Comparative genomics of figworts (Scrophularia, Scrophulariaceae), with implications for the evolution of Scrophularia and Lamiales

Abstract

The figwort genus Scrophularia L. (Scrophulariaceae) comprises 200–300 species and is widespread throughout the temperate Northern Hemisphere. Due to reticulate evolution resulting from hybridization and polyploidization, the taxonomy and phylogeny of Scrophularia is notoriously challenging. Here we report the complete chloroplast (cp) genome sequences of S. henryi Hemsl. and S. dentata Royle ex Benth. and compare them with those of S. takesimensis Nakai and S. buergeriana Miq. The Scrophularia cp genomes ranged from 152 425 to 153 631 bp in length. Each cp genome contained 113 unigenes, consisting of 78 protein‐coding genes, 31 transfer RNA genes, and 4 ribosomal RNA genes. Gene order, gene content, AT content and IR/SC boundary structure were nearly identical among them. Nine cpDNA markers (trnH‐psbA, rps15, rps18‐rpl20, rpl32‐trnL, trnS‐trnG, ycf15‐trnL, rps4‐trnT, ndhF‐rpl32, and rps16‐trnQ) with more than 2% variable sites were identified. Our phylogenetic analyses including 55 genera from Lamiales strongly supported a sister relationship between ((Bignoniaceae + Verbenaceae) + Pedaliaceae) and (Acanthaceae + Lentibulariaceae). Within Scrophulariaceae, a topology of (S. dentata + (S. takesimensis + (S. buergeriana + S. henryi))) was strongly supported. The crown age of Lamiales was estimated to be 85.1 Ma (95% highest posterior density, 70.6–99.8 Ma). The higher core Lamiales originated at 65.6 Ma (95% highest posterior density, 51.4–79.4 Ma), with a subsequent radiation that occurred in the Paleocene (between 55.4 and 62.3 Ma) and gave birth to the diversified families. Our study provides a robust phylogeny and a temporal framework for further investigation of the evolution of Lamiales.

Comparative Chloroplast Genomics of Fritillaria (Liliaceae), Inferences for Phylogenetic Relationships between Fritillaria and Lilium and Plastome Evolution

“…Each Fritillaria plastid genome contained the number of large repeat sequences ranging from 30 to 57 and repeats with highest proportion ranging in size between 30 and 39 bp ( Figure 4D). Repeats situated in homologous regions with identical lengths were recognized as shared repeats [13,26]. Under this criterion, there were 18 repeats shared by all eleven Fritillaria species, 24 repeats shared by ten of the Fritillaria species (except for F. maximowiczii), as well as 27 repeats shared by nine of the Fritillaria species (except for F. maximowiczii and F. davidii).…”

“…They can provide plenty of variable sites among their entire size for phylogenetic analyses [3]. Thus, whole chloroplast genomes show the potential for resolving evolutionary relationships and have been employed to generate highly resolved phylogenies and genetic diversity, especially in the unresolved relationship of some complex taxa or at low taxonomic levels [2,[11][12][13]. Because different regions of the whole chloroplast genomes differed with their evolutionary rates, partitioning the genome by regions or genes might be preferable for phylogenomic analysis [3].…”

Comparative chloroplast genomics of Fritillaria (Liliaceae), inferences for phylogenetic relationships between Fritillaria and Lilium and genome evolution

“…Each Fritillaria plastid genome contained the number of large repeat sequences ranging from 30 to 57 and repeats with highest proportion ranging in size between 30 and 39 bp (Fig.4D). Repeats situated in homologous regions with the identical lengths were recognized as shared repeats [13,26]. Under this criterion, there were18 repeats shared by all eleven Fritillaria species, 24 repeats shared by ten of the Fritillaria species (except for (Table S7).…”

“…They can provide plenty of variable sites among their entire size for phylogenetic analyses [3]. Thus, whole chloroplast genomes show the potential for resolving evolutionary relationships and have been employed to generate highly resolved phylogenies and genetic diversity, especially in unresolved relationship of some complex taxon or at low taxonomic levels [2,[11][12][13]. Because different regions of the whole chloroplast genomes differ with their evolutionary rates, it was preferable for phylogenomic analysis by partition the genome by regions or genes and the concatenated coding genes were by far most widely used [3,14,15].…”

Orthologous nuclear markers and new transcriptomes that broadly cover the phylogenetic diversity of Acanthaceae

“…Furthermore, the phylogenetic relationships in several smaller clades are currently not well understood (e.g., in Avicennia L. [Glasenapp et al., ], Barleria L. [Darbyshire et al., ], Dyschoriste Nees [Chumchim et al., ], Thunbergioideae T. Anderson [Borg et al., ], Ruellia L. [Tripp et al., ]). In addition to this obstacle, the rooting of the Acanthaceae phylogeny is uncertain, as interfamilial relationships in Lamiales remain elusive (Schäferhoff et al., ; Refulio‐Rodriguez and Olmstead, ; Stull et al., ; Wikström et al., ; Chase et al., ; Sarzi et al., ; Xu et al., ). These technical barriers prevent targeted investigations of evolutionary questions within this family.…”