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Jost M, Wanke S. A comparative analysis of plastome evolution in autotrophic Piperales. Am J Bot 2024; 111:e16300. [PMID: 38469876 DOI: 10.1002/ajb2.16300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/13/2024]
Abstract
PREMISE Many plastomes of autotrophic Piperales have been reported to date, describing a variety of differences. Most studies focused only on a few species or a single genus, and extensive, comparative analyses have not been done. Here, we reviewed publicly available plastome reconstructions for autotrophic Piperales, reanalyzed publicly available raw data, and provided new sequence data for all previously missing genera. Comparative plastome genomics of >100 autotrophic Piperales were performed. METHODS We performed de novo assemblies to reconstruct the plastomes of newly generated sequence data. We used Sanger sequencing and read mapping to verify the assemblies and to bridge assembly gaps. Furthermore, we reconstructed the phylogenetic relationships as a foundation for comparative plastome genomics. RESULTS We identified a plethora of assembly and annotation issues in published plastome data, which, if unattended, will lead to an artificial increase of diversity. We were able to detect patterns of missing and incorrect feature annotation and determined that the inverted repeat (IR) boundaries were the major source for erroneous assembly. Accounting for the aforementioned issues, we discovered relatively stable junctions of the IRs and the small single-copy region (SSC), whereas the majority of plastome variations among Piperales stems from fluctuations of the boundaries of the IR and the large single-copy (LSC) region. CONCLUSIONS This study of all available plastomes of autotrophic Piperales, expanded by new data for previously missing genera, highlights the IR-LSC junctions as a potential marker for discrimination of various taxonomic levels. Our data indicates a pseudogene-like status for cemA and ycf15 in various Piperales. Based on a review of published data, we conclude that incorrect IR-SSC boundary identification is the major source for erroneous plastome assembly. We propose a gold standard for assembly and annotation of high-quality plastomes based on de novo assembly methods and appropriate references for gene annotation.
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Affiliation(s)
- Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- Departamento de Botánica, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- Departamento de Botánica, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Botanik und Molekulare Evolutionsforschung, Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt am Main, Germany
- Institut für Ökologie, Evolution und Biodiversität, Goethe-Universität, Frankfurt am Main, Germany
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Wanke S, Wicke S. Editorial: Phylogenomic discordance in plant systematics. Front Plant Sci 2023; 14:1308126. [PMID: 38023848 PMCID: PMC10646189 DOI: 10.3389/fpls.2023.1308126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023]
Affiliation(s)
- Stefan Wanke
- Institute for Botany, Technische Universität Dresden, Dresden, Germany
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Susann Wicke
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
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Zhou S, Wei N, Jost M, Wanke S, Rees M, Liu Y, Zhou R. The Mitochondrial Genome of the Holoparasitic Plant Thonningia sanguinea Provides Insights into the Evolution of the Multichromosomal Structure. Genome Biol Evol 2023; 15:evad155. [PMID: 37603455 PMCID: PMC10476698 DOI: 10.1093/gbe/evad155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/23/2023] Open
Abstract
Multichromosomal mitochondrial genome (mitogenome) structures have repeatedly evolved in many lineages of angiosperms. However, the underlying mechanism remains unclear. The mitogenomes of three genera of Balanophoraceae, namely Lophophytum, Ombrophytum, and Rhopalocnemis, have already been sequenced and assembled, all showing a highly multichromosomal structure, albeit with different genome and chromosome sizes. It is expected that characterization of additional lineages of this family may expand the knowledge of mitogenome diversity and provide insights into the evolution of the plant mitogenome structure and size. Here, we assembled and characterized the mitogenome of Thonningia sanguinea, which, together with Balanophora, forms a clade sister to the clade comprising Lophophytum, Ombrophytum, and Rhopalocnemis. The mitogenome of T. sanguinea possesses a multichromosomal structure of 18 circular chromosomes of 8.7-19.2 kb, with a total size of 246,247 bp. There are very limited shared regions and poor chromosomal correspondence between T. sanguinea and other Balanophoraceae species, suggesting frequent rearrangements and rapid sequence turnover. Numerous medium- and small-sized repeats were identified in the T. sanguinea mitogenome; however, no repeat-mediated recombination was detected, which was verified by Illumina reads mapping and PCR experiments. Intraspecific mitogenome variations in T. sanguinea are mostly insertions and deletions, some of which can lead to degradation of perfect repeats in one or two accessions. Based on the mitogenome features of T. sanguinea, we propose a mechanism to explain the evolution of a multichromosomal mitogenome from a master circle, which involves mutation in organellar DNA replication, recombination and repair genes, decrease of recombination, and repeat degradation.
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Affiliation(s)
- Shuaixi Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Neng Wei
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Mathew Rees
- School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom
- Royal Botanic Garden, Edinburgh, United Kingdom
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, Guangdong, China
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Mkala EM, Jost M, Dong X, Mwachala G, Musili PM, Wanke S, Hu GW, Wang QF. Phylogenetic and comparative analyses of Hydnora abyssinica plastomes provide evidence for hidden diversity within Hydnoraceae. BMC Ecol Evol 2023; 23:34. [PMID: 37464315 PMCID: PMC10353213 DOI: 10.1186/s12862-023-02142-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND To date, plastid genomes have been published for all but two holoparasitic angiosperm families. However, only a single or a few plastomes represent most of these families. Of the approximately 40 genera of holoparasitic angiosperms, a complete plastid genome sequence is available for only about half. In addition, less than 15 species are currently represented with more than one published plastid genome, most of which belong to the Orobanchaceae. Therefore, a significant portion of the holoparasitic plant plastome diversity remains unexplored. This limited information could hinder potential evolutionary pattern recognition as well as the exploration of inter- and intra-species plastid genome diversity in the most extreme holoparasitic angiosperms. RESULTS Here, we report the first plastomes of Kenyan Hydnora abyssinica accessions. The plastomes have a typical quadripartite structure and encode 24 unique genes. Phylogenetic tree reconstruction recovers the Kenyan accessions as monophyletic and together in a clade with the Namibian H. abyssinica accession and the recently published H. arabica from Oman. Hydnora abyssinica as a whole however is recovered as non-monophyletic, with H. arabica nested within. This result is supported by distinct structural plastome synapomorphies as well as pairwise distance estimates that reveal hidden diversity within the Hydnora species in Africa. CONCLUSION We propose to increase efforts to sample widespread holoparasitic species for their plastid genomes, as is the case with H. abyssinica, which is widely distributed in Africa. Morphological reinvestigation and further molecular data are needed to fully investigate the diversity of H. abyssinica along the entire range of distribution, as well as the diversity of currently synonymized taxa.
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Affiliation(s)
- Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China
- University of Chinese Academy of Sciences, Beijing, CN-100049, China
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, 01062, Dresden, Germany
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China
- University of Chinese Academy of Sciences, Beijing, CN-100049, China
| | - Geoffrey Mwachala
- East African Herbarium, National Museums of Kenya, P. O. Box 451660-0100, Nairobi, Kenya
| | - Paul Mutuku Musili
- East African Herbarium, National Museums of Kenya, P. O. Box 451660-0100, Nairobi, Kenya
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, 01062, Dresden, Germany
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China.
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China
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Vera-Paz SI, Granados Mendoza C, Díaz Contreras Díaz DD, Jost M, Salazar GA, Rossado AJ, Montes-Azcué CA, Hernández-Gutiérrez R, Magallón S, Sánchez-González LA, Gouda EJ, Cabrera LI, Ramírez-Morillo IM, Flores-Cruz M, Granados-Aguilar X, Martínez-García AL, Hornung-Leoni CT, Barfuss MH, Wanke S. Plastome phylogenomics reveals an early Pliocene North- and Central America colonization by long-distance dispersal from South America of a highly diverse bromeliad lineage. Front Plant Sci 2023; 14:1205511. [PMID: 37426962 PMCID: PMC10326849 DOI: 10.3389/fpls.2023.1205511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023]
Abstract
Understanding the spatial and temporal frameworks of species diversification is fundamental in evolutionary biology. Assessing the geographic origin and dispersal history of highly diverse lineages of rapid diversification can be hindered by the lack of appropriately sampled, resolved, and strongly supported phylogenetic contexts. The use of currently available cost-efficient sequencing strategies allows for the generation of a substantial amount of sequence data for dense taxonomic samplings, which together with well-curated geographic information and biogeographic models allow us to formally test the mode and tempo of dispersal events occurring in quick succession. Here, we assess the spatial and temporal frameworks for the origin and dispersal history of the expanded clade K, a highly diverse Tillandsia subgenus Tillandsia (Bromeliaceae, Poales) lineage hypothesized to have undergone a rapid radiation across the Neotropics. We assembled full plastomes from Hyb-Seq data for a dense taxon sampling of the expanded clade K plus a careful selection of outgroup species and used them to estimate a time- calibrated phylogenetic framework. This dated phylogenetic hypothesis was then used to perform biogeographic model tests and ancestral area reconstructions based on a comprehensive compilation of geographic information. The expanded clade K colonized North and Central America, specifically the Mexican transition zone and the Mesoamerican dominion, by long-distance dispersal from South America at least 4.86 Mya, when most of the Mexican highlands were already formed. Several dispersal events occurred subsequently northward to the southern Nearctic region, eastward to the Caribbean, and southward to the Pacific dominion during the last 2.8 Mya, a period characterized by pronounced climate fluctuations, derived from glacial-interglacial climate oscillations, and substantial volcanic activity, mainly in the Trans-Mexican Volcanic Belt. Our taxon sampling design allowed us to calibrate for the first time several nodes, not only within the expanded clade K focal group but also in other Tillandsioideae lineages. We expect that this dated phylogenetic framework will facilitate future macroevolutionary studies and provide reference age estimates to perform secondary calibrations for other Tillandsioideae lineages.
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Affiliation(s)
- Sandra I. Vera-Paz
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Daniel D. Díaz Contreras Díaz
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Gerardo A. Salazar
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Andrés J. Rossado
- Laboratorio de Sistemática de Plantas Vasculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Claudia A. Montes-Azcué
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rebeca Hernández-Gutiérrez
- Departament of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis A. Sánchez-González
- Museo de Zoología “Alfonso L. Herrera”, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eric J. Gouda
- Botanical Garden, Utrecht University, Utrecht, Netherlands
| | - Lidia I. Cabrera
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - María Flores-Cruz
- Departamento El Hombre y su Ambiente, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Unidad Xochimilco, Mexico City, Mexico
| | - Xochitl Granados-Aguilar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana L. Martínez-García
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Investigaciones Biológicas, Herbario HGOM, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Hidalgo, Mexico
| | - Claudia T. Hornung-Leoni
- Centro de Investigaciones Biológicas, Herbario HGOM, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Hidalgo, Mexico
| | - Michael H.J. Barfuss
- Departament of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Stefan Wanke
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
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Kim W, Lautenschläger T, Bolin JF, Rees M, Nzuzi A, Zhou R, Wanke S, Jost M. Extreme plastomes in holoparasitic Balanophoraceae are not the norm. BMC Genomics 2023; 24:330. [PMID: 37322447 DOI: 10.1186/s12864-023-09422-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Balanophoraceae plastomes are known for their highly condensed and re-arranged nature alongside the most extreme nucleotide compositional bias known to date, culminating in two independent reconfigurations of their genetic code. Currently, a large portion of the Balanophoraceae diversity remains unexplored, hindering, among others, evolutionary pattern recognition. Here, we explored newly sequenced plastomes of Sarcophyte sanguinea and Thonningia sanguinea. The reconstructed plastomes were analyzed using various methods of comparative genomics based on a representative taxon sampling. RESULTS Sarcophyte, recovered sister to the other sampled Balanophoraceae s. str., has plastomes up to 50% larger than those currently published. Its gene set contains five genes lost in any other species, including matK. Five cis-spliced introns are maintained. In contrast, the Thonningia plastome is similarly reduced to published Balanophoraceae and retains only a single cis-spliced intron. Its protein-coding genes show a more biased codon usage compared to Sarcophyte, with an accumulation of in-frame TAG stop codons. Structural plastome comparison revealed multiple, previously unknown, structural rearrangements within Balanophoraceae. CONCLUSIONS For the "minimal plastomes" of Thonningia, we propose a genetic code change identical to sister genus Balanophora. Sarcophyte however differs drastically from our current understanding on Balanophoraceae plastomes. With a less-extreme nucleotide composition, there is no evidence for an altered genetic code. Using comparative genomics, we identified a hotspot for plastome reconfiguration in Balanophoraceae. Based on previously published and newly identified structural reconfigurations, we propose an updated model of evolutionary plastome trajectories for Balanophoraceae, illustrating a much greater plastome diversity than previously known.
