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The complete plastome of Sorbaria kirilowii: genome structure, comparative analysis, and phylogenetic implications

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Abstract

Sorbaria kirilowii is a deciduous perennial admired for its showy white blossoms. Though of importance for horticultural purposes, the plastomic study concerning this species is still lacking. Here, the plastome of S. kirilowii was de novo assembled using the high-throughput sequencing data. The complete plastome assembly of S. kirilowii was 160,810 bp in length, with a GC content of 36.03%. It featured a typical quadripartite structure, containing a pair of inverted repeats (IRs; 26,338 bp) separated by a large single-copy (LSC; 88,762 bp) and a small single-copy (SSC, 19,372 bp). In total, 132 genes were annotated in the plastome, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Furthermore, 63 SSRs, most of which were AT-rich, were identified in the cp genome of S. kirilowii. 71.7% of the cpSSRs were shown to be located in the intergenic regions. In addition, 49 repeats of varying sizes and types were also identified in the plastome. Through comparison, eight divergence hotspots were identified between the plastome of S. kirilowii and S. sorbifolia var. stellipila. These variable regions could potentially be developed into molecular markers for species delimitation or phylogenetics in future studies. We re-investigated the relationship among 17 Rosaceae species using the plastomic sequences, and S. kirilowii was shown to be a sister to S. sorbifolia var. stellipila. Overall, this study provides plastomic resources which could facilitate marker development and phylogenomics of Rosaceae.

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Data availability

The raw data that support the findings of this research have been deposited in the CNSA (https://db.cngb.org/cnsa/) of CNGBdb under the accession number of CNP0001053.

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Funding

This research was supported by Science and Technology Project of Qinghai Province (2019-ZJ-962Q; 2019-NK-106; 2018-ZJ-963Q; 2017-NK-151; 2016-ZJ-Y01), The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University (2019-ZZ-05), and The Youth Foundation of Qinghai University (2019-QNY-2).

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  1. Le Wang and Jian Liang have contributed equally to this paper.

Authors and Affiliations

  1. State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi’ning, 810016, China

    Le Wang, Jian Liang, Qianhan Shang & Wei Sa

  2. Qinghai Academy of Agricultural Forestry Sciences, Qinghai University, Xi’ning, 810016, China

    Li Wang

  3. Qinghai Plateau Key Laboratory of Tree Genetics and Breeding, Xi’ning, 810016, Qinghai, China

    Li Wang

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  1. Le Wang
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Contributions

LW designed and supervised the project, reviewed drafts of the paper; LW and JL conceived the conception, analyzed the data and wrote the original draft manuscript; LW and QS. analyzed the data and checked and revised the manuscript; JL and WS participated in analyzing the data and drew some figures and tables; LW collected the samples and provided some advice.

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Correspondence to Li Wang.

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(JPG 480 kb). Fig. S1 Verification of the assembly of S. kirilowii plastome.

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Wang, L., Liang, J., Shang, Q. et al. The complete plastome of Sorbaria kirilowii: genome structure, comparative analysis, and phylogenetic implications. Mol Biol Rep 47, 9677–9687 (2020). https://doi.org/10.1007/s11033-020-05976-5

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