Phylogenetic analysis of Chosenia arbutifolia (Pall.) A. Skv. in Salicaceae using complete chloroplast genome sequence

Xudong He; Yu Wang; Jiwei Zheng; Zhongyi Jiao; Jie Zhou; Baosong Wang; Qiang Zhuge

doi:10.15287/afr.2022.2153

Authors

Xudong He Department of Tree Genetics and Breeding, Jiangsu Academy of Forestry, Nanjing, China Willow Nursery of the Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Academy of Forestry, Nanjing, China
Yu Wang Department of Tree Genetics and Breeding, Jiangsu Academy of Forestry, Nanjing, China College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
Jiwei Zheng Department of Tree Genetics and Breeding, Jiangsu Academy of Forestry, Nanjing, China Willow Nursery of the Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Academy of Forestry, Nanjing, China
Zhongyi Jiao Department of Tree Genetics and Breeding, Jiangsu Academy of Forestry, Nanjing, China Willow Nursery of the Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Academy of Forestry, Nanjing, China
Jie Zhou Department of Tree Genetics and Breeding, Jiangsu Academy of Forestry, Nanjing, China Willow Nursery of the Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Academy of Forestry, Nanjing, China
Baosong Wang Department of Tree Genetics and Breeding, Jiangsu Academy of Forestry, Nanjing, China Willow Nursery of the Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Jiangsu Academy of Forestry, Nanjing, China
Qiang Zhuge College of Biology and the Environment, Nanjing Forestry University, Nanjing, China

DOI:

https://doi.org/10.15287/afr.2022.2153

Keywords:

chloroplast genome, comparative analysis, phylogeny, Chosenia arbutifolia, Salix

Abstract

As a unique and endangered species in the family Salicaceae, Chosenia arbutifolia (Pall.) A. Skv. has great potential for use in ornamental and industrial purposes. Despite its comprehensive importance, the phylogenetic position of C. arbutifolia within Salicaceae is still ambiguous. In the present study, the whole chloroplast genome of C. arbutifolia was sequenced and compared with the genome of other Salicaceae species. A phylogenetic tree was established based on the maximum-likelihood (ML) methods. The de novo assemblies generated 155684 bp in length for the completed cp genome of C. arbutifolia, including a large single-copy region of 84551 bp, a small single-copy region of 16217 bp, and two inverted repeat regions of 27458 bp each. In total, 130 genes were predicted, of which 85 protein-coding genes were annotated in at least one of the five reference databases. In the repeat analysis, 23 forward, 15 palindromic, one complement, one reverse long repeats, and 221 putative SSRs were identified. The results of genome comparison showed that the large single copy region (LSC) region was more divergent than the small single copy region (SSC) and inverted repeated (IR) regions, and a higher divergence occurred in non-coding regions than in coding regions. Significant contractions or expansions were also observed at the IR-LSC/SSC boundaries. Phylogenetic analysis of 20 Salicaceae species confirmed that C. arbutifolia is closely related to Salix species and may therefore be treated as a member of the genus Salix. The complete C. arbutifolia chloroplast genome will provide insight into the chloroplast architecture, function, and evolution of this species and provide additional resources for future research

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