Plastid Phylogenomics and Plastome Evolution of Nandinoideae (Berberidaceae)
Subfamily Nandinoideae Heintze (Berberidaceae), comprising four genera and ca. 19 species, is disjunctively distributed in eastern North America vs. Eurasia (eastern Asia, Central Asia, Middle East, and southeastern Europe), and represents an ideal taxon to explore plastid phylogenomics and plastome...
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Frontiers Media S.A.
2022-06-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.913011/full |
| _version_ | 1818466090035970048 |
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| author | Shiqiang Song Shiqiang Song Dmitriy Zubov Hans Peter Comes Haiwen Li Xuelian Liu Xin Zhong Joongku Lee Zhaoping Yang Pan Li Pan Li |
| author_facet | Shiqiang Song Shiqiang Song Dmitriy Zubov Hans Peter Comes Haiwen Li Xuelian Liu Xin Zhong Joongku Lee Zhaoping Yang Pan Li Pan Li |
| author_sort | Shiqiang Song |
| collection | DOAJ |
| description | Subfamily Nandinoideae Heintze (Berberidaceae), comprising four genera and ca. 19 species, is disjunctively distributed in eastern North America vs. Eurasia (eastern Asia, Central Asia, Middle East, and southeastern Europe), and represents an ideal taxon to explore plastid phylogenomics and plastome evolution in Berberidaceae. Many species of this subfamily have been listed as national or international rare and endangered plants. In this study, we sequenced and assembled 20 complete plastomes, representing three genera and 13 species of Nandinoideae. Together with six plastomes from GenBank, a total of 26 plastomes, representing all four genera and 16 species of Nandinoideae, were used for comparative genomic and phylogenomic analyses. These plastomes showed significant differences in overall size (156,626–161,406 bp), which is mainly due to the expansion in inverted repeat (IR) regions and/or insertion/deletion (indel) events in intergenic spacer (IGS) regions. A 75-bp deletion in the ndhF gene occurred in Leontice and Gymnospermium when compared with Nandina and Caulophyllum. We found a severe truncation at the 5’ end of ycf1 in three G. altaicum plastomes, and a premature termination of ropC1 in G. microrrhynchum. Our phylogenomic results support the topology of {Nandina, [Caulophyllum, (Leontice, Gymnospermium)]}. Within the core genus Gymnospermium, we identified G. microrrhynchum from northeastern Asia (Clade A) as the earliest diverging species, followed by G. kiangnanense from eastern China (Clade B), while the rest species clustered into the two sister clades (C and D). Clade C included three species from West Tianshan (G. albertii, G. darwasicum, G. vitellinum). Clade D consisted of G. altaicum from northern Central Asia, plus one species from the Caucasus Mountains (G. smirnovii) and three from southeastern Europe (G. odessanum, G. peloponnesiacum, G. scipetarum). Overall, we identified 21 highly variable plastome regions, including two coding genes (rpl22, ycf1) and 19 intergenic spacer (IGS) regions, all with nucleotide diversity (Pi) values > 0.02. These molecular markers should serve as powerful tools (including DNA barcodes) for future phylogenetic, phylogeographic and conservation genetic studies. |
| first_indexed | 2024-04-13T20:54:49Z |
| format | Article |
| id | doaj.art-9ed61fa8a83546f5834b6d00d6d3cf01 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-13T20:54:49Z |
| publishDate | 2022-06-01 |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-9ed61fa8a83546f5834b6d00d6d3cf012022-12-22T02:30:22ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-06-011310.3389/fpls.2022.913011913011Plastid Phylogenomics and Plastome Evolution of Nandinoideae (Berberidaceae)Shiqiang Song0Shiqiang Song1Dmitriy Zubov2Hans Peter Comes3Haiwen Li4Xuelian Liu5Xin Zhong6Joongku Lee7Zhaoping Yang8Pan Li9Pan Li10College of Life Sciences and Technologies, Tarim University, Alar, ChinaLaboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, ChinaNational Academy of Medical Sciences of Ukraine, Kyiv, UkraineDepartment of Environment & Biodiversity, University of Salzburg, Salzburg, AustriaCollege