Abstract
The taxonomy and evolutionary history of Sophora L., a genus with high economic and medicinal value, remain uncertain due to the absence of genetic resource (especially in China) and low polymorphism of molecular markers. Our aim was to elucidate the molecular evolution and phylogenetic relationships in chloroplast genomes of Sophora species in the early-diverging legume subfamily Papilionoideae (Fabaceae). We reported nine Sophora chloroplast genome from China using Illumina sequencing. We performed a series of analyses with previously published genomes of Sophora species to investigate their genomic characteristics, identified simple sequence repeats, large repeat sequences, tandem repeats, and highly polymorphic loci. The genomes were 152,953–158,087 bp in length, and contained 111–113 unique genes, including 76–78 protein coding, 31 tRNA, and 4 rRNA. The expansion of inverted repeat boundary of Sophora resulted in rps12 entering into the LSC region and loss of trnT-CGU gene in some species. Also, we found an approximately 23 kb inversion between trnC-GCA and trnF-GAA within the genus. In addition, we identified seven highly polymorphic loci (pi (π) > 0.035) suitable for inferring the phylogeny of Sophora species. Among these, three regions also co-occurred with large repeat sequences and support use of repeats as a proxy for the identification of polymorphic loci. Based on whole chloroplast genome and protein-coding sequences data-set, a well-supported phylogenetic tree of Sophora and related taxa showed that this genus is monophyletic, but sect. Disamaea and sect. Sophora, are incongruent with traditional taxonomic classifications based on fruit morphology. Our finding provides significant genetic resources to support further investigation into the phylogenetic relationship and evolution of the genus Sophora.
Highlights
The plastid genome of photosynthetic flowering plants is generally extremely conserved in terms of structural organization, gene content (115–160 genes), gene arrangement, and GC content (34–40%; Palmer, 1985; Mower and Vickrey, 2018)
S. dunnii Prain, S. franchetiana Dunn, S. moorcroftiana (Benth.) Benth. ex Baker, S. prazeri Prain, S. tomentosa L., S. velutina Lindl., and S. wilsonii Craib assemblies. These plastomes ranged from 152,953 bp (S. moorcroftiana) to 158,087 bp (S. wilsonii; Supplementary Table S2) and exhibited the typical quadripartite structure, including two inverted repeat (IR) regions of 25,800–30,609 bp separated by an large single-copy region (LSC) region of 83,138–85,127 bp and an small single-copy region (SSC) region of 13,466–18,342 bp (Supplementary Table S2)
The GC content of the newly assembled plastomes ranged from 36.1% (S. wilsonii) to 36.7% (S. davidii and S. moorcroftiana; Supplementary Table S2)
Summary
The plastid genome (plastome) of photosynthetic flowering plants is generally extremely conserved in terms of structural organization, gene content (115–160 genes), gene arrangement, and GC content (34–40%; Palmer, 1985; Mower and Vickrey, 2018). Several mutational events occur in plastomes, including indels, inversions, substitutions, contractions, and expansions of the inverted repeats. These mutations affect the gene content of plastomes through gene duplication, gene loss, and pseudogenization (Guisinger et al, 2011; Vieira et al, 2014; Abdullah, Mehmood, et al, 2020a; Alqahtani and Jansen, 2021). Rearrangements have been found in the Asteraceae (Kim et al, 2005; Sablok et al, 2019), Bignoniaceae (Fonseca and Lohmann, 2017), Campanulaceae (Haberle et al, 2008; Uribe–Convers et al, 2017), Fabaceae (Lavin et al, 1990; Cai et al, 2008; Schwarz et al, 2015; Keller et al, 2017; Wang et al, 2018; Jin et al, 2019; Oyebanji et al, 2020), Geraniaceae (Wicke et al, 2011; Röschenbleck et al, 2017), Oleaceae (Lee et al, 2007), Plantaginaceae (Zhu et al, 2016; Asaf et al, 2020), and Poaceae (Burke et al, 2016; Liu et al, 2020)
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