Comparative Chloroplast Genomics of Sophora Species: Evolution and Phylogenetic Relationships in the Early-Diverging Legume Subfamily Papilionoideae (Fabaceae)

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.

Complete Chloroplast Genomes Provide Insights Into Evolution and Phylogeny of Campylotropis (Fabaceae)

“…140–160 kb; Oyebanji et al, 2020 ). Other genome features, including lengths of LSC, SSC, and IRs, expansion and contraction of IR boundaries, number of genes, GC content, the pattern of SSRs also varied little within this genus, which is comparable to other genera from the legume family (e.g., Oyebanji et al, 2020 ; Liao et al, 2021 ).…”

“…The 21 newly assembled and one previously published Campylotropis cp genomes showed little variation in genome structure and genome length, as found in other legume species ( Wang et al, 2018 ; Oyebanji et al, 2020 ; Zhang et al, 2020 ; Liao et al, 2021 ). The Campylotropis cp genomes exhibit the typical quadripartite structure and no large structural variant was found ( Table 1 ).…”

“…Consequently, all 13 candidate molecular markers were located in the LSC region, which may be useful in further studies of species delimitation, phylogenetic, and population genetic studies ( Table 3 ). Many of these molecular markers have been reported in other studies, such as trnH-psbA ( Li et al, 2021 ), accD-psaI ( Chen et al, 2021 ), and petN-trnD ( Liao et al, 2021 ). Notably, the matK gene, which encodes a protein essential for in vivo splicing of Group II introns ( Ahlert et al, 2006 ), is a pseudogene in C. bonii .…”

“…Voucher specimens were deposited in the Herbarium of the Chengdu Institute of Biology (CDBI; Supplementary Table S1 ). The extraction of total genomic DNA, library preparation, and Illumina sequencing for each accession were described in our previous study ( Liao et al, 2021 ).…”

Comparative analysis of the chloroplast genomes of eight Piper species and insights into the utilization of structural variation in phylogenetic analysis

“…This genus occupies a special taxonomic position as a branch of the basal or sub-basal angiosperms ( Group, 2016 ), and factors such as its origin, taxonomic position in angiosperms, unique traits, global distribution, and availability of high diversity in some areas makes Piper a genus of great scientific interest ( Jaramillo et al, 2008 ; Asmarayani, 2018 ; Sen et al, 2019 ). Notably, the morphological features of plants can be greatly affected by environmental conditions, which makes it challenging to elucidate some aspects of taxonomy and evolution by means of classical methods that depend on leaf morphology, fruit morphology, and seed color ( Tsoong Pu-Chiu, 1981 ; Ma, 1990 ; Liao et al, 2021 ). Chloroplasts are maternally-inherited organelles that have a conserved gene structure and undergo less gene recombination, which offers natural advantages in solving the problems of species classification and evolution ( de Vries and Archibald, 2018 ; Nick, 2020 ).…”