Plastome Evolution in Saxifragaceae and Multiple Plastid Capture Events Involving Heuchera and Tiarella

Abstract

Saxifragaceae, a family of over 600 species and approximately 30 genera of herbaceous perennials, is well-known for intergeneric hybridization. Of the main lineages in this family, the Heuchera group represents a valuable model for the analysis of plastid capture and its impact on phylogeny reconstruction. In this study, we investigated plastome evolution across the family, reconstructed the phylogeny of the Heuchera group and examined putative plastid capture between Heuchera and Tiarella. Seven species (11 individuals) representing Tiarella, as well as Mitella and Heuchera, were selected for genome skimming. We assembled the plastomes, and then compared these to six others published for Saxifragaceae; the plastomes were found to be highly similar in overall size, structure, gene order and content. Moreover, ycf15 was lost due to pseudogenization and rpl2 lost its only intron for all the analyzed plastomes. Comparative plastome analysis revealed that size variations of the plastomes are purely ascribed to the length differences of LSC, SSC, and IRs regions. Using nuclear ITS + ETS and the complete plastome, we fully resolved the species relationships of Tiarella, finding that the genus is monophyletic and the Asian species is most closely related to the western North American species. However, the position of the Heuchera species was highly incongruent between nuclear and plastid data. Comparisons of nuclear and plastid phylogenies revealed that multiple plastid capture events have occurred between Heuchera and Tiarella, through putative ancient hybridization. Moreover, we developed numerous molecular markers for Tiarella (e.g., plastid hotspot and polymorphic nuclear SSRs), which will be useful for future studies on the population genetics and phylogeography of this disjunct genus.

Sequencing and comparative analysis of the chloroplast genome of Ribes odoratum provide insights for marker development and phylogenetics in Ribes

“…This consistency was also observed in the cp genome of Saxifragaceae (Dong et al 2018), in which Grossulariaceae was formerly included as a subfamily. A recent report by Liu et al (2020) have pointed out that Saxifragaceae plastomes showed high similarity in size, gene content and order, and ycf15 was lost as a result of pseudogenization. The loss of ycf15, and the intron of rpl2 as well, was also observed in the two Ribes plastomes.…”

Characterization of the complete chloroplast genome of Peltoboykinia tellimoides (Saxifragaceae)

“…( 2017 ) and Liu et al. ( 2020 ). Maximum likelihood (ML) method was applied to reconstruct the phylogenetic tree for 22 whole cp genome sequences of Saxifragaceae species, with two Grossulariaceae species as outgroup.…”

Plastomes of two Rehmannia species： comparative genomic and phylogenetic analyses

“…Then 125-bp Paired-end reads were sequenced on the Illumina HiSeq 2500 platform. Complete plastomes were assembled and confirmed using NOVOPlasty (Dierckxsens et al 2017) and CLC Genomics Workbench 11 (Zhang et al 2019;Liu et al 2020). Gene annotation was performed using program PGA (Qu et al 2019) with Rehmannia henryi (GenBank accession numbers: KX636158) as a reference.…”