The Conservation of Chloroplast Genome Structure and Improved Resolution of Infrafamilial Relationships of Crassulaceae.

Hong Chang,Xiaoting Xu,Jianquan Liu,Zhenxiang Xi,Lei Zhang,Huanhuan Xie

doi:10.3389/fpls.2021.631884

Hong Chang, Xiaoting Xu + Show 4 more

Open Access

https://doi.org/10.3389/fpls.2021.631884

Copy DOI

Abstract

Crassulaceae are the largest family in the angiosperm order Saxifragales. Species of this family are characterized by succulent leaves and a unique photosynthetic pathway known as Crassulacean acid metabolism (CAM). Although the inter- and intrageneric relationships have been extensively studied over the last few decades, the infrafamilial relationships of Crassulaceae remain partially obscured. Here, we report nine newly sequenced chloroplast genomes, which comprise several key lineages of Crassulaceae. Our comparative analyses and positive selection analyses of Crassulaceae species indicate that the overall gene organization and function of the chloroplast genome are highly conserved across the family. No positively selected gene was statistically supported in Crassulaceae lineage using likelihood ratio test (LRT) based on branch-site models. Among the three subfamilies of Crassulaceae, our phylogenetic analyses of chloroplast protein-coding genes support Crassuloideae as sister to Kalanchoideae plus Sempervivoideae. Furthermore, within Sempervivoideae, our analyses unambiguously resolved five clades that are successively sister lineages, i.e., Telephium clade, Sempervivum clade, Aeonium clade, Leucosedum clade, and Acre clade. Overall, this study enhances our understanding of the infrafamilial relationships and the conservation of chloroplast genomes within Crassulaceae.

Highlights

The angiosperm family Crassulaceae, known as the stonecrop family, belongs to the order Saxifragales and include 34 genera and approximately 1,400 species (APG IV, 2016; Messerschmid et al, 2020), which are predominantly perennial herbs, subshrubs, or shrubs (Thiede and Eggli, 2007)
Numerous phylogenetic studies have been performed to evaluate the infrafamilial relationships of Crassulaceae with a broad taxon sampling (e.g., Berger, 1930; van Ham and Hart, 1998; Mort et al, 2001; Mayuzumi and Ohba, 2004; Gontcharova et al, 2006, 2008; Folk et al, 2019; Messerschmid et al, 2020), which have led to the establishment of three subfamilies by Thiede and Eggli (2007), i.e., Crassuloideae, Kalanchoideae, and Sempervivoideae
After quality control and pre-processing, at least four gigabases (Gb) of whole-genome sequencing data were obtained for each of the nine species (Table 1). These clean reads were assembled into high-quality chloroplast genomes using a reference-guided approach, and the resulting coverage ranged from 1,115 × (i.e., Cotyledon tomentosa) to 12,687 × (i.e., Kalanchoe fedtschenkoi)

Summary

Introduction

The angiosperm family Crassulaceae, known as the stonecrop family, belongs to the order Saxifragales and include 34 genera and approximately 1,400 species (APG IV, 2016; Messerschmid et al, 2020), which are predominantly perennial herbs, subshrubs, or shrubs (Thiede and Eggli, 2007). Numerous phylogenetic studies have been performed to evaluate the infrafamilial relationships of Crassulaceae with a broad taxon sampling (e.g., Berger, 1930; van Ham and Hart, 1998; Mort et al, 2001; Mayuzumi and Ohba, 2004; Gontcharova et al, 2006, 2008; Folk et al, 2019; Messerschmid et al, 2020), which have led to the establishment of three subfamilies by Thiede and Eggli (2007), i.e., Crassuloideae, Kalanchoideae, and Sempervivoideae. Despite the significant progress made in the tribal and generic circumscription of Crassulaceae, phylogenetic relationships among tribes and major clades remain poorly to moderately supported or sometimes contradicted, especially within Sempervivoideae (Supplementary Figure 1)

Methods

Results

Conclusion