates) was constructed in MEGA 7.0, which includes 10 Rosaceae plants and 11 exophytes. The results showed Prunus sibirica belongs to Rosaceae (Figure 1). The relationship between Prunus sibirica and Prunus salicina is closer. Previous studies suggested that the relationship between Prunus vulgaris and Prunus mume is close (Zhang et al. 2018), but we found that Prunus sibirica and Prunus salicina is closer, suggesting there is a wide range of genetic variation in apricot plants.

Figure 1.

Figure 1.

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The phylogenetic tree (1000 replicates) of 10 Rosaceae plants and 11 Exophytes.

In conclusion, the complete chloroplast genome in this study supports the phylogeny study of Rosaceae.

Acknowledgments

The authors certify that they have participated sufficiently in the work to take public responsibility for the appropriateness of the experimental design and method and the collection, analysis, and interpretation of the data. This manuscript has not been published in whole or in part nor is it being considered for publication elsewhere. The authors declare that there are no financial or other relationships that might lead to a conflict of interest in the present article. All authors have reviewed the final version of the manuscript and approved it for publication.

Funding Statement

This work was supported by the Liaoning Special Professor Fund Project (2012) and the National Forestry Public Welfare Industry Research Project (201004034).

Disclosure statement

No potential conflict of interest was reported by the authors.

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