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Affiliation(s)
- Woorin Kim
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Thea Lautenschläger
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- Botanischer Garten Hamburg, Universität Hamburg, Hamburg, Germany
| | - Jay F Bolin
- Department of Biology, Catawba College, Salisbury, USA
| | - Mathew Rees
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden, Edinburgh, UK
| | - Albertina Nzuzi
- Instituto Nacional da Biodiversidade e Conservação, Luanda, Angola
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, China
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany.
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Benítez-Villaseñor A, Granados Mendoza C, Wanke S, Peñafiel Cevallos M, Freire ME, Lemmon EM, Lemmon AR, Magallón S. The use of Anchored Hybrid Enrichment data to resolve higher-level phylogenetic relationships: A proof-of-concept applied to Asterales (Eudicotyledoneae; Angiosperms). Mol Phylogenet Evol 2023; 181:107714. [PMID: 36708940 DOI: 10.1016/j.ympev.2023.107714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/28/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023]
Abstract
Anchored Hybrid Enrichment (AHE) is a tool for capturing orthologous regions of the nuclear genome shared in low or single copy across lineages. Despite the increasing number of studies using this method, its usefulness to estimate relationships at deeper taxonomic levels in plants has not been fully explored. Here we present a proof of concept about the performance of nuclear loci obtained with AHE to infer phylogenetic relationships and explore the use of gene sampling schemes to estimate divergence times in Asterales. We recovered low-copy nuclear loci using the AHE method from herbarium material and silica-preserved samples. Maximum likelihood, Bayesian inference, and coalescence approaches were used to reconstruct phylogenomic relationships. Dating analyses were conducted under a multispecies coalescent approach by jointly inferring species tree and divergence times with random gene sampling schemes and multiple calibrations. We recovered 403 low-copy nuclear loci for 63 species representing nine out of eleven families of Asterales. Phylogenetic hypotheses were congruent among the applied methods and previously published results. Analyses with concatenated datasets were strongly supported, but coalescence-based analyses showed low support for the phylogenetic position of families Argophyllaceae and Alseuosmiaceae. Estimated family ages were congruent among gene sampling schemes, with the mean age for Asterales around 130 Myr. Our study documents the usefulness of AHE for resolving phylogenetic relationships at deep phylogenetic levels in Asterales. Observed phylogenetic inconsistencies were possibly due to the non-inclusion of families Phellinceae and Pentaphragmataceae. Random gene sampling schemes produced consistent age estimates with coalescence and species tree relaxed clock approaches.
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Affiliation(s)
- Adriana Benítez-Villaseñor
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, A. P. 70-153, C.P.04510 Ciudad de México, Mexico.
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Stefan Wanke
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Marcia Peñafiel Cevallos
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - M Efraín Freire
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - Emily Moriarty Lemmon
- Department of Biology, Florida State University 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL 32306-4295, United States.
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306-4120, United States.
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico.
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Yu R, Chen X, Long L, Jost M, Zhao R, Liu L, Mower JP, dePamphilis CW, Wanke S, Jiao Y. De novo Assembly and Comparative Analyses of Mitochondrial Genomes in Piperales. Genome Biol Evol 2023; 15:7075204. [PMID: 36896589 PMCID: PMC10036691 DOI: 10.1093/gbe/evad041] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/20/2023] [Accepted: 02/19/2023] [Indexed: 03/11/2023] Open
Abstract
The mitochondrial genome of Liriodendron tulipifera exhibits many ancestral angiosperm features and a remarkably slow evolutionary rate, while mitochondrial genomes of other magnoliids remain yet to be characterized. We assembled nine new mitochondrial genomes, representing all genera of perianth-bearing Piperales, as well as for a member of the sister clade: three complete or nearly complete mitochondrial genomes from Aristolochiaceae and six additional draft assemblies including Thottea, Asaraceae, Lactoridaceae, and Hydnoraceae. For comparative purpose, a complete mitochondrial genome was assembled for Saururus, a member of the perianth-less Piperales. The average number of short repeats (50-99 bp) was much larger in genus Aristolochia than in other angiosperm mitochondrial genomes, and approximately 30% of repeats (<350 bp) were found to have the capacity to mediate recombination. We found mitochondrial genomes in perianth-bearing Piperales comprising conserved repertories of protein-coding genes and rRNAs but variable copy numbers of tRNA genes. We identified several shifts from cis- to trans-splicing of the Group II introns of nad1i728, cox2i373, and nad7i209. Two short regions of the cox1 and atp8 genes were likely derived from independent horizontal gene transfer events in perianth-bearing Piperales. We found biased enrichment of specific substitution types in different lineages of magnoliids and the Aristolochiaceae family showed the highest ratio of A:T > T:A substitutions of all other investigated angiosperm groups. Our study reports the first mitochondrial genomes for Piperales and uses this new information for a better understanding of the evolutionary patterns of magnoliids and angiosperms in general.
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Affiliation(s)
- Runxian Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xudong Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Lingjie Long
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Matthias Jost
- Institute of Botany, Dresden University of Technology, Dresden, Germany
| | - Ran Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Lumei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jeffrey P Mower
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska
| | - Claude W dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Stefan Wanke
- Institute of Botany, Dresden University of Technology, Dresden, Germany
- Departamento de Botanica, Instituto de Biología, Universidad Nacional Autonoma de Mexico, Coyoacan, Distrito Federal, Mexico
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
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Makuch WA, Wanke S, Ditsch B, Richter F, Herklotz V, Ahlborn J, Ritz CM. Population genetics and plant growth experiments as prerequisite for conservation measures of the rare European aquatic plant Luronium natans (Alismataceae). Front Plant Sci 2023; 13:1069842. [PMID: 36714738 PMCID: PMC9880460 DOI: 10.3389/fpls.2022.1069842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
Information provided by population genetic studies is often necessary to effectively protect endangered species. In general, such data is scarce for aquatic plants and this holds also for Luronium natans, an aquatic macrophyte endemic to northwestern and western Europe. It is threatened across its whole distribution range due to human influences, in particular due to eutrophication and intensive fish farming. In spite of habitat protection populations continue to decline and re-introductions are one possibility to prevent the species' extinction. Therefore, insights in genetic diversity and relatedness of source populations is warranted. Thus, we performed Amplified Fragment-Length Polymorphism (AFLP) on two large populations in Saxony, Germany (Großenhainer Pflege and Niederspree), complemented with numerous additional occurrences from Europe. In addition, we conducted experiments on plant growth to assess optimal conditions for ex-situ cultivation taking water temperature, water level and substrate into account. We revealed considerably high levels of genetic diversity within populations (Shannon Indices ranged from 0.367 to 0.416) implying that populations are not restricted to clonal growth only but reproduce also by open-pollinated flowers. Remarkably, the two geographically close Saxon populations were genetically distant to each other but subpopulations within a locality were completely intermingled. Concerning optimal cultivation conditions, longest roots were obtained at temperatures >14°C and saturated, but not submerging water levels. Thus, our findings advocate for a re-introduction scheme from nearby source populations and provide detailed information on successful ex-situ cultivation.
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Affiliation(s)
- Weronika A. Makuch
- Institute of Biology, Geobotany and Botanical Garden, Martin-Luther University Halle, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institut für Botanik, Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| | - Stefan Wanke
- Institut für Botanik, Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
- Departamento de Botanica, Instituto de Biología, Universidad Nacional Autonoma de Mexico, Distrito Federal, Mexico
| | - Barbara Ditsch
- Botanischer Garten der Technischen Universität Dresden, Dresden, Germany
| | - Frank Richter
- Sächsisches Landesamt für Umwelt, Landwirtschaft und Geologie, Dresden, Germany
| | - Veit Herklotz
- Senckenberg Museum for Natural History Görlitz, Senckenberg – Member of the Leibniz Association, Görlitz, Germany
| | - Julian Ahlborn
- Senckenberg Museum for Natural History Görlitz, Senckenberg – Member of the Leibniz Association, Görlitz, Germany
| | - Christiane M. Ritz
- Senckenberg Museum for Natural History Görlitz, Senckenberg – Member of the Leibniz Association, Görlitz, Germany
- Professur für Biodiversität der Pflanzen, Internationales Hochschulinstitut (IHI) Zittau, Technische Universität Dresden, Zittau, Germany
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10
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Kusuma YWC, Matsuo A, Suyama Y, Wanke S, Isagi Y. Conservation genetics of three Rafflesia species in Java Island, Indonesia using SNP markers obtained from MIG-seq. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01470-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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Vera-Paz SI, Díaz Contreras Díaz DD, Jost M, Wanke S, Rossado AJ, Hernández-Gutiérrez R, Salazar GA, Magallón S, Gouda EJ, Ramírez-Morillo IM, Donadío S, Granados Mendoza C. New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy. Front Plant Sci 2022; 13:924922. [PMID: 35982706 PMCID: PMC9378858 DOI: 10.3389/fpls.2022.924922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Full plastome sequences for land plants have become readily accessible thanks to the development of Next Generation Sequencing (NGS) techniques and powerful bioinformatic tools. Despite this vast amount of genomic data, some lineages remain understudied. Full plastome sequences from the highly diverse (>1,500 spp.) subfamily Tillandsioideae (Bromeliaceae, Poales) have been published for only three (i.e., Guzmania, Tillandsia, and Vriesea) out of 22 currently recognized genera. Here, we focus on core Tillandsioideae, a clade within subfamily Tillandsioideae, and explore the contribution of individual plastid markers and data categories to inform deep divergences of a plastome phylogeny. We generated 37 high quality plastome assemblies and performed a comparative analysis in terms of plastome structure, size, gene content and order, GC content, as well as number and type of repeat motifs. Using the obtained phylogenetic context, we reconstructed the evolution of these plastome attributes and assessed if significant shifts on the evolutionary traits' rates have occurred in the evolution of the core Tillandsioideae. Our results agree with previously published phylogenetic hypotheses based on plastid data, providing stronger statistical support for some recalcitrant nodes. However, phylogenetic discordance with previously published nuclear marker-based hypotheses was found. Several plastid markers that have been consistently used to address phylogenetic relationships within Tillandsioideae were highly informative for the retrieved plastome phylogeny and further loci are here identified as promising additional markers for future studies. New lineage-specific plastome rearrangements were found to support recently adopted taxonomic groups, including large inversions, as well as expansions and contractions of the inverted repeats. Evolutionary trait rate shifts associated with changes in size and GC content of the plastome regions were found across the phylogeny of core Tillandsioideae.
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Affiliation(s)
- Sandra I. Vera-Paz
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Daniel D. Díaz Contreras Díaz
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Stefan Wanke
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Andrés J. Rossado
- Laboratorio de Sistemática de Plantas Vasculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Rebeca Hernández-Gutiérrez
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA, United States
| | - Gerardo A. Salazar
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eric J. Gouda
- Botanical Garden, Utrecht University, Utrecht, Netherlands
| | | | - Sabina Donadío
- Instituto de Botánica Darwinion (CONICET-ANCEFN), Buenos Aires, Argentina
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
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12
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Mkala EM, Jost M, Wanke S, Ngarega BK, Hughes A, Mutinda ES, Waswa EN, Mwanzia VM, Oulo MA, Wanga VO, Ngumbau VM, Mwachala G, Hu GW, Wang QF. How vulnerable are holoparasitic plants with obligate hosts to negative climate change impacts? ECOL INFORM 2022; 69:101636. [DOI: https:/doi.org/10.1016/j.ecoinf.2022.101636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
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13
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Mkala EM, Jost M, Wanke S, Ngarega BK, Hughes A, Mutinda ES, Waswa EN, Mwanzia VM, Oulo MA, Wanga VO, Ngumbau VM, Mwachala G, Hu GW, Wang QF. How vulnerable are holoparasitic plants with obligate hosts to negative climate change impacts? ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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14
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Jost M, Naumann J, Bolin JF, Martel C, Rocamundi N, Cocucci AA, Lupton D, Neinhuis C, Wanke S. Structural plastome evolution in holoparasitic Hydnoraceae with special focus on inverted and direct repeats. Genome Biol Evol 2022; 14:6602284. [PMID: 35660863 PMCID: PMC9168662 DOI: 10.1093/gbe/evac077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 11/14/2022] Open
Abstract
Plastome condensation during adaptation to a heterotrophic lifestyle is generally well understood and lineage-independent models have been derived. However, understanding the evolutionary trajectories of comparatively old heterotrophic lineages, that are on the cusp of a minimal plastomes, is essential to complement and expand current knowledge. We study Hydnoraceae, one of the oldest and least investigated parasitic angiosperm lineages. Plastome comparative genomics, using seven out of eight known species of the genus Hydnora and three species of Prosopanche, reveal a high degree of structural similarity and shared gene content; contrasted by striking dissimilarities with respect to repeat content (inverted and direct repeats). We identified varying IR content and positions, likely resulting from multiple, independent evolutionary events and a direct repeat gain in Prosopanche. Considering different evolutionary trajectories and based on a fully resolved and supported species-level phylogenetic hypothesis, we describe three possible, distinct models to explain the Hydnoraceae plastome states. For comparative purposes we also report the first plastid genomes for the closely related autotrophic genera Lactoris (Lactoridaceae) and Thottea (Aristolochiaceae).
