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Weng L, Jiang Y, Wang Y, Zhang X, Zhou P, Wu M, Li H, Sun H, Chen S. Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae). BMC PLANT BIOLOGY 2023; 23:284. [PMID: 37246219 DOI: 10.1186/s12870-023-04271-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/07/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND The Sinodielsia clade of the subfamily Apioideae (Apiacieae) was established in 2008, and it is composed of 37 species from 17 genera. Its circumscription is still poorly delimited and unstable, and interspecific relationships in the clade lack comprehensive analysis. Chloroplast (cp.) genomes provide valuable and informative data sources for evolutionary biology and have been widely used in studies on plant phylogeny. To infer the phylogenetic history of the Sinodielsia clade, we assembled complete cp. genomes of 39 species and then performed phylogenetic analysis based on these cp. genome sequence data combined with 66 published cp. genomes from 16 genera relative to the Sinodielsia clade. RESULTS These 39 newly assembled genomes had a typical quadripartite structure with two inverted repeat regions (IRs: 17,599-31,486 bp) separated by a large single-copy region (LSC: 82,048-94,046 bp) and a small single-copy region (SSC: 16,343-17,917 bp). The phylogenetic analysis showed that 19 species were clustered into the Sinodielsia clade, and they were divided into two subclades. Six mutation hotspot regions were detected from the whole cp. genomes among the Sinodielsia clade, namely, rbcL-accD, ycf4-cemA, petA-psbJ, ycf1-ndhF, ndhF-rpl32 and ycf1, and it was found that ndhF-rpl32 and ycf1 were highly variable in the 105 sampled cp. genomes. CONCLUSION The Sinodielsia clade was subdivided into two subclades relevant to geographical distributions, except for cultivated and introduced species. Six mutation hotspot regions, especially ndhF-rpl32 and ycf1, could be used as potential DNA markers in the identification and phylogenetic analyses of the Sinodielsia clade and Apioideae. Our study provided new insights into the phylogeny of the Sinodielsia clade and valuable information on cp. genome evolution in Apioideae.
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Affiliation(s)
- Long Weng
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Yunhui Jiang
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Yong Wang
- Yunnan Institute of Forest Inventory and Planning, Kunming, 650051, China
| | - Xuemei Zhang
- Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Ping Zhou
- College of Basic Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Mei Wu
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Hongzhe Li
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shaotian Chen
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
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Ogoma CA, Liu J, Stull GW, Wambulwa MC, Oyebanji O, Milne RI, Monro AK, Zhao Y, Li DZ, Wu ZY. Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:870949. [PMID: 35668809 PMCID: PMC9164014 DOI: 10.3389/fpls.2022.870949] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/15/2022] [Indexed: 05/09/2023]
Abstract
Urticeae s.l., a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling in previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. To address these concerns, we used genome skimming data-CP genome and nuclear ribosomal DNA (18S-ITS1-5.8S-ITS2-26S); 106 accessions-for the very first time to attempt resolving the recalcitrant relationships and to explore chloroplast structural evolution across the group. Furthermore, we assembled a taxon rich two-locus dataset of trnL-F spacer and ITS sequences across 291 accessions to complement our genome skimming dataset. We found that Urticeae plastomes exhibit the tetrad structure typical of angiosperms, with sizes ranging from 145 to 161 kb and encoding a set of 110-112 unique genes. The studied plastomes have also undergone several structural variations, including inverted repeat (IR) expansions and contractions, inversion of the trnN-GUU gene, losses of the rps19 gene, and the rpl2 intron, and the proliferation of multiple repeat types; 11 hypervariable regions were also identified. Our phylogenomic analyses largely resolved major relationships across tribe Urticeae, supporting the monophyly of the tribe and most of its genera except for Laportea, Urera, and Urtica, which were recovered as polyphyletic with strong support. Our analyses also resolved with strong support several previously contentious branches: (1) Girardinia as a sister to the Dendrocnide-Discocnide-Laportea-Nanocnide-Zhengyia-Urtica-Hesperocnide clade and (2) Poikilospermum as sister to the recently transcribed Urera sensu stricto. Analyses of the taxon-rich, two-locus dataset showed lower support but was largely congruent with results from the CP genome and nuclear ribosomal DNA dataset. Collectively, our study highlights the power of genome skimming data to ameliorate phylogenetic resolution and provides new insights into phylogenetic relationships and chloroplast structural evolution in Urticeae.
