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Open AccessArticle

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

1
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
2
University of Chinese Academy of Sciences, Beijing 100049, China
3
Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
4
East African Herbarium, National Museums of Kenya, P.O. Box 45166-00100 Nairobi, Kenya
*
Author to whom correspondence should be addressed.
Plants 2020, 9(4), 456; https://doi.org/10.3390/plants9040456
Received: 2 March 2020 / Revised: 29 March 2020 / Accepted: 2 April 2020 / Published: 4 April 2020
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics)
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. View Full-Text
Keywords: Streptocarpus ionanthus; section Saintpaulia; divergence hotspots; phylogeny; polymorphism; simple sequence repeats (SSRs); genome structure Streptocarpus ionanthus; section Saintpaulia; divergence hotspots; phylogeny; polymorphism; simple sequence repeats (SSRs); genome structure
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Kyalo, C.M.; Li, Z.-Z.; Mkala, E.M.; Malombe, I.; Hu, G.-W.; Wang, Q.-F. The First Glimpse of Streptocarpus ionanthus (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes. Plants 2020, 9, 456.

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