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Affiliation(s)
- Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Germany
| | - Julia Naumann
- Institut für Botanik, Technische Universität Dresden, Germany
| | | | - Carlos Martel
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.,Instituto de Ciencias Ómicas y Biotecnología Aplicada, Pontificia Universidad Católica del Perú, Peru
| | - Nicolás Rocamundi
- Laboratorio de Ecología Evolutiva y Biología Floral, IMBIV, CONICET and Universidad Nacional de Córdoba, Argentina
| | - Andrea A Cocucci
- Laboratorio de Ecología Evolutiva y Biología Floral, IMBIV, CONICET and Universidad Nacional de Córdoba, Argentina
| | - Darach Lupton
- Oman Botanic Garden, Sultanate of Oman.,National Botanic Gardens, Glasnevin, Ireland
| | | | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Germany.,Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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15
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Krause C, Oelschlägel B, Mahfoud H, Frank D, Lecocq G, Shuka L, Neinhuis C, Vargas P, Tosunoglu A, Thiv M, Wanke S. The evolution of the
Aristolochia pallida
complex (Aristolochiaceae) challenges traditional taxonomy and reflects large‐scale glacial refugia in the Mediterranean. Ecol Evol 2022; 12:e8765. [PMID: 35386874 PMCID: PMC8969917 DOI: 10.1002/ece3.8765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/08/2022] [Accepted: 03/08/2022] [Indexed: 11/08/2022] Open
Abstract
The taxonomy of the Mediterranean Aristolochia pallida complex has been under debate since several decades with the following species currently recognized: A. pallida, A. lutea, A. nardiana, A. microstoma, A. merxmuelleri, A. croatica, and A. castellana. These taxa are distributed from Iberia to Turkey. To reconstruct phylogenetic and biogeographic patterns, we employed cpDNA sequence variation using both noncoding (intron and spacer) and protein‐coding regions (i.e., trnK intron, matK gene, and trnK‐psbA spacer). Our results show that the morphology‐based traditional taxonomy was not corroborated by our phylogenetic analyses. Aristolochia pallida, A. lutea, A. nardiana, and A. microstoma were not monophyletic. Instead, strong geographic signals were detected. Two major clades, one exclusively occurring in Greece and a second one of pan‐Mediterranean distribution, were found. Several subclades distributed in Greece, NW Turkey, Italy, as well as amphi‐Adriatic subclades, and a subgroup of southern France and Spain, were revealed. The distribution areas of these groups are in close vicinity to hypothesized glacial refugia areas in the Mediterranean. According to molecular clock analyses the diversification of this complex started around 3–3.3 my, before the onset of glaciation cycles, and the further evolution of and within major lineages falls into the Pleistocene. Based on these data, we conclude that the Aristolochia pallida alliance survived in different Mediterranean refugia rarely with low, but often with a high potential for range extension, and a high degree of morphological diversity.
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Affiliation(s)
- Cornelia Krause
- Botany Department State Museum of Natural History Stuttgart Stuttgart Germany
| | | | - Hafez Mahfoud
- Institut für Botanik Technische Universität Dresden Dresden Germany
| | - Dominik Frank
- Botany Department State Museum of Natural History Stuttgart Stuttgart Germany
| | | | - Lulëzim Shuka
- Department of Biology, Faculty of Natural Sciences Tirana University Tiranë Albania
| | | | | | - Aycan Tosunoglu
- Department of Biology Faculty of Arts and Science Bursa Uludag University Bursa Turkey
| | - Mike Thiv
- Botany Department State Museum of Natural History Stuttgart Stuttgart Germany
| | - Stefan Wanke
- Institut für Botanik Technische Universität Dresden Dresden Germany
- Departamento de Botánica, Instituto de Biología Universidad Nacional Autónoma de México Mexico City Mexico
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16
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Qin L, Hu Y, Wang J, Wang X, Zhao R, Shan H, Li K, Xu P, Wu H, Yan X, Liu L, Yi X, Wanke S, Bowers JE, Leebens-Mack JH, dePamphilis CW, Soltis PS, Soltis DE, Kong H, Jiao Y. Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome. Nat Plants 2021; 7:1239-1253. [PMID: 34475528 PMCID: PMC8445822 DOI: 10.1038/s41477-021-00990-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 07/22/2021] [Indexed: 05/04/2023]
Abstract
Aristolochia, a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata, a species that, similar to Amborella trichopoda, lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata. Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata.
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Affiliation(s)
- Liuyu Qin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiheng Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinpeng Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaoliang Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ran Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Kunpeng Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hanying Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Xueqing Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lumei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Yi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Stefan Wanke
- Institute of Botany, Dresden University of Technology, Dresden, Germany
| | - John E Bowers
- Department of Plant Biology, University of Georgia, Athens, GA, USA
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | | | - Claude W dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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17
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Granados Mendoza C, Martínez Salas EM, Goetghebeur P, Wanke S, Samain MS. Molecular Phylogeny, Character Evolution, and Biogeography of Hydrangea Section Cornidia, Hydrangeaceae. Front Plant Sci 2021; 12:661522. [PMID: 34267769 PMCID: PMC8276264 DOI: 10.3389/fpls.2021.661522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Background: Hydrangea section Cornidia consists of 26 currently accepted species and a yet undefined number of new species and erroneously synonymized taxa. This clade consists of (sub)tropical lianas occurring from northern Mexico to southern Chile and Argentina, and one species from Southeast Asia. Currently, no molecular phylogenetic hypothesis is available that includes more than a few species of this section. Hence, a resolved and well-sampled molecular phylogenetic hypothesis may help to enforce taxonomic decisions. In this study, we present a phylogenetic framework based on sequences from two low copy nuclear genes from a comprehensive taxon sampling of H. section Cornidia and a selection of outgroups. Our phylogenetic reconstructions prove the non-monophyly of the traditionally recognized subsections Monosegia and Polysegia and their corresponding series, Speciosae and Aphananthae, and Synstyleae and Chorystyleae, respectively. Three morphologically defined species were recovered with high support as monophyletic, namely, Hydrangea panamensis, Hydrangea serratifolia, and Hydrangea tarapotensis. However, statistical support for some shallow nodes did not allow to refute, with high support, the monophyly of several of the herein recognized species for which more than one individual could be analyzed. Based on the obtained phylogenetic framework, we reconstructed the evolution of selected reproductive characters. Hydrangea section Cornidia is the only genus section for which dioecism has been extensively documented. Our character reconstruction of sexual dimorphism shows that dioecism is the ancestral state in this section and that this was reversed to monoecy in Hydrangea seemannii and Hydrangea integrifolia. Character reconstruction for the enlarged marginal flowers recovered their presence as the ancestral character state in H. section Cornidia, although at least three internal lineages independently lost them; thus, losses were reconstructed to be more likely than gain. With respect to the flower color, more species exhibit white than red flowers, and white is reconstructed as the ancestral state. Cornidia also shows an unusual disjunct geographic distribution between Asia and Central Mesoamerica-South America, as it is not present in the USA and Canada. The origin of Cornidia is reconstructed to be the New World with higher probability, and the presence of one species in Asia is likely due to long-distance dispersal.
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Affiliation(s)
- Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Research Group Spermatophytes, Ghent University, Gent, Belgium
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Esteban Manuel Martínez Salas
- Herbario Nacional de México, Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Paul Goetghebeur
- Ghent University Museum, Botanical Garden, Ghent University, Gent, Belgium
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Marie-Stéphanie Samain
- Red de Diversidad Biológica del Occidente Mexicano, Centro Regional del Bajío, Instituto de Ecología, A.C., Pátzcuaro, Michoacán, Mexico
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, Gent, Belgium
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18
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Rupp T, Oelschlägel B, Rabitsch K, Mahfoud H, Wenke T, Disney RHL, Neinhuis C, Wanke S, Dötterl S. Flowers of Deceptive Aristolochia microstoma Are Pollinated by Phorid Flies and Emit Volatiles Known From Invertebrate Carrion. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.658441] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Deceptive flowers decoy pollinators by advertising a reward, which finally is not provided. Numerous deceptive plants are pollinated by Diptera, but the attractive cues and deceptive strategies are only identified in a few cases. A typical fly-deceptive plant genus is Aristolochia, which evolved sophisticated trap flowers to temporarily capture pollinators. Though rarely demonstrated by experimental approaches, Aristolochia species are believed to chemically mimic brood sites, food sources for adult flies, or utilize sexual deception. Indeed, for most species, studies on scent composition and attractive signals are lacking. In this study, we focused on Aristolochia microstoma, a peculiar Greek endemic with flowers that are presented at ground level in the leaf litter or between rocks and are characterized by a unique morphology. We analyzed flower visitor and pollinator spectra and identified the floral scent composition using dynamic headspace and gas chromatography coupled to mass spectrometry (GC/MS). Female and male phorid flies (Phoridae) are the exclusive pollinators, although the flowers are also frequently visited by Sciaridae, as well as typical ground-dwelling arthropods, such as Collembola and arachnids. The carrion-like floral scent mainly consists of the oligosulphide dimethyldisulfide and the nitrogen-bearing compound 2,5-dimethylpyrazine. These compounds together are known to be released from decomposing insects, and thus, we conclude that pollinators are likely deceived by chemical imitation of invertebrate carrion, a deceptive strategy not described from another plant species so far.
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19
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Jost M, Samain MS, Marques I, Graham SW, Wanke S. Discordant Phylogenomic Placement of Hydnoraceae and Lactoridaceae Within Piperales Using Data From All Three Genomes. Front Plant Sci 2021; 12:642598. [PMID: 33912209 PMCID: PMC8072514 DOI: 10.3389/fpls.2021.642598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/17/2021] [Indexed: 05/08/2023]
Abstract
Phylogenetic relationships within the magnoliid order Piperales have been studied extensively, yet the relationships of the monotypic family Lactoridaceae and the holoparasitic Hydnoraceae to the remainder of the order remain a matter of debate. Since the first confident molecular phylogenetic placement of Hydnoraceae among Piperales, different studies have recovered various contradictory topologies. Most phylogenetic hypotheses were inferred using only a few loci and have had incomplete taxon sampling at the genus level. Based on these results and an online survey of taxonomic opinion, the Angiosperm Phylogeny Group lumped both Hydnoraceae and Lactoridaceae in Aristolochiaceae; however, the latter family continues to have unclear relationships to the aforementioned taxa. Here we present extensive phylogenomic tree reconstructions based on up to 137 loci from all three subcellular genomes for all genera of Piperales. We infer relationships based on a variety of phylogenetic methods, explore instances of phylogenomic discordance between the subcellular genomes, and test alternative topologies. Consistent with these phylogenomic results and a consideration of the principles of phylogenetic classification, we propose to exclude Hydnoraceae and Lactoridaceae from the broad circumscription of Aristolochiaceae, and instead favor recognition of four monophyletic and morphologically well circumscribed families in the perianth-bearing Piperales: Aristolochiaceae, Asaraceae, Hydnoraceae, and Lactoridaceae, with a total of six families in the order.
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Affiliation(s)
- Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Marie-Stéphanie Samain
- Instituto de Ecología, A.C., Red de Diversidad Biológica del Occidente Mexicano, Pátzcuaro, Mexico
| | - Isabel Marques
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- Plant-Environment Interactions and Biodiversity Lab, Forest Research Centre, Instituto Superior de Agronomia, Universidadede Lisboa, Lisbon, Portugal
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
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Allio R, Nabholz B, Wanke S, Chomicki G, Pérez-Escobar OA, Cotton AM, Clamens AL, Kergoat GJ, Sperling FAH, Condamine FL. Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants. Nat Commun 2021; 12:354. [PMID: 33441560 PMCID: PMC7806994 DOI: 10.1038/s41467-020-20507-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/03/2020] [Indexed: 01/29/2023] Open
Abstract
The mega-diversity of herbivorous insects is attributed to their co-evolutionary associations with plants. Despite abundant studies on insect-plant interactions, we do not know whether host-plant shifts have impacted both genomic adaptation and species diversification over geological times. We show that the antagonistic insect-plant interaction between swallowtail butterflies and the highly toxic birthworts began 55 million years ago in Beringia, followed by several major ancient host-plant shifts. This evolutionary framework provides a valuable opportunity for repeated tests of genomic signatures of macroevolutionary changes and estimation of diversification rates across their phylogeny. We find that host-plant shifts in butterflies are associated with both genome-wide adaptive molecular evolution (more genes under positive selection) and repeated bursts of speciation rates, contributing to an increase in global diversification through time. Our study links ecological changes, genome-wide adaptations and macroevolutionary consequences, lending support to the importance of ecological interactions as evolutionary drivers over long time periods.
