Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications

Abstract

Background Ceratostigma, a genus in the Plumbaginaceae, is an ecologically dominant group of shrubs, subshrub and herb mainly distributed in Qinghai-Tibet Plateau and North China. Ceratostigma has been the focal group in several studies, owing to their importance in economic and ecological value and unique breeding styles. Despite this, the genome information is limited and interspecific relationships within the genus Cerotastigma remains unexplored. Here we sequenced, assembled and characterized the 14 plastomes of five species, and conducted phylogenetic analyses of Cerotastigma using plastomes and nuclear ribosomal DNA (nrDNA) data. Results Fourteen Cerotastigma plastomes possess typical quadripartite structures with lengths from 164,076 to 168,355 bp that consist of a large single copy, a small single copy and a pair of inverted repeats, and contain 127–128 genes, including 82–83 protein coding genes, 37 transfer RNAs and eight ribosomal RNAs. All plastomes are highly conservative and similar in gene order, simple sequence repeats (SSRs), long repeat repeats and codon usage patterns, but some structural variations in the border of single copy and inverted repeats. Mutation hotspots in coding (Pi values > 0.01: matK, ycf3, rps11, rps3, rpl22 and ndhF) and non-coding regions (Pi values > 0.02: trnH-psbA, rps16-trnQ, ndhF-rpl32 and rpl32-trnL) were identified among plastid genomes that could be served as potential molecular markers for species delimitation and genetic variation studies in Cerotastigma. Gene selective pressure analysis showed that most protein-coding genes have been under purifying selection except two genes. Phylogenetic analyses based on whole plastomes and nrDNA strongly support that the five species formed a monophyletic clade. Moreover, interspecific delimitation was well resolved except C. minus, individuals of which clustered into two main clades corresponding to their geographic distributions. The topology inferred from the nrDNA dataset was not congruent with the tree derived from the analyses of the plastid dataset. Conclusion These findings represent the first important step in elucidating plastome evolution in this widespread distribution genus Cerotastigma in the Qinghai-Tibet Plateau. The detailed information could provide a valuable resource for understanding the molecular dynamics and phylogenetic relationship in the family Plumbaginaceae. Lineage genetic divergence within C. minus was perhaps promoted by geographic barriers in the Himalaya and Hengduan Mountains region, but introgression or hybridization could not be completely excluded.

The complete chloroplast genome of the medicinally important plant Plumbago zeylanica L. (plumbaginaceae) and phylogenetic analysis

“… 2023 ), ceratostigma ulicinum NC071211 (Zhao et al. 2023 ), plumbago auriculata NC041245 (Yao et al. 2019 ), plumbago zeylanica OR712438 (in this study), limonium bicolor NC059915 (Darshetkar et al.…”

“…The following sequences were used: Ceratostigma willmottianum OP967034 (Zhao et al. 2023 ), ceratostigma plumbaginoides NC071212 (Zhao et al. 2023 ), ceratostigma minus NC071214 (Zhao et al.…”

“… 2023 ), ceratostigma plumbaginoides NC071212 (Zhao et al. 2023 ), ceratostigma minus NC071214 (Zhao et al. 2023 ), ceratostigma griffithii NC071213 (Zhao et al.…”

“… 2023 ), ceratostigma griffithii NC071213 (Zhao et al. 2023 ), ceratostigma ulicinum NC071211 (Zhao et al. 2023 ), plumbago auriculata NC041245 (Yao et al.…”

Figure 1 from: Malekmohammadi M, Koutroumpa K, Crespo MB, Domina G, Korotkova N, Akhani H, von Mering S, Borsch T, Berendsohn WG (2024) A taxonomic backbone for the Plumbaginaceae (Caryophyllales). PhytoKeys 243: 67-103. https://doi.org/10.3897/phytokeys.243.122784

“…material 2). In Plumbagineae, highly supported monophyly is inferred for Ceratostigma (Koutroumpa et al 2018;Zhao et al 2023) and Dyerophytum (Koutroumpa et al 2018). Plumbago is non-monophyletic (Lledó et al 2001(Lledó et al , 2005aKoutroumpa et al 2018) and Plumbagella is a monospecific genus, therefore, monophyly at the genus level cannot be tested.…”