The First Glimpse of <i>Streptocarpus ionanthus</i> (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes
<i>Streptocarpus ionanthus</i> (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of <i>Str. ionanthus</i> is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to un...
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MDPI AG
2020-04-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/9/4/456 |
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| author | Cornelius M. Kyalo Zhi-Zhong Li Elijah M. Mkala Itambo Malombe Guang-Wan Hu Qing-Feng Wang |
| author_facet | Cornelius M. Kyalo Zhi-Zhong Li Elijah M. Mkala Itambo Malombe Guang-Wan Hu Qing-Feng Wang |
| author_sort | Cornelius M. Kyalo |
| collection | DOAJ |
| description | <i>Streptocarpus ionanthus</i> (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of <i>Str. ionanthus</i> is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to understand the molecular variation within <i>Str. ionanthus</i> using a phylogenomic approach. We sequence the chloroplast genomes of five subspecies of <i>Str. ionanthus</i>, 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 (<i>psb</i>M, <i>rps</i>3, <i>atp</i>F<i>-atp</i>H, <i>psb</i>C<i>-psb</i>Z and <i>psa</i>A<i>-ycf</i>3) and five genes with a high number of polymorphic sites (<i>rps</i>16, <i>rpo</i>C2, <i>rpo</i>B, <i>ycf</i>1 and <i>ndh</i>A) which could be investigated further for phylogenetic utility in <i>Str. ionanthus.</i> Phylogenomic analyses here exhibit low polymorphism within <i>Str. ionanthus</i> 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 <i>Str. ionanthus</i> phylogenetic relationships. |
| first_indexed | 2024-03-10T20:40:58Z |
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| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T20:40:58Z |
| publishDate | 2020-04-01 |
| publisher | MDPI AG |
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| series | Plants |
| spelling | doaj.art-5a3310a0d4824231ab8ec0363c7003752023-11-19T20:42:26ZengMDPI AGPlants2223-77472020-04-019445610.3390/plants9040456The First Glimpse of <i>Streptocarpus ionanthus</i> (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast GenomesCornelius M. Kyalo0Zhi-Zhong Li1Elijah M. Mkala2Itambo Malombe3Guang-Wan Hu4Qing-Feng Wang5Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, ChinaUniversity of Chinese Academy of Sciences, Beijing 100049, ChinaKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, ChinaEast African Herbarium, National Museums of Kenya, P.O. Box 45166-00100 Nairobi, KenyaKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, ChinaKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China<i>Streptocarpus ionanthus</i> (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of <i>Str. ionanthus</i> is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to understand the molecular variation within <i>Str. ionanthus</i> using a phylogenomic approach. We sequence the chloroplast genomes of five subspecies of <i>Str. ionanthus</i>, 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 (<i>psb</i>M, <i>rps</i>3, <i>atp</i>F<i>-atp</i>H, <i>psb</i>C<i>-psb</i>Z and <i>psa</i>A<i>-ycf</i>3) and five genes with a high number of polymorphic sites (<i>rps</i>16, <i>rpo</i>C2, <i>rpo</i>B, <i>ycf</i>1 and <i>ndh</i>A) which could be investigated further for phylogenetic utility in <i>Str. ionanthus.</i> Phylogenomic analyses here exhibit low polymorphism within <i>Str. ionanthus</i> 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 <i>Str. ionanthus</i> phylogenetic relationships.https://www.mdpi.com/2223-7747/9/4/456<i>Streptocarpus ionanthus</i>section <i>Saintpaulia</i>divergence hotspotsphylogenypolymorphismsimple sequence repeats (SSRs) |
| spellingShingle | Cornelius M. Kyalo Zhi-Zhong Li Elijah M. Mkala Itambo Malombe Guang-Wan Hu Qing-Feng Wang The First Glimpse of <i>Streptocarpus ionanthus</i> (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes Plants <i>Streptocarpus ionanthus</i> section <i>Saintpaulia</i> divergence hotspots phylogeny polymorphism simple sequence repeats (SSRs) |
| title | The First Glimpse of <i>Streptocarpus ionanthus</i> (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes |
| title_full | The First Glimpse of <i>Streptocarpus ionanthus</i> (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes |
| title_fullStr | The First Glimpse of <i>Streptocarpus ionanthus</i> (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes |
| title_full_unstemmed | The First Glimpse of <i>Streptocarpus ionanthus</i> (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes |
| title_short | The First Glimpse of <i>Streptocarpus ionanthus</i> (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes |
| title_sort | first glimpse of i streptocarpus ionanthus i gesneriaceae phylogenomics analysis of five subspecies chloroplast genomes |
| topic | <i>Streptocarpus ionanthus</i> section <i>Saintpaulia</i> divergence hotspots phylogeny polymorphism simple sequence repeats (SSRs) |
| url | https://www.mdpi.com/2223-7747/9/4/456 |
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