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Affiliation(s)
- Rémi Allio
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
| | - Benoit Nabholz
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany
| | - Guillaume Chomicki
- Department of Bioscience, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | | | - Adam M Cotton
- 86/2 Moo 5, Tambon Nong Kwai, Hang Dong, Chiang Mai, Thailand
| | - Anne-Laure Clamens
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Gaël J Kergoat
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, AB, Canada
| | - Fabien L Condamine
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, AB, Canada.
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Pabón-Mora N, Madrigal Y, Alzate JF, Ambrose BA, Ferrándiz C, Wanke S, Neinhuis C, González F. Evolution of Class II TCP genes in perianth bearing Piperales and their contribution to the bilateral calyx in Aristolochia. New Phytol 2020; 228:752-769. [PMID: 32491205 DOI: 10.1111/nph.16719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/20/2020] [Indexed: 05/21/2023]
Abstract
Controlled spatiotemporal cell division and expansion are responsible for floral bilateral symmetry. Genetic studies have pointed to class II TCP genes as major regulators of cell division and floral patterning in model core eudicots. Here we study their evolution in perianth-bearing Piperales and their expression in Aristolochia, a rare occurrence of bilateral perianth outside eudicots and monocots. The evolution of class II TCP genes reveals single-copy CYCLOIDEA-like genes and three paralogs of CINCINNATA (CIN) in early diverging angiosperms. All class II TCP genes have independently duplicated in Aristolochia subgenus Siphisia. Also CIN2 genes duplicated before the diversification of Saruma and Asarum. Sequence analysis shows that CIN1 and CIN3 share motifs with Cyclin proteins and CIN2 genes have lost the miRNA319a binding site. Expression analyses of all paralogs of class II TCP genes in Aristolochia fimbriata point to a role of CYC and CIN genes in maintaining differential perianth expansion during mid- and late flower developmental stages by promoting cell division in the distal and ventral portion of the limb. It is likely that class II TCP genes also contribute to cell division in the leaf, the gynoecium and the ovules in A. fimbriata.
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Affiliation(s)
- Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, Medellín, 050010, Colombia
- Technische Universität Dresden, Institut für Botanik, Dresden, 01062, Germany
| | - Yesenia Madrigal
- Instituto de Biología, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Juan F Alzate
- Facultad de Medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| | | | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Valencia, 46022, Spain
| | - Stefan Wanke
- Technische Universität Dresden, Institut für Botanik, Dresden, 01062, Germany
| | - Christoph Neinhuis
- Technische Universität Dresden, Institut für Botanik, Dresden, 01062, Germany
| | - Favio González
- Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
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Granados Mendoza C, Jost M, Hágsater E, Magallón S, van den Berg C, Lemmon EM, Lemmon AR, Salazar GA, Wanke S. Target Nuclear and Off-Target Plastid Hybrid Enrichment Data Inform a Range of Evolutionary Depths in the Orchid Genus Epidendrum. Front Plant Sci 2020; 10:1761. [PMID: 32063915 PMCID: PMC7000662 DOI: 10.3389/fpls.2019.01761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/16/2019] [Indexed: 05/12/2023]
Abstract
Universal angiosperm enrichment probe sets designed to enrich hundreds of putatively orthologous nuclear single-copy loci are increasingly being applied to infer phylogenetic relationships of different lineages of angiosperms at a range of evolutionary depths. Studies applying such probe sets have focused on testing the universality and performance of the target nuclear loci, but they have not taken advantage of off-target data from other genome compartments generated alongside the nuclear loci. Here we do so to infer phylogenetic relationships in the orchid genus Epidendrum and closely related genera of subtribe Laeliinae. Our aims are to: 1) test the technical viability of applying the plant anchored hybrid enrichment (AHE) method (Angiosperm v.1 probe kit) to our focal group, 2) mine plastid protein coding genes from off-target reads; and 3) evaluate the performance of the target nuclear and off-target plastid loci in resolving and supporting phylogenetic relationships along a range of taxonomical depths. Phylogenetic relationships were inferred from the nuclear data set through coalescent summary and site-based methods, whereas plastid loci were analyzed in a concatenated partitioned matrix under maximum likelihood. The usefulness of target and flanking non-target nuclear regions and plastid loci was assessed through the estimation of their phylogenetic informativeness. Our study successfully applied the plant AHE probe kit to Epidendrum, supporting the universality of this kit in angiosperms. Moreover, it demonstrated the feasibility of mining plastome loci from off-target reads generated with the Angiosperm v.1 probe kit to obtain additional, uniparentally inherited sequence data at no extra sequencing cost. Our analyses detected some strongly supported incongruences between nuclear and plastid data sets at shallow divergences, an indication of potential lineage sorting, hybridization, or introgression events in the group. Lastly, we found that the per site phylogenetic informativeness of the ycf1 plastid gene surpasses that of all other plastid genes and several nuclear loci, making it an excellent candidate for assessing phylogenetic relationships at medium to low taxonomic levels in orchids.
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Affiliation(s)
- Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Eric Hágsater
- Herbario AMO, Instituto Chinoin, A.C., Mexico City, Mexico
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, United States
| | - Gerardo A. Salazar
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
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Li S, Hao GY, Niinemets Ü, Harley PC, Wanke S, Lens F, Zhang YJ, Cao KF. The effects of intervessel pit characteristics on xylem hydraulic efficiency and photosynthesis in hemiepiphytic and non-hemiepiphytic Ficus species. Physiol Plant 2019; 167:661-675. [PMID: 30637766 DOI: 10.1111/ppl.12923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/21/2018] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
Xylem vulnerability to cavitation and hydraulic efficiency are directly linked to fine-scale bordered pit features in water-conducting cells of vascular plants. However, it is unclear how pit characteristics influence water transport and carbon economy in tropical species. The primary aim of this study was to evaluate functional implications of changes in pit characteristics for water relations and photosynthetic traits in tropical Ficus species with different growth forms (i.e. hemiepiphytic and non-hemiepiphytic) grown under common conditions. Intervessel pit characteristics were measured using scanning electron microscopy in five hemiepiphytic and five non-hemiepiphytic Ficus species to determine whether these traits were related to hydraulics, leaf photosynthesis, stomatal conductance and wood density. Ficus species varied greatly in intervessel pit structure, hydraulic conductivity and leaf physiology, and clear differences were observed between the two growth forms. The area and diameter of pit aperture were negatively correlated with sapwood-specific hydraulic conductivity, mass-based net assimilation rate, stomatal conductance (gs ), intercellular CO2 concentration (Ci ) and the petiole vessel lumen diameters (Dv ), but positively correlated with wood density. Pit morphology was only negatively correlated with sapwood- and leaf-specific hydraulic conductivity and Dv . Pit density was positively correlated with gs , Ci and Dv , but negatively with intrinsic leaf water-use efficiency. Pit and pit aperture shape were not significantly correlated with any of the physiological traits. These findings indicate a significant role of pit characteristics in xylem water transport, carbon assimilation and ecophysiological adaptation of Ficus species in tropical rain forests.
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Affiliation(s)
- Shuai Li
- Department of Plant Physiology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, 51014, Estonia
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Guang-You Hao
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Liaoning, Shenyang, 110016, China
| | - Ülo Niinemets
- Department of Plant Physiology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, 51014, Estonia
| | - Peter C Harley
- Department of Plant Physiology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, 51014, Estonia
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, 01062, Germany
| | - Frederic Lens
- Naturalis Biodiversity Center, Leiden University, PO Box 9517, 2300RA, Leiden, The Netherlands
| | - Yong-Jiang Zhang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- School of Biology and Ecology, University of Maine, Orono, ME, 04469, USA
| | - Kun-Fang Cao
- College of Forestry, Guangxi University, Plant Ecophysiology and Evolution Group, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Forest Ecology and Conservation, Nanning, Guangxi, 530004, China
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Tränkner C, Krüger J, Wanke S, Naumann J, Wenke T, Engel F. Rapid identification of inflorescence type markers by genotyping-by-sequencing of diploid and triploid F 1 plants of Hydrangea macrophylla. BMC Genet 2019; 20:60. [PMID: 31337331 PMCID: PMC6651981 DOI: 10.1186/s12863-019-0764-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/08/2019] [Indexed: 11/17/2022] Open
Abstract
Background The ornamental crop Hydrangea macrophylla develops highly attractive lacecap (wild type) or mophead inflorescences. The mophead trait, which is mostly favored by consumers, is recessively inherited by the INFLORESCENCE TYPE locus (INF). If lacecap cultivars are crossed with mophead cultivars, then either 50% or all progenies develop lacecap inflorescences, depending on the zygosity at the INF locus. For most cultivars, the zygosity at the INF locus is unknown. Furthermore, the determination of the inflorescence type in offspring populations is time-consuming, because seedlings flower the first time in the 2nd year after sowing. Within this study, we aimed to develop DNA-based markers that allow to determine the zygosity at the INF locus of prospective parental plants and to predict the inflorescence phenotype of seedlings already in the non-flowering stage. Results By crossing a mophead and a lacecap cultivar of H. macrophylla, we produced a pseudo-backcross F1 population consisting of 422 plants. These plants segregated into 279 lacecap, 73 mophead, 3 intermediate and 67 non-flowering plants, differing significantly from the expected 1:1 segregation ratio. Surprisingly, 75% of these plants were triploid, although both parents were diploid. We found that the lacecap parent produced unreduced pollen, which induced the formation of triploids. 380 randomly selected F1 plants were genotyped by genotyping-by-sequencing (GbS). Using a genome assembly of cultivar ‘Sir Joseph Banks’, we performed subsequently a bulk sequence analysis with pooled GbS data of diploid versus mophead plants. We identified directly 2 markers tightly linked with the INF locus, each of them explaining 99.7% of the inflorescence phenotype. Using a collection consisting of 56 diploid, triploid or tetraploid H. macrophylla varieties, we detected 6 sequence variants for one of these markers. Two variants were associated with the mophead phenotype. Furthermore, we found by marker analysis a co-segregation between the mophead and the non-flowering trait, which indicates a major flowering time locus next to the INF locus. Conclusion Through bulk sequence analysis of pooled GbS data from diploid and polyploid F1 plants, we identify rapidly tightly linked markers for the inflorescence type, a dominant-recessively inherited trait in the non-model plant species H. macrophylla. Electronic supplementary material The online version of this article (10.1186/s12863-019-0764-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Conny Tränkner
- Leibniz Institute of Vegetable and Ornamental Crops, Kühnhäuser Straße 101, 99090, Erfurt, Germany. .,Present Address: Erfurt Research Centre for Horticultural Crops, Erfurt University of Applied Sciences, Kühnhäuser Straße 101, 99090, Erfurt, Germany.
| | - Jörg Krüger
- Leibniz Institute of Vegetable and Ornamental Crops, Kühnhäuser Straße 101, 99090, Erfurt, Germany.,Present Address: Erfurt Research Centre for Horticultural Crops, Erfurt University of Applied Sciences, Kühnhäuser Straße 101, 99090, Erfurt, Germany
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany
| | - Julia Naumann
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany
| | - Torsten Wenke
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany.,ASGEN GmbH & Co. KG, Egon-Erwin-Kisch-Str. 6, 01069, Dresden, Germany
| | - Frauke Engel
- Gartenbau Kötterheinrich Hortensienkulturen, Hohner Mark 20, 49525, Lengerich, Germany
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Salomo K, Smith JF, Feild TS, Samain MS, Bond L, Davidson C, Zimmers J, Neinhuis C, Wanke S. The Emergence of Earliest Angiosperms may be Earlier than Fossil Evidence Indicates. Syst Bot 2017; 42:607-619. [PMID: 29398773 PMCID: PMC5792071 DOI: 10.1600/036364417x696438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Gaps between molecular ages and fossils undermine the validity of time-calibrated molecular phylogenies. An example of the time gap surrounds the age of angiosperm's origin. We calculate molecular ages of the earliest flowering plant lineages using 22 fossil calibrations (101 genera, 40 families). Our results reveal the origin of angiosperms at the late Permian, ~275 million years ago. Different prior probability curves of molecular age calculations on dense calibration point distributions had little effect on overall age estimates compared to the effects of altered calibration points. The same is true for reasonable root age constraints. We conclude that our age estimates based on multiple datasets, priors, and calibration points are robust and the true ages are likely between our extremes. Our results, when integrated with the ecophysiological evolution of early angiosperms, imply that the ecology of the earliest angiosperms is critical to understand the pre-Cretaceous evolution of flowering plants.
