Chloroplast phylogenomics and the taxonomy of Saxifraga section Ciliatae (Saxifragaceae)

Rui Yuan; Xiaolei Ma; Zhuoxin Zhang; Richard J Gornall; Yongcui Wang; Shilong Chen; Qingbo Gao

doi:10.1002/ece3.9694

Chloroplast phylogenomics and the taxonomy of Saxifraga section Ciliatae (Saxifragaceae)

Ecol Evol. 2023 Jan 6;13(1):e9694. doi: 10.1002/ece3.9694. eCollection 2023 Jan.

Authors

Rui Yuan^{1

2}, Xiaolei Ma^{1

2}, Zhuoxin Zhang³, Richard J Gornall⁴, Yongcui Wang¹, Shilong Chen¹, Qingbo Gao^{1

5}

Affiliations

¹ Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park Chinese Academy of Sciences Xining China.
² University of Chinese Academy of Sciences Beijing China.
³ College of Forestry and Landscape Architecture South China Agricultual University Guanzhou China.
⁴ Department of Genetics University of Leicester Leicester UK.
⁵ Qinghai Provincial Key Laboratory of Crop Molecular Breeding Xining China.

Abstract

Comprising ca. 200 species, Saxifraga sect. Ciliatae is the most species-rich section of Saxifraga s.str., whose center of diversity is in the Tibeto-Himalayan region. The infra-sectional classification of sect. Ciliatae is still in debate due to the high level of species richness, as well as remarkable variations of habitat, morphology, physiology and life cycles. Subdivisions of this section proposed in various taxonomic systems have not been adequately tested in previous phylogenetic studies, partly due to low taxonomic sampling density, but also to the use of few DNA markers. In order to achieve a more robust infra-sectional classification of sect. Ciliatae, complete chloroplast genomes of 94 taxa from this section were analyzed, of which 93 were newly sequenced, assembled and annotated. The length of the 94 plastomes of sect. Ciliatae taxa range from 143,479 to 159,938 bp, encoding 75 to 79 unique protein-coding genes (PCGs). Analyses of the 94 plastomes revealed high conservation in structural organization, gene arrangement, and gene content. Gene loss and changes of IR boundaries were detected but in extremely low frequency. The molecular phylogenetic tree from concatenated PCGs and complete chloroplast genome sequences exhibited high resolution and support values and confirms that sect. Ciliatae is monophyletic. Three well-supported clades were revealed within the section that agree relatively well with the subsectional taxonomy of Gornall (1987), but some minor modifications should be made. Firstly, the monotypic subsection Cinerascentes should be abandoned and its constituent species, S. cinerascens, assigned to subsect. Gemmiparae. Secondly, subsections Rosulares and Serpyllifoliae should be merged and become subsect. Rosulares. Section Ciliatae thus comprises: subsect. Hirculoideae Engl. & Irmsch.; subsect. Rosulares Gornall; subsect. Gemmiparae Engl. & Irmsch.; subsect. Flagellares (C. B. Clarke) Engl. & Irmsch. and subsect. Hemisphaericae (Engl. & Irmsch.) Gornall.

Keywords: Saxifraga; chloroplast; phylogeny; plastome; sect. Ciliatae.