of Life Sciences and Technologies, Tarim University, Alar, ChinaCollege of Life Science, Tonghua Normal University, Tonghua, ChinaShanghai Chenshan Botanical Garden, Shanghai, ChinaDepartment of Environment and Forest Resources, Chungnam National University, Daejeon, South KoreaCollege of Life Sciences and Technologies, Tarim University, Alar, ChinaLaboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, ChinaKey Laboratory of Biosystem Homeostasis and Protection, Ministry of Education, Zhejiang University, Hangzhou, ChinaSubfamily Nandinoideae Heintze (Berberidaceae), comprising four genera and ca. 19 species, is disjunctively distributed in eastern North America vs. Eurasia (eastern Asia, Central Asia, Middle East, and southeastern Europe), and represents an ideal taxon to explore plastid phylogenomics and plastome evolution in Berberidaceae. Many species of this subfamily have been listed as national or international rare and endangered plants. In this study, we sequenced and assembled 20 complete plastomes, representing three genera and 13 species of Nandinoideae. Together with six plastomes from GenBank, a total of 26 plastomes, representing all four genera and 16 species of Nandinoideae, were used for comparative genomic and phylogenomic analyses. These plastomes showed significant differences in overall size (156,626–161,406 bp), which is mainly due to the expansion in inverted repeat (IR) regions and/or insertion/deletion (indel) events in intergenic spacer (IGS) regions. A 75-bp deletion in the ndhF gene occurred in Leontice and Gymnospermium when compared with Nandina and Caulophyllum. We found a severe truncation at the 5’ end of ycf1 in three G. altaicum plastomes, and a premature termination of ropC1 in G. microrrhynchum. Our phylogenomic results support the topology of {Nandina, [Caulophyllum, (Leontice, Gymnospermium)]}. Within the core genus Gymnospermium, we identified G. microrrhynchum from northeastern Asia (Clade A) as the earliest diverging species, followed by G. kiangnanense from eastern China (Clade B), while the rest species clustered into the two sister clades (C and D). Clade C included three species from West Tianshan (G. albertii, G. darwasicum, G. vitellinum). Clade D consisted of G. altaicum from northern Central Asia, plus one species from the Caucasus Mountains (G. smirnovii) and three from southeastern Europe (G. odessanum, G. peloponnesiacum, G. scipetarum). Overall, we identified 21 highly variable plastome regions, including two coding genes (rpl22, ycf1) and 19 intergenic spacer (IGS) regions, all with nucleotide diversity (Pi) values > 0.02. These molecular markers should serve as powerful tools (including DNA barcodes) for future phylogenetic, phylogeographic and conservation genetic studies.https://www.frontiersin.org/articles/10.3389/fpls.2022.913011/fullCaulophyllumGymnospermiumLeonticeNorth America-Eurasia disjunctionphylogenomicsplastome evolution |
| spellingShingle | Shiqiang Song Shiqiang Song Dmitriy Zubov Hans Peter Comes Haiwen Li Xuelian Liu Xin Zhong Joongku Lee Zhaoping Yang Pan Li Pan Li Plastid Phylogenomics and Plastome Evolution of Nandinoideae (Berberidaceae) Frontiers in Plant Science Caulophyllum Gymnospermium Leontice North America-Eurasia disjunction phylogenomics plastome evolution |
| title | Plastid Phylogenomics and Plastome Evolution of Nandinoideae (Berberidaceae) |
| title_full | Plastid Phylogenomics and Plastome Evolution of Nandinoideae (Berberidaceae) |
| title_fullStr | Plastid Phylogenomics and Plastome Evolution of Nandinoideae (Berberidaceae) |
| title_full_unstemmed | Plastid Phylogenomics and Plastome Evolution of Nandinoideae (Berberidaceae) |
| title_short | Plastid Phylogenomics and Plastome Evolution of Nandinoideae (Berberidaceae) |
| title_sort | plastid phylogenomics and plastome evolution of nandinoideae berberidaceae |
| topic | Caulophyllum Gymnospermium Leontice North America-Eurasia disjunction phylogenomics plastome evolution |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.913011/full |
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