The First Glimpse of Streptocarpus ionanthus (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes

Abstract

Streptocarpus ionanthus (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of Str. ionanthus is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to understand the molecular variation within Str. ionanthus using a phylogenomic approach. We sequence the chloroplast genomes of five subspecies of Str. ionanthus, compare their structural features and identify divergent regions. The five genomes are identical, with a conserved structure, a narrow size range (170 base pairs (bp)) and 115 unique genes (80 protein-coding, 31 tRNAs and 4 rRNAs). Genome alignment exhibits high synteny while the number of Simple Sequence Repeats (SSRs) are observed to be low (varying from 37 to 41), indicating high similarity. We identify ten divergent regions, including five variable regions (psbM, rps3, atpF-atpH, psbC-psbZ and psaA-ycf3) and five genes with a high number of polymorphic sites (rps16, rpoC2, rpoB, ycf1 and ndhA) which could be investigated further for phylogenetic utility in Str. ionanthus. Phylogenomic analyses here exhibit low polymorphism within Str. ionanthus and poor phylogenetic separation, which might be attributed to recent divergence. The complete chloroplast genome sequence data concerning the five subspecies provides genomic resources which can be expanded for future elucidation of Str. ionanthus phylogenetic relationships.

Taxonomy, comparative genomics of Mullein (Verbascum, Scrophulariaceae), with implications for the evolution of Verbascum and Lamiales

“…In comparison to chloroplast DNA markers, plastome studies provide more comprehensive genetic data [5,37,38]. Plastomes have been recently used as a useful tool in phylogenetic studies and genetic diversity [39][40][41]. Additionally, the variable regions of plastomes can be used as molecular markers for future phylogenetic and genetic diversity studies [41].…”

“…Plastomes have been recently used as a useful tool in phylogenetic studies and genetic diversity [39][40][41]. Additionally, the variable regions of plastomes can be used as molecular markers for future phylogenetic and genetic diversity studies [41]. In this study, we sequenced and analyzed the whole plastomes of V. sinaiticum, V. brevipedicellatum, V. thapsus, V. songaricum, V. blattaria, V. chaixii, V. phoeniceum including two additional sequences from NCBI (NC050920 and MT610040).…”

Plastome Characterization and Phylogenomics of East Asian Beeches with a Special Emphasis on Fagus multinervis on Ulleung Island, Korea

“…In addition, plastome sequencing has revealed considerable variation within and between plant species [ 16 ]. Therefore, such information is particularly fundamental to provide a greater resolution and stronger support at lower taxonomic levels [ 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. Recently, several studies have reported the whole plastome sequences of Fagus and related genera, such as Quercus and Castanea , in Fagaceae [ 30 , 31 , 32 , 33 , 34 ].…”

Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan

“…Achieving adequate resolutions on the basis of the phylogenetic analyses of several concatenated regions has been difficult, especially for recently diverged plant species, because of limited sequence variations in several coding and noncoding regions of chloroplast DNA [24][25][26] . With the advent of next-generation sequencing (NGS) tools, considerable genome-wide variations in phylogenomics have significantly enhanced our understanding of patterns and processes in plant evolution, especially at lower taxonomic levels [27][28][29][30][31][32] . Since the first report of three partial Rubus plastomes being part of the Rosaceae phylogeny 33 , several complete chloroplast genomes belonging to different subgenera, i.e., Anoplobatus and Idaeobatus, have been recently reported, and useful hotspot regions for phylogenetic analysis have been suggested [34][35][36][37][38][39] .…”