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Affiliation(s)
- Catherine A. Ogoma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Gregory W. Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Moses C. Wambulwa
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui, Kenya
| | - Oyetola Oyebanji
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Richard I. Milne
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Ying Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- *Correspondence: De-Zhu Li,
| | - Zeng-Yuan Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Zeng-Yuan Wu,
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Benítez-Benítez C, Otero A, Ford KA, García-Moro P, Donadío S, Luceño M, Martín-Bravo S, Jiménez-Mejías P. An Evolutionary Study of Carex Subg. Psyllophorae (Cyperaceae) Sheds Light on a Strikingly Disjunct Distribution in the Southern Hemisphere, With Emphasis on Its Patagonian Diversification. FRONTIERS IN PLANT SCIENCE 2021; 12:735302. [PMID: 34819937 PMCID: PMC8606891 DOI: 10.3389/fpls.2021.735302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Carex subgenus Psyllophorae is an engaging study group due to its early diversification compared to most Carex lineages, and its remarkable disjunct distribution in four continents corresponding to three independent sections: sect. Psyllophorae in Western Palearctic, sect. Schoenoxiphium in Afrotropical region, and sect. Junciformes in South America (SA) and SW Pacific. The latter section is mainly distributed in Patagonia and the Andes, where it is one of the few Carex groups with a significant in situ diversification. We assess the role of historical geo-climatic events in the evolutionary history of the group, particularly intercontinental colonization events and diversification processes, with an emphasis on SA. We performed an integrative study using phylogenetic (four DNA regions), divergence times, diversification rates, biogeographic reconstruction, and bioclimatic niche evolution analyses. The crown age of subg. Psyllophorae (early Miocene) supports this lineage as one of the oldest within Carex. The diversification rate probably decreased over time in the whole subgenus. Geography seems to have played a primary role in the diversification of subg. Psyllophorae. Inferred divergence times imply a diversification scenario away from primary Gondwanan vicariance hypotheses and suggest long-distance dispersal-mediated allopatric diversification. Section Junciformes remained in Northern Patagonia since its divergence until Plio-Pleistocene glaciations. Andean orogeny appears to have acted as a northward corridor, which contrasts with the general pattern of North-to-South migration for temperate-adapted organisms. A striking niche conservatism characterizes the evolution of this section. Colonization of the SW Pacific took place on a single long-distance dispersal event from SA. The little ecological changes involved in the trans-Pacific disjunction imply the preadaptation of the group prior to the colonization of the SW Pacific. The high species number of the section results from simple accumulation of morphological changes (disparification), rather than shifts in ecological niche related to increased diversification rates (radiation).
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Affiliation(s)
- Carmen Benítez-Benítez
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Ana Otero
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL, United States
| | - Kerry A. Ford
- Allan Herbarium, Manaaki-Whenua Landcare Research, Lincoln, New Zealand
| | - Pablo García-Moro
- Department of Biology (Botany), Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Sabina Donadío
- Instituto de Botánica Darwinion (ANCEFN-CONICET), San Isidro, Argentina
| | - Modesto Luceño
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Santiago Martín-Bravo
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Pedro Jiménez-Mejías
- Department of Biology (Botany), Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
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Cai XL, Landis JB, Wang HX, Wang JH, Zhu ZX, Wang HF. Plastome structure and phylogenetic relationships of Styracaceae (Ericales). BMC Ecol Evol 2021; 21:103. [PMID: 34049486 PMCID: PMC8161964 DOI: 10.1186/s12862-021-01827-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 05/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Styracaceae are a woody, dicotyledonous family containing 12 genera and an estimated 160 species. Recent studies have shown that Styrax and Sinojackia are monophyletic, Alniphyllum and Bruinsmia cluster into a clade with an approximately 20-kb inversion in the Large Single-Copy (LSC) region. Halesia and Pterostyrax are not supported as monophyletic, while Melliodendron and Changiostyrax always form sister clades. Perkinsiodendron and Changiostyrax are newly established genera of Styracaceae. However, the phylogenetic relationship of Styracaceae at the generic level needs further research. RESULTS We collected 28 complete plastomes of Styracaceae, including 12 sequences newly reported here and 16 publicly available sequences, comprising 11 of the 12 genera of Styracaceae. All species possessed the typical quadripartite structure of angiosperm plastomes, with sequence differences being minor, except for a large 20-kb (14 genes) inversion found in Alniphyllum and Bruinsmia. Seven coding sequences (rps4, rpl23, accD, rpoC1, psaA, rpoA and ndhH) were identified to possess positively selected sites. Phylogenetic reconstructions based on seven data sets (i.e., LSC, SSC, IR, Coding, Non-coding, combination of LSC + SSC and concatenation of LSC + SSC + one IR) produced similar topologies. In our analyses, all genera were strongly supported as monophyletic. Styrax was sister to the remaining genera. Alniphyllum and Bruinsmia form a clade. Halesia diptera does not cluster with Perkinsiodendron, while Perkinsiodendron and Rehderodendron form a clade. Changiostyrax is sister to a clade of Pterostyrax and Sinojackia. CONCLUSION Overall, our results demonstrate the power of plastid phylogenomics in improving estimates of phylogenetic relationships among genera. This study also provides insight into plastome evolution across Styracaceae.
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Affiliation(s)
- Xiu-Lian Cai
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14850, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Hong-Xin Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Jian-Hua Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Zhi-Xin Zhu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Hua-Feng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China.