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Affiliation(s)
- Karsten Salomo
- Technische Universität Dresden, Technische Universität Dresden, Zellescher Weg 20b, 01062 Dresden, Germany
| | - James F. Smith
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, Idaho, 83725, U. S. A
| | - Taylor S. Feild
- School of Marine and Tropical Biology, James Cook University, Townsville, Queensland, Australia
| | - Marie-Stéphanie Samain
- Instituto de Ecología A.C., Centro Regional del Bajío, Avenida Lázaro Cárdenas 253, 61600 Pátzcuaro, Mexico
- Ghent University, Department of Biology, Research Group Spermatophytes, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Laura Bond
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, Idaho, 83725, U. S. A
| | | | - Jay Zimmers
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, Idaho, 83725, U. S. A
| | - Christoph Neinhuis
- Technische Universität Dresden, Technische Universität Dresden, Zellescher Weg 20b, 01062 Dresden, Germany
| | - Stefan Wanke
- Technische Universität Dresden, Technische Universität Dresden, Zellescher Weg 20b, 01062 Dresden, Germany
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Wanke S, Granados Mendoza C, Müller S, Paizanni Guillén A, Neinhuis C, Lemmon AR, Lemmon EM, Samain MS. Recalcitrant deep and shallow nodes in Aristolochia (Aristolochiaceae) illuminated using anchored hybrid enrichment. Mol Phylogenet Evol 2017; 117:111-123. [DOI: 10.1016/j.ympev.2017.05.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/05/2023]
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Pytlik N, Kaden J, Finger M, Naumann J, Wanke S, Machill S, Brunner E. Biological synthesis of gold nanoparticles by the diatom Stephanopyxis turris and in vivo SERS analyses. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.10.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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De Smet Y, De Clerck O, Uemachi T, Granados Mendoza C, Wanke S, Goetghebeur P, Samain MS. Multilocus coalescent species delimitation to evaluate traditionally defined morphotypes in Hydrangea sect. Asperae (Hydrangeaceae). Mol Phylogenet Evol 2017; 114:415-425. [PMID: 28606445 DOI: 10.1016/j.ympev.2017.05.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 05/23/2017] [Accepted: 05/23/2017] [Indexed: 11/29/2022]
Abstract
The number of species recognized in section Asperae of the flowering plant genus Hydrangea differs widely between subsequent revisions. This variation is largely centered around the H. aspera species complex, with numbers of recognized species varying from one to nearly a dozen. Despite indications of molecular variation in this complex, no sequence-based species delimitation methods have been employed to evaluate the primarily morphology-based species boundaries. In the present study, a multi-locus coalescent-based approach to species delimitation is employed in order to identify separate evolutionary lines within H. sect. Asperae, using four chloroplast and four nuclear molecular markers. Eight lineages were recovered within the focal group, of which five correspond with named morphotypes. The other three lineages illustrate types of conflict between molecular species delimitation and traditional morphology-based taxonomy. One molecular lineage comprises two named morphotypes, which possibly diverged recently enough to not have developed sufficient molecular divergence. A second conflict is found in H. strigosa. This morphotype is recovered as a separate lineage when occurring in geographic isolation, but when occurring in sympatry with two other morphotypes (H. aspera and H. robusta), the coalescent species delimitation lumps these taxa into a single putative species.
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Affiliation(s)
- Yannick De Smet
- Ghent University, Department of Biology, Research Group Spermatophytes, K.L. Ledeganckstraat 35, 9000 Gent, Belgium.
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), 9000 Gent, Belgium
| | - Tatsuya Uemachi
- School of Environmental Science, The University of Shiga Prefecture, Hikone 522-8533, Japan
| | - Carolina Granados Mendoza
- Ghent University, Department of Biology, Research Group Spermatophytes, K.L. Ledeganckstraat 35, 9000 Gent, Belgium; Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-367, 04510 Coyoacán, Distrito Federal, Mexico; CONACyT División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica AC, Camino a la Presa de San José 2055, Lomas 4a. sección, C.P. 78216 San Luis Potosí, San Luis Potosí, Mexico
| | - Stefan Wanke
- Technische Universität Dresden, Institut für Botanik, Zellescher Weg 20b, 01062 Dresden, Germany
| | - Paul Goetghebeur
- Ghent University, Department of Biology, Research Group Spermatophytes, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Marie-Stéphanie Samain
- Ghent University, Department of Biology, Research Group Spermatophytes, K.L. Ledeganckstraat 35, 9000 Gent, Belgium; Instituto de Ecología, A.C., Centro Regional del Bajío, Avenida Lázaro Cárdenas 253, 61600 Pátzcuaro, Michoacán, Mexico(1)
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Oelschlägel B, von Tschirnhaus M, Nuss M, Nikolić T, Wanke S, Dötterl S, Neinhuis C. Spatio-temporal patterns in pollination of deceptive Aristolochia rotunda L. (Aristolochiaceae). Plant Biol (Stuttg) 2016; 18:928-937. [PMID: 27566447 DOI: 10.1111/plb.12503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/22/2016] [Indexed: 05/23/2023]
Abstract
Pollination success of highly specialised flowers is susceptible to fluctuations of the pollinator fauna. Mediterranean Aristolochia rotunda has deceptive trap flowers exhibiting a highly specialised pollination system. The sole pollinators are kleptoparasitic flies in search of food. This study investigates these pollinators on a spatio-temporal scale and the impact of weather conditions on their availability. Two potential strategies of the plants to cope with pollinator limitation, i.e. autonomous selfing and an increased floral life span, were tested. A total of 6156 flowers were investigated for entrapped pollinators in 10 Croatian populations. Availability of the main pollinator was correlated to meteorological data. Artificial pollination experiments were conducted and the floral life span was recorded in two populations according to pollinator availability. Trachysiphonella ruficeps (Chloropidae) was identified as dominant pollinator, along with less abundant species of Chloropidae, Ceratopogonidae and Milichiidae. Pollinator compositions varied among populations. Weather conditions 15-30 days before pollination had a significant effect on availability of the main pollinator. Flowers were not autonomously selfing, and the floral life span exhibited considerable plasticity depending on pollinator availability. A. rotunda flowers rely on insect pollen vectors. Plants are specialised on a guild of kleptoparasitic flies, rather than on a single species. Pollinator variability may result in differing selection pressures among populations. The availability/abundance of pollinators depends on weather conditions during their larval development. Flowers show a prolonged trapping flower stage that likely increases outcrossing success during periods of pollinator limitation.
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Affiliation(s)
- B Oelschlägel
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany.
| | | | - M Nuss
- Senckenberg Naturhistorische Sammlungen Dresden & Museum für Tierkunde, Dresden, Germany
| | - T Nikolić
- Department of Botany, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - S Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - S Dötterl
- Department of Ecology & Evolution, University of Salzburg, Salzburg, Austria
| | - C Neinhuis
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
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Frenzke L, Goetghebeur P, Neinhuis C, Samain MS, Wanke S. Evolution of Epiphytism and Fruit Traits Act Unevenly on the Diversification of the Species-Rich Genus Peperomia (Piperaceae). Front Plant Sci 2016; 7:1145. [PMID: 27555851 PMCID: PMC4977276 DOI: 10.3389/fpls.2016.01145] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/18/2016] [Indexed: 05/23/2023]
Abstract
The species-rich genus Peperomia (Black Pepper relatives) is the only genus among early diverging angiosperms where epiphytism evolved. The majority of fruits of Peperomia release sticky secretions or exhibit hook-shaped appendages indicative of epizoochorous dispersal, which is in contrast to other flowering plants, where epiphytes are generally characterized by fruit morphological adaptations for anemochory or endozoochory. We investigate fruit characters using Cryo-SEM. Comparative phylogenetic analyses are applied for the first time to include life form and fruit character information to study diversification in Peperomia. Likelihood ratio tests uncover correlated character evolution. We demonstrate that diversification within Peperomia is not homogenous across its phylogeny, and that net diversification rates increase by twofold within the most species-rich subgenus. In contrast to former land plant studies that provide general evidence for increased diversification in epiphytic lineages, we demonstrate that the evolution of epiphytism within Peperomia predates the diversification shift. An epiphytic-dependent diversification is only observed for the background phylogeny. An elevated frequency of life form transitions between epiphytes and terrestrials and thus evolutionary flexibility of life forms is uncovered to coincide with the diversification shift. The evolution of fruits showing dispersal related structures is key to diversification in the foreground region of the phylogeny and postdates the evolution of epiphytism. We conclude that the success of Peperomia, measured in species numbers, is likely the result of enhanced vertical and horizontal dispersal ability and life form flexibility but not the evolution of epiphytism itself.
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Affiliation(s)
- Lena Frenzke
- Department of Biology, Institut für Botanik, Technische Universität DresdenDresden, Germany
| | - Paul Goetghebeur
- Department of Biology, Research Group Spermatophytes, Ghent UniversityGent, Belgium
| | - Christoph Neinhuis
- Department of Biology, Institut für Botanik, Technische Universität DresdenDresden, Germany
| | | | - Stefan Wanke
- Department of Biology, Institut für Botanik, Technische Universität DresdenDresden, Germany
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Michl J, Kite GC, Wanke S, Zierau O, Vollmer G, Neinhuis C, Simmonds MSJ, Heinrich M. LC-MS- and (1)H NMR-Based Metabolomic Analysis and in Vitro Toxicological Assessment of 43 Aristolochia Species. J Nat Prod 2016; 79:30-7. [PMID: 26706944 DOI: 10.1021/acs.jnatprod.5b00556] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Species of Aristolochia are used as herbal medicines worldwide. They cause aristolochic acid nephropathy (AAN), a devastating disease associated with kidney failure and renal cancer. Aristolochic acids I and II (1 and 2) are considered to be responsible for these nephrotoxic and carcinogenic effects. A wide range of other aristolochic acid analogues (AAAs) exist, and their implication in AAN may have been overlooked. An LC-MS- and (1)H NMR-based metabolomic analysis was carried out on 43 medicinally used Aristolochia species. The cytotoxicity and genotoxicity of 28 Aristolochia extracts were measured in human kidney (HK-2) cells. Compounds 1 and 2 were found to be the most common AAAs. However, AA IV (3), aristolactam I (4), and aristolactam BI (5) were also widespread. No correlation was found between the amounts of 1 or 2 and extract cytotoxicity against HK-2 cells. The genotoxicity and cytotoxicity of the extracts could be linked to their contents of 5, AA D (8), and AA IIIa (10). These results undermine the assumption that 1 and 2 are exclusively responsible for the toxicity of Aristolochia species. Other analogues are likely to contribute to their toxicity and need to be considered as nephrotoxic agents. These findings facilitate understanding of the nephrotoxic mechanisms of Aristolochia and have significance for the regulation of herbal medicines.
