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.

Keywords: Streptocarpus ionanthus; divergence hotspots; genome structure; phylogeny; polymorphism; section Saintpaulia; simple sequence repeats (SSRs).

Figure 1

Linear chloroplast genome maps of six taxa of sect. Saintpaulia ((A) Str. teitensis; (B) subsp. velutinus; (C) subsp. grandifolius; (D) subsp. orbicularis; (E) subsp. grotei and (F) subsp. rupicola). The genes above the black line (names on top of the figure) represent clockwise transcription while genes below (names at the bottom) are transcribed counter-clockwise. Genes of different functional categories are colored according to the legend at the bottom.

Figure 2

Multiple genome alignment of six sect. Saintpaulia taxa. The red bars represent sequence similarity among different genomes. The bottom bar is a visualization of the sequences’ consensus identities with the green color symbolizing homology while the yellow vertical lines signify variation spots. LSC: Large Single Copy region; IRA: Inverted Repeat A; SSC: Small Single Copy region and IRB: Inverted Repeat B.

Figure 3

Comparison of the Inverted Repeat/ Single Copy (IR/SC) junctions’ characteristics among the six sect. Saintpaulia genomes. The genes below and above are transcribed in clockwise and counter-clockwise directions, respectively. The setting is not to scale.

Figure 4

Nucleotide variability (Pi) values among chloroplast genomes of the five Str. ionanthus subspecies for (A) Coding sequences and (B) Intergenic spacer regions.

Figure 5

Simple Sequence Repeats (SSRs) in six sect. Saintpaulia chloroplast genomes. (A) Number of identified SSRs at different repeat motifs, (B) Percentage contribution of each repeat type.

Figure 6

The phylogenetic relationship within five Str. ionanthus subspecies and the relationship with other Gesneriaceae based on (A) complete genome sequence and (B) coding genes and (C) intergenic regions. The bootstrap support values are given for both Maximum Likelihood (ML) and Bayesian Inference (BI) trees (ML/BI) and * denote maximum support values for both ML/BI.

Figure 7

Morphological heterogeneity in Streptocarpus ionanthus; (A) Str. ionanthus subsp. velutinus, (B) Str. ionanthus subsp. orbicularis, (C) Str. ionanthus subsp. grandifolius, (D) Str. ionanthus subsp. rupicola, (E) Str. ionanthus subsp. grotei (trailing habit) and (F) Str. ionanthus subsp. grotei (rosulate habit).