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Valdez L, D’Elía G. Genetic Diversity and Demographic History of the Shaggy Soft-Haired Mouse Abrothrix hirta (Cricetidae; Abrotrichini). Front Genet 2021; 12:642504. [PMID: 33841502 PMCID: PMC8024643 DOI: 10.3389/fgene.2021.642504] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/28/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic information on species can inform decision making regarding conservation of biodiversity since the response of organisms to changing environments depend, in part, on their genetic makeup. Territories of central-southern Chile and Argentina have undergone a varying degree of impact during the Quaternary, where the response of local fauna and flora was rather species-specific. Here, we focus on the sigmodontine rodent Abrothrix hirta, distributed from 35° S in Chile and Argentina to northern Tierra del Fuego. Based on 119,226 transcriptome-derived SNP loci from 46 individuals of A. hirta, we described the geographic distribution of the genetic diversity of this species using a maximum likelihood tree, principal component and admixture analyses. We also addressed the demographic history of the main intraspecific lineages of A. hirta using GADMA. We found that A. hirta exhibited four allopatric intraspecific lineages. Three main genetic groups were identified by a Principal Component Analysis and by Ancestry analysis. The demographic history of A. hirta was characterized by recent population stability for populations at the northernmost part of the range, while southern populations experienced a recent population expansion.
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Affiliation(s)
- Lourdes Valdez
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Colección de Mamíferos, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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Biogeography, phylogenetic relationships and morphological analyses of the South American genus Mutisia L.f. (Asteraceae) shows early connections of two disjunct biodiversity hotspots. ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00454-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Connection, isolation and reconnection: Quaternary climatic oscillations and the Andes shaped the phylogeographical patterns of the Patagonian bee Centris cineraria (Apidae). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe joint effect of the Andes as a geographical barrier and the Quaternary glaciations as promoters of genetic divergence remains virtually unexplored in southern South America. To help fill this knowledge gap, in this study we investigated the demographic history of Centris cineraria, a solitary bee mainly distributed in Patagonia. We used mitochondrial and nuclear markers and performed phylogeographical and dating analyses, adjusted spatio-temporal diffusion and species distribution models, and used Approximate Bayesian Computation to identify likely historical demographic scenarios. Our results revealed that during glacial periods the Andes represented a barrier due to the extent of the ice-sheets and the occurrence of unsuitable habitats, while interglacials allowed for gene flow across the Andes. Secondary contact between previously isolated lineages was evident across at least two low-altitude Andean areas, the northern one being a putative glacial refugium. Our findings also suggest that C. cineraria has persisted in situ in four periglacial refugia located along a north–south transect, congruent with the maximum extent of the ice sheet during the Greatest Patagonian Glaciation. As the first phylogeographical study of Patagonian insects, our work reveals that the interaction between Quaternary climatic oscillations and the Andes as a barrier was the main driver of the spatial and demographic history of C. cineraria.
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Diversification and Evolutionary Histories of Patagonian Steppe Lizards. NATURAL AND SOCIAL SCIENCES OF PATAGONIA 2020. [DOI: 10.1007/978-3-030-42752-8_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Plastid phylogenomic insights into the evolution of the Caprifoliaceae s.l. (Dipsacales). Mol Phylogenet Evol 2019; 142:106641. [PMID: 31605813 DOI: 10.1016/j.ympev.2019.106641] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/02/2019] [Accepted: 10/06/2019] [Indexed: 12/20/2022]
Abstract
The family Caprifoliaceae s.l. is an asterid angiosperm clade of ca. 960 species, most of which are distributed in temperate regions of the northern hemisphere. Recent studies show that the family comprises seven major clades: Linnaeoideae, Zabelia, Morinoideae, Dipsacoideae, Valerianoideae, Caprifolioideae, and Diervilloideae. However, its phylogeny at the subfamily or genus level remains controversial, and the backbone relationships among subfamilies are incompletely resolved. In this study, we utilized complete plastome sequencing to resolve the relationships among the subfamilies of the Caprifoliaceae s.l. and clarify several long-standing controversies. We generated and analyzed plastomes of 48 accessions of Caprifoliaceae s.l., representing 44 species, six subfamilies and one genus. Combined with available Caprifoliaceae s.l. plastomes on GenBank and 12 outgroups, we analyzed a final dataset of 68 accessions. Genome structure was strongly conserved in general, although the boundaries between the Inverted Repeat were found to have contracted across Caprifoliaceae s.l. to exclude rpl2, rps19, and ycf1, all or parts of which are typically present in the IR of most angiosperms. The ndhF gene was found to have been inverted in all plastomes of Adoxaceae. Phylogenomic analyses of 68 complete plastomes yielded a highly supported topology that strongly supported the monophyly of Zabelia and its sister relationship to Morinoideae. Moreover, a clade of Valerianoideae + Dipsacoideae was recovered as sister to a clade of Linnaeoideae + Zabelia + Morinoideae clade, and Heptacodium was sister to remaining Caprifolioideae. The Diervilloideae and Caprifolioideae were successively sister to all other Caprifoliaceae s.l. Major lineages of Caprifoliaceae s.l. were estimated to have diverged from the Upper Cretaceous to the Eocene (50-100 Ma), whereas within-genus diversification was dated to the Oligocene and later, concomitant with global cooling and drying. Our results demonstrate the power of plastid phylogenomics in improving estimates of phylogeny among genera and subfamilies, and provide new insights into plastome evolution across Caprifoliaceae s.l.
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