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Affiliation(s)
- Johanna Michl
- Research Cluster Biodiversity and Medicines/Centre for Pharmacognosy and Phytotherapy, UCL School of Pharmacy , 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
| | - Geoffrey C Kite
- Royal Botanic Gardens , Kew, Richmond, Surrey, TW9 3AB, United Kingdom
| | | | | | | | | | | | - Michael Heinrich
- Research Cluster Biodiversity and Medicines/Centre for Pharmacognosy and Phytotherapy, UCL School of Pharmacy , 29-39 Brunswick Square, London, WC1N 1AX, United Kingdom
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Naumann J, Der JP, Wafula EK, Jones SS, Wagner ST, Honaas LA, Ralph PE, Bolin JF, Maass E, Neinhuis C, Wanke S, dePamphilis CW. Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae). Genome Biol Evol 2016; 8:345-63. [PMID: 26739167 PMCID: PMC4779604 DOI: 10.1093/gbe/evv256] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2015] [Indexed: 11/14/2022] Open
Abstract
Plastid genomes of photosynthetic flowering plants are usually highly conserved in both structure and gene content. However, the plastomes of parasitic and mycoheterotrophic plants may be released from selective constraint due to the reduction or loss of photosynthetic ability. Here we present the greatly reduced and highly divergent, yet functional, plastome of the nonphotosynthetic holoparasite Hydnora visseri (Hydnoraceae, Piperales). The plastome is 27 kb in length, with 24 genes encoding ribosomal proteins, ribosomal RNAs, tRNAs, and a few nonbioenergetic genes, but no genes related to photosynthesis. The inverted repeat and the small single copy region are only approximately 1.5 kb, and intergenic regions have been drastically reduced. Despite extreme reduction, gene order and orientation are highly similar to the plastome of Piper cenocladum, a related photosynthetic plant in Piperales. Gene sequences in Hydnora are highly divergent and several complementary approaches using the highest possible sensitivity were required for identification and annotation of this plastome. Active transcription is detected for all of the protein-coding genes in the plastid genome, and one of two introns is appropriately spliced out of rps12 transcripts. The whole-genome shotgun read depth is 1,400× coverage for the plastome, whereas the mitochondrial genome is covered at 40× and the nuclear genome at 2×. Despite the extreme reduction of the genome and high sequence divergence, the presence of syntenic, long transcriptionally active open-reading frames with distant similarity to other plastid genomes and a high plastome stoichiometry relative to the mitochondrial and nuclear genomes suggests that the plastome remains functional in H. visseri. A four-stage model of gene reduction, including the potential for complete plastome loss, is proposed to account for the range of plastid genomes in nonphotosynthetic plants.
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Affiliation(s)
- Julia Naumann
- Institut für Botanik, Technische Universität Dresden, Germany Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University
| | - Joshua P Der
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Department of Biological Science, California State University Fullerton
| | - Eric K Wafula
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University
| | - Samuel S Jones
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Plant Biology, The Pennsylvania State University
| | - Sarah T Wagner
- Institut für Botanik, Technische Universität Dresden, Germany
| | - Loren A Honaas
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University
| | - Paula E Ralph
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University
| | | | - Erika Maass
- Department of Biological Sciences, University of Namibia, Windhoek, Namibia
| | | | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Germany
| | - Claude W dePamphilis
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Plant Biology, The Pennsylvania State University
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Heitkam T, Petrasch S, Zakrzewski F, Kögler A, Wenke T, Wanke S, Schmidt T. Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe’s oldest Camellia japonica. Chromosome Res 2015; 23:791-806. [DOI: 10.1007/s10577-015-9500-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 11/30/2022]
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Granados Mendoza C, Naumann J, Samain MS, Goetghebeur P, De Smet Y, Wanke S. A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea. BMC Evol Biol 2015; 15:132. [PMID: 26141718 PMCID: PMC4491267 DOI: 10.1186/s12862-015-0416-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/09/2015] [Indexed: 12/21/2022] Open
Abstract
Background Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low- or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Taking advantage of public transcriptome data from the One Thousand Plant Project (1KP), we developed a genome-scale mining strategy for recovering potentially orthologous single-copy markers to address low-scale phylogenetics. Our marker design targeted the amplification of intron-rich nuclear single-copy regions from genomic DNA. As a case study we used Hydrangea section Cornidia, one of the most recently diverged lineages within Hydrangeaceae (Cornales), for comparing the performance of three of these nuclear markers to other “fast” evolving plastid markers. Results Our data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales. The three assessed nuclear markers showed considerably more phylogenetic signal for shallow evolutionary depths than conventional plastid markers. Phylogenetic signal in plastid markers increased less markedly towards deeper evolutionary divergences. Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths. In contrast, plastid markers showed higher probabilities for introducing phylogenetic noise than signal at the deepest evolutionary divergences within the tribe Hydrangeeae (Hydrangeaceae). Conclusions While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution. The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0416-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carolina Granados Mendoza
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium. .,Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-367, 04510, Coyoacán, Distrito Federal, Mexico.
| | - Julia Naumann
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany.
| | - Marie-Stéphanie Samain
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium. .,Instituto de Ecología, A.C., Centro Regional del Bajío, Avenida Lázaro Cárdenas 253, 61600, Pátzcuaro, Michoacán, Mexico.
| | - Paul Goetghebeur
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Yannick De Smet
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany.
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Oelschlägel B, Nuss M, von Tschirnhaus M, Pätzold C, Neinhuis C, Dötterl S, Wanke S. The betrayed thief - the extraordinary strategy of Aristolochia rotunda to deceive its pollinators. New Phytol 2015; 206:342-351. [PMID: 25488155 PMCID: PMC4357391 DOI: 10.1111/nph.13210] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/06/2014] [Indexed: 05/10/2023]
Abstract
Pollination of several angiosperms is based on deceit. In such systems, the flowers advertise a reward that ultimately is not provided. We report on a previously unknown pollination/mimicry system discovered in deceptive Aristolochia rotunda (Aristolochiaceae). Pollinators were collected in the natural habitat and identified. Flower scent and the volatiles of insects (models) potentially mimicked were analyzed by chemical analytical techniques. Electrophysiological and behavioral tests on the pollinators identified the components that mediate the plant-pollinator interaction and revealed the model of the mimicry system. The main pollinators of A. rotunda were female Chloropidae. They are food thieves that feed on secretions of true bugs (Miridae) while these are eaten by arthropod predators. Freshly killed mirids and Aristolochia flowers released the same scent components that chloropids use to find their food sources. Aristolochia exploits these components to deceive their chloropid pollinators. Aristolochia and other trap flowers were believed to lure saprophilous flies and mimic brood sites of pollinators. We demonstrate for A. rotunda, and hypothesize for other deceptive angiosperms, the evolution of a different, kleptomyiophilous pollination strategy. It involves scent mimicry and the exploitation of kleptoparasitic flies as pollinators. Our findings suggest a reconsideration of plants assumed to show sapromyiophilous pollination.
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Affiliation(s)
- Birgit Oelschlägel
- Institut für Botanik, Technische Universität DresdenZellescher Weg 20b, 01062, Dresden, Germany
- Birgit Oelschlägel, Tel: +49 351 463 34070,
| | - Matthias Nuss
- Senckenberg Naturhistorische Sammlungen Dresden & Museum für TierkundeKönigsbrücker Landstraße 159, 01109, Dresden, Germany
| | | | - Claudia Pätzold
- Institut für Botanik, Technische Universität DresdenZellescher Weg 20b, 01062, Dresden, Germany
| | - Christoph Neinhuis
- Institut für Botanik, Technische Universität DresdenZellescher Weg 20b, 01062, Dresden, Germany
| | - Stefan Dötterl
- Lehrstuhl für Pflanzensystematik, Universität BayreuthUniversitätsstraße 30, 95447, Bayreuth, Germany
- Authors for correspondence: Stefan Dötterl, Tel: +43 662 8044 5527,
| | - Stefan Wanke
- Institut für Botanik, Technische Universität DresdenZellescher Weg 20b, 01062, Dresden, Germany
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Müller S, Salomo K, Salazar J, Naumann J, Jaramillo MA, Neinhuis C, Feild TS, Wanke S. Intercontinental long-distance dispersal of Canellaceae from the New to the Old World revealed by a nuclear single copy gene and chloroplast loci. Mol Phylogenet Evol 2015; 84:205-19. [PMID: 25579657 DOI: 10.1016/j.ympev.2014.12.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 10/24/2022]
Abstract
Canellales, a clade consisting of Winteraceae and Canellaceae, represent the smallest order of magnoliid angiosperms. The clade shows a broad distribution throughout the Southern Hemisphere, across a diverse range of dry to wet tropical forests. In contrast to their sister-group, Winteraceae, the phylogenetic relations and biogeography within Canellaceae remain poorly studied. Here we present the phylogenetic relationships of all currently recognized genera of Canellales with a special focus on the Old World Canellaceae using a combined dataset consisting of the chloroplast trnK-matK-trnK-psbA and the nuclear single copy gene mag1 (Maigo 1). Within Canellaceae we found high statistical support for the monophyly of Warburgia and Cinnamosma. However, we also found relationships that differ from previous studies. Cinnamodendron splitted into two clades, a South American clade and a second clade confined to the Antilles and adjacent areas. Cinnamodendron from the Antilles, as well as Capsicodendron, South American Cinnamodendron and Pleodendron were not monophyletic. Consequently, Capsicodendron should be included in the South American Cinnamodendron clade and the genus Pleodendron merged with the Cinnamodendron clade from the Antilles. We also found that Warburgia (restricted to mainland eastern Africa) together with the South American Cinnamodendron and Capsicodendron are sister to the Malagasy genus Cinnamosma. In addition to the unexpected geographical relationships, both biogeographic and molecular clock analyses suggest vicariance, extinction, and at least one intercontinental long-distance-dispersal event. Our dating result contrasts previous work on Winteraceae. Diversification of Winteraceae took place in the Paleocene, predating the Canellaceae diversification by 13 MA in the Eocene. The phylogenetic relationships for Canellaceae supported here offer a solid framework for a future taxonomic revision of the Canellaceae.
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Affiliation(s)
- Sebastian Müller
- Technische Universität Dresden, Institut für Botanik, Zellescher Weg 20b, 01062 Dresden, Germany
| | - Karsten Salomo
- Technische Universität Dresden, Institut für Botanik, Zellescher Weg 20b, 01062 Dresden, Germany
| | - Jackeline Salazar
- Escuela de Biología, Universidad Autónoma de Santo Domingo (UASD), C/Bartolomé Mitre, Santo Domingo, Dominican Republic
| | - Julia Naumann
- Technische Universität Dresden, Institut für Botanik, Zellescher Weg 20b, 01062 Dresden, Germany
| | | | - Christoph Neinhuis
- Technische Universität Dresden, Institut für Botanik, Zellescher Weg 20b, 01062 Dresden, Germany
| | - Taylor S Feild
- Centre for Tropical Biodiversity and Climate Change, College of Marine and Environmental Science, Townsville 4810, Campus Townsville, Australia
| | - Stefan Wanke
- Technische Universität Dresden, Institut für Botanik, Zellescher Weg 20b, 01062 Dresden, Germany.
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Wagner ST, Hesse L, Isnard S, Samain MS, Bolin J, Maass E, Neinhuis C, Rowe NP, Wanke S. Major trends in stem anatomy and growth forms in the perianth-bearing Piperales, with special focus on Aristolochia. Ann Bot 2014; 113:1139-54. [PMID: 24694829 PMCID: PMC4030810 DOI: 10.1093/aob/mcu044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/18/2014] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS The order Piperales has the highest diversity of growth forms among the earliest angiosperm lineages, including trees, shrubs, climbers and herbs. However, within the perianth-bearing Piperales (Asarum, Saruma, Lactoris, Hydnora, Prosopanche, Thottea and Aristolochia), climbing species only occur in the most species-rich genus Aristolochia. This study traces anatomical and morphological traits among these lineages, to detect trends in growth form evolution and developmental processes. METHODS Transverse stem sections of different developmental stages of representatives of Asarum, Saruma, Lactoris, Hydnora, Thottea and Aristolochia were compared and anatomical traits were linked to growth form evolution. Biomechanical properties of representative climbers were determined in three-point bending tests and are discussed based on the anatomical observations. Growth form evolution of the perianth-bearing Piperales was reconstructed by ancestral character state reconstruction using Mesquite. KEY RESULTS While species of Asarum and Saruma are exclusively herbaceous, species of the remaining genera show a higher diversity of growth habit and anatomy. This growth form diversity is accompanied by a more complex stem anatomy and appropriate biomechanical properties. The ancestral growth form of the perianth-bearing Piperales is reconstructed with either a shrub-like or herbaceous character state, while the following three backbone nodes in the reconstruction show a shrub-like character state. Accordingly, the climbing habit most probably evolved in the ancestor of Aristolochia. CONCLUSIONS Since the ancestor of the perianth-bearing Piperales has been reconstructed with a herb- or shrub-like habit, it is proposed that the climbing habit is a derived growth form, which evolved with the diversification of Aristolochia, and might have been a key feature for its diversification. Observed anatomical synapomorphies, such as the perivascular fibres in Lactoris, Thottea and Aristolochia, support the phylogenetic relationship of several lineages within the perianth-bearing Piperales. In addition, the hypothesis that the vegetative organs of the holoparasitic Hydnoraceae are most probably rhizomes is confirmed.
