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Plant Diversity and Resources

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

Wu-Qin Xu1, Jocelyn Losh1, Chuan Chen2*, Pan Li1*, Rui-Hong Wang3, Yun-Peng Zhao1, Ying-Xiong Qiu1, and Cheng-Xin Fu1

1Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China

2Hangzhou Botanical Garden (Hangzhou Research Institute of Garden Science), Hangzhou 310013, China

3Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China

Keywords: chloroplast genome, divergence time, genomic structure, phylogenomics, phylogeny.


The figwort genus Scrophularia (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 and S. dentata and compare them with those of S. takesimensis and S. buergeriana. 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 four ribosomal RNA genes. Gene order, gene content, AT content and IR/SC boundary structure were nearly identical among them. Nine cp DNA markers (trnH-psbA, rps15, rps18-rpl20, rpl32-trnL, trnS-trnG, ycf15-trnL, rps4-trnT, ndhF-rpl32, 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% HPD: 70.6–99.8 Ma). The higher core Lamiales originated at 65.6 Ma (95% HPD: 51.4–79.4 Ma), with a subsequent radiation which occurred in the Paleocene (between 55.4–62.3 Ma) and gave birth to the diversified families. Our study provides a robust phylogeny and a temporal framework for further investigation on the evolution of Lamiales.

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