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Affiliation(s)
- Sarah T Wagner
- Institut für Botanik, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Linnea Hesse
- Institut für Botanik, Technische Universität Dresden, D-01062 Dresden, Germany Institut für Spezielle Botanik, Johannes Gutenberg-Universität Mainz, D-55112 Mainz, Germany
| | - Sandrine Isnard
- IRD, UMR-AMAP, Laboratoire de Botanique et d'Écologie Végétale Appliquées, BPA5, 98800, Nouméa, New Caledonia
| | - Marie-Stéphanie Samain
- Instituto de Ecología, A.C., Centro Regional del Bajío, 61600 Pátzcuaro, Michoacán, Mexico
| | - Jay Bolin
- Department of Biology, Catawba College, Salisbury, NC 28144, USA
| | - Erika Maass
- Department of Biological Sciences, University of Namibia, Windhoek, Namibia
| | - Christoph Neinhuis
- Institut für Botanik, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Nick P Rowe
- Université Montpellier 2, UMR-AMAP, Montpellier, F-34000 France; CNRS, UMR AMAP, Montpellier, F-34000, France
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, D-01062 Dresden, Germany
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Wanke S, Reuter H, Pfister R, Michels G. Public-Access-Defibrillation: erfolgreiche Reanimation durch Einsatz eines automatischen externen Defibrillators nach Verkehrsunfall. Dtsch Med Wochenschr 2014; 139:638-40. [DOI: 10.1055/s-0034-1369864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- S. Wanke
- Klinik III für Innere Medizin, Herzzentrum der Uniklinik Köln, Köln
| | - H. Reuter
- Klinik III für Innere Medizin, Herzzentrum der Uniklinik Köln, Köln
| | - R. Pfister
- Klinik III für Innere Medizin, Herzzentrum der Uniklinik Köln, Köln
| | - G. Michels
- Klinik III für Innere Medizin, Herzzentrum der Uniklinik Köln, Köln
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Do TV, Nghiem TD, Wanke S, Neinhuis C. Aristolochia quangbinhensis (Aristolochiaceae), a new species from Central Vietnam. PhytoKeys 2014:51-9. [PMID: 24526848 PMCID: PMC3921559 DOI: 10.3897/phytokeys.33.6094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 01/13/2014] [Indexed: 05/14/2023]
Abstract
Aristolochia quangbinhensis T.V. Do, a new species from Central Vietnam, is described and illustrated. According to morphology, the species belongs to Aristolochia subgenus Isotrema. A detailed description, along with line drawings, photographs, ecology, distribution, conservation status as well as a comparison to morphologically similar species is provided.
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Affiliation(s)
- Truong Van Do
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, D–01062 Dresden, Germany
- Vietnam National Museum of Nature, Vietnam Academy of Science & Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam
| | - Trong Duc Nghiem
- Department of Botany, Hanoi University of Pharmacy, 13–15 Le Thanh Tong, Hanoi, Vietnam
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, D–01062 Dresden, Germany
| | - Christoph Neinhuis
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, D–01062 Dresden, Germany
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40
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Naumann J, Salomo K, Der JP, Wafula EK, Bolin JF, Maass E, Frenzke L, Samain MS, Neinhuis C, dePamphilis CW, Wanke S. Single-copy nuclear genes place haustorial Hydnoraceae within piperales and reveal a cretaceous origin of multiple parasitic angiosperm lineages. PLoS One 2013; 8:e79204. [PMID: 24265760 PMCID: PMC3827129 DOI: 10.1371/journal.pone.0079204] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 09/20/2013] [Indexed: 11/19/2022] Open
Abstract
Extreme haustorial parasites have long captured the interest of naturalists and scientists with their greatly reduced and highly specialized morphology. Along with the reduction or loss of photosynthesis, the plastid genome often decays as photosynthetic genes are released from selective constraint. This makes it challenging to use traditional plastid genes for parasitic plant phylogenetics, and has driven the search for alternative phylogenetic and molecular evolutionary markers. Thus, evolutionary studies, such as molecular clock-based age estimates, are not yet available for all parasitic lineages. In the present study, we extracted 14 nuclear single copy genes (nSCG) from Illumina transcriptome data from one of the “strangest plants in the world”, Hydnora visseri (Hydnoraceae). A ∼15,000 character molecular dataset, based on all three genomic compartments, shows the utility of nSCG for reconstructing phylogenetic relationships in parasitic lineages. A relaxed molecular clock approach with the same multi-locus dataset, revealed an ancient age of ∼91 MYA for Hydnoraceae. We then estimated the stem ages of all independently originated parasitic angiosperm lineages using a published dataset, which also revealed a Cretaceous origin for Balanophoraceae, Cynomoriaceae and Apodanthaceae. With the exception of Santalales, older parasite lineages tend to be more specialized with respect to trophic level and have lower species diversity. We thus propose the “temporal specialization hypothesis” (TSH) implementing multiple independent specialization processes over time during parasitic angiosperm evolution.
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Affiliation(s)
- Julia Naumann
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- * E-mail: (JN); (SW)
| | - Karsten Salomo
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Joshua P. Der
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Eric K. Wafula
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jay F. Bolin
- Department of Biology, Catawba College, Salisbury, North Carolina, United States of America
| | - Erika Maass
- Department of Biological Sciences, University of Namibia, Windhoek, Namibia
| | - Lena Frenzke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | | | | | - Claude W. dePamphilis
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- * E-mail: (JN); (SW)
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Bliss BJ, Wanke S, Barakat A, Ayyampalayam S, Wickett N, Wall PK, Jiao Y, Landherr L, Ralph PE, Hu Y, Neinhuis C, Leebens-Mack J, Arumuganathan K, Clifton SW, Maximova SN, Ma H, dePamphilis CW. Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies. BMC Plant Biol 2013; 13:13. [PMID: 23347749 PMCID: PMC3621149 DOI: 10.1186/1471-2229-13-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 12/12/2012] [Indexed: 05/15/2023]
Abstract
BACKGROUND Previous studies in basal angiosperms have provided insight into the diversity within the angiosperm lineage and helped to polarize analyses of flowering plant evolution. However, there is still not an experimental system for genetic studies among basal angiosperms to facilitate comparative studies and functional investigation. It would be desirable to identify a basal angiosperm experimental system that possesses many of the features found in existing plant model systems (e.g., Arabidopsis and Oryza). RESULTS We have considered all basal angiosperm families for general characteristics important for experimental systems, including availability to the scientific community, growth habit, and membership in a large basal angiosperm group that displays a wide spectrum of phenotypic diversity. Most basal angiosperms are woody or aquatic, thus are not well-suited for large scale cultivation, and were excluded. We further investigated members of Aristolochiaceae for ease of culture, life cycle, genome size, and chromosome number. We demonstrated self-compatibility for Aristolochia elegans and A. fimbriata, and transformation with a GFP reporter construct for Saruma henryi and A. fimbriata. Furthermore, A. fimbriata was easily cultivated with a life cycle of just three months, could be regenerated in a tissue culture system, and had one of the smallest genomes among basal angiosperms. An extensive multi-tissue EST dataset was produced for A. fimbriata that includes over 3.8 million 454 sequence reads. CONCLUSIONS Aristolochia fimbriata has numerous features that facilitate genetic studies and is suggested as a potential model system for use with a wide variety of technologies. Emerging genetic and genomic tools for A. fimbriata and closely related species can aid the investigation of floral biology, developmental genetics, biochemical pathways important in plant-insect interactions as well as human health, and various other features present in early angiosperms.
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Affiliation(s)
- Barbara J Bliss
- Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, 201 Life Sciences Building, Pennsylvania State University, University Park, PA 16802, USA
- USDA ARS PBARC, 64 Nowelo St., Hilo, HI 96720, USA
| | - Stefan Wanke
- Technische Universität Dresden, Institut für Botanik, D-01062, Dresden, Germany
| | - Abdelali Barakat
- Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, 201 Life Sciences Building, Pennsylvania State University, University Park, PA 16802, USA
- 100 Jordan Hall, Clemson University, Clemson, SC, 29634, USA
| | | | - Norman Wickett
- Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, 201 Life Sciences Building, Pennsylvania State University, University Park, PA 16802, USA
- Chicago Botanic Garden, Glencoe, IL, 27709, USA
| | - P Kerr Wall
- Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, 201 Life Sciences Building, Pennsylvania State University, University Park, PA 16802, USA
- BASF Plant Science, 26 Davis Drive, Research Triangle Park, NC, 27709, USA
| | - Yuannian Jiao
- Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, 201 Life Sciences Building, Pennsylvania State University, University Park, PA 16802, USA
| | - Lena Landherr
- Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, 201 Life Sciences Building, Pennsylvania State University, University Park, PA 16802, USA
| | - Paula E Ralph
- Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, 201 Life Sciences Building, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi Hu
- Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, 201 Life Sciences Building, Pennsylvania State University, University Park, PA 16802, USA
| | - Christoph Neinhuis
- Technische Universität Dresden, Institut für Botanik, D-01062, Dresden, Germany
| | - Jim Leebens-Mack
- Department of Plant Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Kathiravetpilla Arumuganathan
- Benaroya Research Institute at Virginia Mason, Flow Cytometry and Imaging Core Laboratory, 1201 Ninth Avenue, Seattle, WA, 98101, USA
| | - Sandra W Clifton
- The Genome Institute,Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO, 63108, USA
- Stephenson Research and Technology Center, Advanced Center for Genome Technology, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, 73019, USA
| | - Siela N Maximova
- Department of Horticulture, 421 Life Sciences Building, Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, 201 Life Sciences Building, Pennsylvania State University, University Park, PA 16802, USA
- State Key Laboratory of Genetic Engineering and the Institute of Plant Biology, the Center for Evolutionary Biology, the School of Life Sciences, Fudan University, Shanghai, 200433, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Claude W dePamphilis
- Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, 201 Life Sciences Building, Pennsylvania State University, University Park, PA 16802, USA
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Wagner ST, Isnard S, Rowe NP, Samain MS, Neinhuis C, Wanke S. Escaping the lianoid habit: evolution of shrub-like growth forms in Aristolochia subgenus Isotrema (Aristolochiaceae). Am J Bot 2012; 99:1609-29. [PMID: 22984094 DOI: 10.3732/ajb.1200244] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
PREMISE OF THE STUDY A large range of growth forms is a notable aspect of angiosperm diversity and arguably a key element of their success. However, few studies within a phylogenetic context have explored how anatomical, developmental, and biomechanical traits are linked with growth form evolution. Aristolochia (∼500 species) consists predominantly of climbers, but a handful of shrub-like species are known from Aristolochia subgenus Isotrema (hereafter, shortened to Isotrema). We test hypotheses proposing that the establishment of functional traits linked to lianescence might limit the ability to evolve structurally diverse growth forms, particularly self-supporting forms. • METHODS We focus on the origin of the shrub habit in Isotrema, from which we sampled representatives from climbing to self-supporting forms. Morphological, anatomical, and biomechanical characters are optimized on a chloroplast- and nuclear-derived phylogeny. • KEY RESULTS Character-state reconstructions revealed that the climbing habit is plesiomorphic in Isotrema and shrub-like forms are derived from climbers. However, shrubs do not constitute a monophyletic group. Both shrubs and climbers show large multiseriate rays, but differ in terms of vessel size and proportion of fibers and soft tissues. • CONCLUSION We suggest that while shrub-like species might have partly escaped from the constraints of life as lianas; their height size and stability are not typical of self-supporting shrubs and trees. Shrubs retained lianoid stem characters that are known to promote flexibility such as ray parenchyma. The transitions to a shrub-like form likely involved relatively simple, developmental changes that may be attributed to heterochronic processes.
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Affiliation(s)
- Sarah T Wagner
- Institut für Botanik, Technische Universität Dresden, D-01062 Dresden, Germany.
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Horner HT, Wanke S, Samain MS. A comparison of leaf crystal macropatterns in the two sister genera Piper and Peperomia (Piperaceae). Am J Bot 2012; 99:983-997. [PMID: 22623612 DOI: 10.3732/ajb.1200007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY This is the first large-scale study comparing leaf crystal macropatterns of the species-rich sister genera Piper and Peperomia. It focuses on identifying types of calcium oxalate crystals and their macropatterns in leaves of both genera. The Piper results are placed in a phylogenetic context to show evolutionary patterns. This information will expand knowledge about crystals and provide specific examples to help study their form and function. One example is the first-time observation of Piper crystal sand tumbling in chlorenchyma vacuoles. METHODS Herbarium and fresh leaves were cleared of cytoplasmic content and examined with polarizing microscopy to identify types of crystals and their macropatterns. Selected hydrated herbarium and fresh leaf punches were processed for scanning electron microscopy and x-ray elemental analysis. Vibratome sections of living Piper and Peperomia leaves were observed for anatomical features and crystal movement. KEY RESULTS Both genera have different leaf anatomies. Piper displays four crystal types in chlorenchyma-crystal sand, raphides, styloids, and druses, whereas Peperomia displays three types-druses, raphides, and prisms. Because of different leaf anatomies and crystal types between the genera, macropatterns are completely different. Crystal macropattern evolution in both is characterized by increasing complexity, and both may use their crystals for light gathering and reflection for efficient photosynthesis under low-intensity light environments. CONCLUSIONS Both genera have different leaf anatomies, types of crystals and crystal macropatterns. Based on Piper crystals associated with photosynthetic tissues and low-intensity light, further study of their function and association with surrounding chloroplasts is warranted, especially active crystal movement.
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Affiliation(s)
- Harry T Horner
- Department of Genetics, Development and Cell Biology & Microscopy and NanoImaging Facility, Iowa State University, Ames, Iowa 50011-1020 USA
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Naumann J, Symmank L, Samain MS, Müller KF, Neinhuis C, dePamphilis CW, Wanke S. Chasing the hare - evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level within the species rich group Peperomia (Piperaceae). BMC Evol Biol 2011; 11:357. [PMID: 22151585 PMCID: PMC3252395 DOI: 10.1186/1471-2148-11-357] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 12/12/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The rapidly increasing number of available plant genomes opens up almost unlimited prospects for biology in general and molecular phylogenetics in particular. A recent study took advantage of this data and identified a set of nuclear genes that occur in single copy in multiple sequenced angiosperms. The present study is the first to apply genomic sequence of one of these low copy genes, agt1, as a phylogenetic marker for species-level phylogenetics. Its utility is compared to the performance of several coding and non-coding chloroplast loci that have been suggested as most applicable for this taxonomic level. As a model group, we chose Tildenia, a subgenus of Peperomia (Piperaceae), one of the largest plant genera. Relationships are particularly difficult to resolve within these species rich groups due to low levels of polymorphisms and fast or recent radiation. Therefore, Tildenia is a perfect test case for applying new phylogenetic tools. RESULTS We show that the nuclear marker agt1, and in particular the agt1 introns, provide a significantly increased phylogenetic signal compared to chloroplast markers commonly used for low level phylogenetics. 25% of aligned characters from agt1 intron sequence are parsimony informative. In comparison, the introns and spacer of several common chloroplast markers (trnK intron, trnK-psbA spacer, ndhF-rpl32 spacer, rpl32-trnL spacer, psbA-trnH spacer) provide less than 10% parsimony informative characters. The agt1 dataset provides a deeper resolution than the chloroplast markers in Tildenia. CONCLUSIONS Single (or very low) copy nuclear genes are of immense value in plant phylogenetics. Compared to other nuclear genes that are members of gene families of all sizes, lab effort, such as cloning, can be kept to a minimum. They also provide regions with different phylogenetic content deriving from coding and non-coding parts of different length. Thus, they can be applied to a wide range of taxonomic levels from family down to population level. As more plant genomes are sequenced, we will obtain increasingly precise information about which genes return to single copy most rapidly following gene duplication and may be most useful across a wide range of plant groups.
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Affiliation(s)
- Julia Naumann
- Technische Universität Dresden, Institut für Botanik, D-01062 Dresden, Germany.
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Mathieu G, Symmank L, Callejas R, Wanke S, Neinhuis C, Goetghebeur P, Stéphanie Samain M. Nuevas especies geofíticas de Peperomia (Piperaceae) de México, Belice y Costa Rica. REV MEX BIODIVERS 2011. [DOI: 10.22201/ib.20078706e.2011.2.1199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Samain MS, Vrijdaghs A, Hesse M, Goetghebeur P, Jiménez Rodríguez F, Stoll A, Neinhuis C, Wanke S. Verhuellia is a segregate lineage in Piperaceae: more evidence from flower, fruit and pollen morphology, anatomy and development. Ann Bot 2010; 105:677-88. [PMID: 20237114 PMCID: PMC2859909 DOI: 10.1093/aob/mcq031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 01/04/2010] [Accepted: 01/08/2010] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS The perianthless Piperales, i.e. Saururaceae and Piperaceae, have simple reduced flowers strikingly different from the other families of the order (e.g. Aristolochiaceae). Recent molecular phylogenies proved Verhuellia to be the first branch in Piperaceae, making it a promising subject to study the detailed structure and development of the flowers. Based on recently collected material, the first detailed study since 1872 was conducted with respect to morphology, anatomy and development of the inflorescence, pollen ultrastructure and fruit anatomy. METHODS Original scanning electron microscopy (SEM), transmission electron microscopy (TEM) and light microscopy (LM) observations on Verhuellia lunaria were compared with those of Piperaceae, Saururaceae and fossils. KEY RESULTS The inflorescence is an indeterminate spike with sessile flowers, each in the axil of a bract, developing in acropetal, helical succession. Flowers consist of two (occasionally three) stamens with basifixed tetrasporangiate anthers and latrorse dehiscence by a longitudinal slit. The gynoecium lacks a style but has 3-4 stigma branches and a single, basal orthotropous and unitegmic ovule. The fruit is a drupe with large multicellular epidermal protuberances. The pollen is very small, inaperturate and areolate, with hemispherical microechinate exine elements. CONCLUSIONS Despite the superficial similarities with different genera of Piperaceae and Saururaceae, the segregate position of Verhuellia revealed by molecular phylogenetics is supported by morphological, developmental and anatomical data presented here. Unitegmic ovules and inaperturate pollen, which are synapomorphies for the genus Peperomia, are also present in Verhuellia.
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Affiliation(s)
- Marie-Stéphanie Samain
- Ghent University, Department of Biology, Research Group Spermatophytes, B-9000 Gent, Belgium.
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Oelschlägel B, Gorb S, Wanke S, Neinhuis C. Structure and biomechanics of trapping flower trichomes and their role in the pollination biology of Aristolochia plants (Aristolochiaceae). New Phytol 2009; 184:988-1002. [PMID: 19761495 DOI: 10.1111/j.1469-8137.2009.03013.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
*Catching insects to ensure pollination is one of the most elaborate and specialized mechanisms of insect-plant interactions. Phylogenetically, Aristolochiaceae represent the first angiosperm lineage that developed trap flowers. Here we report the structure and function of specific trichomes contributing to the highly specialized trapping devices. *Investigations were carried out on six Mediterranean Aristolochia species. The morphology and arrangement of the trapping trichomes were investigated by scanning electron microscopy (SEM) and cryo-SEM. To demonstrate frictional anisotropy of the trapping trichome array, a microtribological approach was used. *The results of our experiments support a hypothesis long proposed, but never tested, regarding the trapping mechanism in proterogynous Aristolochia flowers: that an array of highly specialized trichomes arranged eccentrically to the underlying surface is responsible for the easy entrance of insects into flowers but impedes their escape. As they enter the male stage of anthesis, flowers significantly modify their inner surface characteristics, allowing insects to leave. *We have demonstrated the substantial contribution of trapping trichomes to the capture, retention and release of pollinators, an important prerequisite for making cross-pollination possible in most Aristolochia species. Finally, we compare trapping trichomes of Aristolochia with similar structures found in other trapping flowers as well as in pitchers of carnivorous plants not optimized for insect release.
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Heinrich M, Chan J, Wanke S, Neinhuis C, Simmonds MSJ. Local uses of Aristolochia species and content of nephrotoxic aristolochic acid 1 and 2--a global assessment based on bibliographic sources. J Ethnopharmacol 2009; 125:108-44. [PMID: 19505558 DOI: 10.1016/j.jep.2009.05.028] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 05/20/2009] [Accepted: 05/28/2009] [Indexed: 05/21/2023]
Abstract
AIMS OF THE STUDY More than 100 cases of nephropathy over the last 10 years caused by the systemic and longer term application of Chinese snakeroot (Aristolochia fangchi) highlighted the risk of using preparations which contain aristolochic acids. On the other hand anecdotal evidence highlights the widespread use of Aristolochia species (Aristolochiaceae) in many regions of the world. Therefore, it was our objective to systematically assess the scientific literature available on the local and traditional use of Aristolochia spp. on a worldwide scale. Our review identifies core species which need to be investigated and which may need monitoring (esp. in national and international trade). METHODS An extensive review of the literature available in libraries in London on the uses of species of Aristolochia was undertaken. Relevant information was extracted and entered into a database for analysis. RESULTS Based on the assessment of 566 reference sources 685 individual sets of data were recorded. Seven species--Aristolochia indica L. (Asia), Aristolochia serpentaria L. (North America), Aristolochia debilis Sieb & Zucch. (China), Aristolochia acuminata Lam (India), Aristolochia trilobata L. (Central/South America, Caribbean), Aristolochia clematitis L. (Europe) and Aristolochia bracteolata Lam. (Africa)--are reported widely as being used medicinally. The medical uses vary, but of particular interest are uses in case of gastrointestinal problems, which is likely to result in repeated exposure to the botanical drugs by an individual. About half of all records relate to uses of Aristolochia species in Asia, one-third to the Americas, a continent which has so far received practically no attention in terms of assessing the risk of using species of Aristolochia. Of the 99 species (plus several identified at genus level only) for which we were able to summarise ethnobotanical information, preliminary phytochemical information is only available for 24 species and some of the most common ones including Aristolochia acuminata have so far not been studied phytochemically. CONCLUSIONS Species of Aristolochia are used medicinally in many regions of the world and both from an ethnopharmacological and a public health perspective this poses a risk. A systematic assessment of the content of aristolochic acids in the most widely used species is needed to evaluate whether their uses pose a potential health risk. In China and Europe species of Aristolochia have been associated with nephropathy and it is important to evaluate whether nephropathy occurs in other parts of the world, especially India and Central America where the use of species of Aristolochia are reported to be commonly used in traditional medicine.
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Affiliation(s)
- Michael Heinrich
- Centre for Pharmacognosy and Phytotherapy, The School of Pharmacy, University London, 29-39 Brunswick Square, London WC1N1AX, UK.
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Wanke S, Vanderschaeve L, Mathieu G, Neinhuis C, Goetghebeur P, Samain MS. From forgotten taxon to a missing link? The position of the genus Verhuellia (piperaceae) revealed by molecules. Ann Bot 2007; 99:1231-8. [PMID: 17513306 PMCID: PMC3243581 DOI: 10.1093/aob/mcm063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS The species-poor and little-studied genus Verhuellia has often been treated as a synonym of the genus Peperomia, downplaying its significance in the relationships and evolutionary aspects in Piperaceae and Piperales. The lack of knowledge concerning Verhuellia is largely due to its restricted distribution, poorly known collection localities, limited availability in herbaria and absence in botanical gardens and lack of material suitable for molecular phylogenetic studies until recently. Because Verhuellia has some of the most reduced flowers in Piperales, the reconstruction of floral evolution which shows strong trends towards reduction in all lineages needs to be revised. METHODS Verhuellia is included in a molecular phylogenetic analysis of Piperales (trnT-trnL-trnF and trnK/matK), based on nearly 6000 aligned characters and more than 1400 potentially parsimony-informative sites which were partly generated for the present study. Character states for stamen and carpel number are mapped on the combined molecular tree to reconstruct the ancestral states. KEY RESULTS The genus Peperomia is generally considered to have the most reduced flowers in Piperales but this study shows that this is only partially true. Verhuellia, with almost equally reduced flowers, is not part of or sister to Peperomia as expected, but is revealed as sister to all other Piperaceae in all analyses, putting character evolution in this family and in the perianthless Piperales in a different light. A robust phylogenetic analysis including all relevant taxa is presented as a framework for inferring patterns and processes of evolution in Piperales and Piperaceae. CONCLUSIONS Verhuellia is a further example of how a molecular phylogenetic study can elucidate the relationships of an unplaced taxon. When more material becomes available, it will be possible to investigate character evolution in Piperales more thoroughly and to answer some evolutionary questions concerning Piperaceae.
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Affiliation(s)
- S Wanke
- Technische Universität Dresden, Institut für Botanik, D-01062 Dresden, Germany
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Wanke S, Jaramillo MA, Borsch T, Samain MS, Quandt D, Neinhuis C. Evolution of Piperales—matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Mol Phylogenet Evol 2007; 42:477-97. [PMID: 16978885 DOI: 10.1016/j.ympev.2006.07.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Revised: 07/07/2006] [Accepted: 07/11/2006] [Indexed: 10/24/2022]
Abstract
Piperales represent the largest basal angiosperm order with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 2000 species), Peperomia (ca. 1500-1700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of six amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogeneity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia.
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Affiliation(s)
- Stefan Wanke
- Institut für Botanik, Plant Phylogenetics and Phylogenomics Group, Technische Universität Dresden, 01062 Dresden, Germany.
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