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Jost M, Wanke S. A comparative analysis of plastome evolution in autotrophic Piperales. AMERICAN JOURNAL OF BOTANY 2024; 111:e16300. [PMID: 38469876 DOI: 10.1002/ajb2.16300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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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] [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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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] [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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Klimpert NJ, Mayer JLS, Sarzi DS, Prosdocimi F, Pinheiro F, Graham SW. Phylogenomics and plastome evolution of a Brazilian mycoheterotrophic orchid, Pogoniopsis schenckii. AMERICAN JOURNAL OF BOTANY 2022; 109:2030-2050. [PMID: 36254561 DOI: 10.1002/ajb2.16084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Pogoniopsis likely represents an independent photosynthesis loss in orchids. We use phylogenomic data to better identify the phylogenetic placement of this fully mycoheterotrophic taxon, and investigate its molecular evolution. METHODS We performed likelihood analysis of plastid and mitochondrial phylogenomic data to localize the position of Pogoniopsis schenckii in orchid phylogeny, and investigated the evolution of its plastid genome. RESULTS All analyses place Pogoniopsis in subfamily Epidendroideae, with strongest support from mitochondrial data, which also place it near tribe Sobralieae with moderately strong support. Extreme rate elevation in Pogoniopsis plastid genes broadly depresses branch support; in contrast, mitochondrial genes are only mildly rate elevated and display very modest and localized reductions in bootstrap support. Despite considerable genome reduction, including loss of photosynthesis genes and multiple translation apparatus genes, gene order in Pogoniopsis plastomes is identical to related autotrophs, apart from moderately shifted inverted repeat (IR) boundaries. All cis-spliced introns have been lost in retained genes. Two plastid genes (accD, rpl2) show significant strengthening of purifying selection. A retained plastid tRNA gene (trnE-UUC) of Pogoniopsis lacks an anticodon; we predict that it no longer functions in translation but retains a secondary role in heme biosynthesis. CONCLUSIONS Slowly evolving mitochondrial genes clarify the placement of Pogoniopsis in orchid phylogeny, a strong contrast with analysis of rate-elevated plastome data. We documented the effects of the novel loss of photosynthesis: for example, despite massive gene loss, its plastome is fully colinear with other orchids, and it displays only moderate shifts in selective pressure in retained genes.
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Affiliation(s)
- Nathaniel J Klimpert
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Juliana Lischka Sampaio Mayer
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Deise Schroder Sarzi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, UFRJ/CCS/Bloco B33, Rio de Janeiro, RJ, 21.941-902, Brazil
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, UFRJ/CCS/Bloco B33, Rio de Janeiro, RJ, 21.941-902, Brazil
| | - Fábio Pinheiro
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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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] [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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Yang T, Sahu SK, Yang L, Liu Y, Mu W, Liu X, Strube ML, Liu H, Zhong B. Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:808156. [PMID: 35498716 PMCID: PMC9038950 DOI: 10.3389/fpls.2022.808156] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/07/2022] [Indexed: 05/03/2023]
Abstract
The plastid organelle is essential for many vital cellular processes and the growth and development of plants. The availability of a large number of complete plastid genomes could be effectively utilized to understand the evolution of the plastid genomes and phylogenetic relationships among plants. We comprehensively analyzed the plastid genomes of Viridiplantae comprising 3,654 taxa from 298 families and 111 orders and compared the genomic organizations in their plastid genomic DNA among major clades, which include gene gain/loss, gene copy number, GC content, and gene blocks. We discovered that some important genes that exhibit similar functions likely formed gene blocks, such as the psb family presumably showing co-occurrence and forming gene blocks in Viridiplantae. The inverted repeats (IRs) in plastid genomes have doubled in size across land plants, and their GC content is substantially higher than non-IR genes. By employing three different data sets [all nucleotide positions (nt123), only the first and second codon positions (nt12), and amino acids (AA)], our phylogenomic analyses revealed Chlorokybales + Mesostigmatales as the earliest-branching lineage of streptophytes. Hornworts, mosses, and liverworts forming a monophylum were identified as the sister lineage of tracheophytes. Based on nt12 and AA data sets, monocots, Chloranthales and magnoliids are successive sister lineages to the eudicots + Ceratophyllales clade. The comprehensive taxon sampling and analysis of different data sets from plastid genomes recovered well-supported relationships of green plants, thereby contributing to resolving some long-standing uncertainties in the plant phylogeny.
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Affiliation(s)
- Ting Yang
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sunil Kumar Sahu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- *Correspondence: Sunil Kumar Sahu,
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yang Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Weixue Mu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Xin Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Huan Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Bojian Zhong,
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Lyko P, Wicke S. Genomic reconfiguration in parasitic plants involves considerable gene losses alongside global genome size inflation and gene births. PLANT PHYSIOLOGY 2021; 186:1412-1423. [PMID: 33909907 PMCID: PMC8260112 DOI: 10.1093/plphys/kiab192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/13/2021] [Indexed: 05/02/2023]
Abstract
Parasitic plant genomes and transcriptomes reveal numerous genetic innovations, the functional-evolutionary relevance and roles of which open unprecedented research avenues.
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Affiliation(s)
- Peter Lyko
- Institute for Biology, Humboldt-University of Berlin, Germany
| | - Susann Wicke
- Institute for Biology, Humboldt-University of Berlin, Germany
- Author for communication:
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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. FRONTIERS IN PLANT SCIENCE 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] [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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11
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Mkala EM, Mutungi MM, Mutinda ES, Oulo MA, Wanga VO, Mwachala G, Hu GW. Understanding the Ethnobotany, Chemistry, Pharmacology, and Distribution of Genus Hydnora (Aristolochiaceae). PLANTS (BASEL, SWITZERLAND) 2021; 10:494. [PMID: 33807757 PMCID: PMC8001087 DOI: 10.3390/plants10030494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022]
Abstract
The genus Hydnora (Hydnoraceae) is one of the basal angiosperms in the order Piperales, found in the semi-arid regions of Africa, and the Southern Arabian Peninsula. Plants in this genus play essential roles in communities around the world as revealed by various studies. Currently, there are eight species of the genus Hydnora; seven in Africa and one in the Arabian Peninsula. Notably, Hydnora abyssinica A.Br. and Hydnora africana Thunb. are widely distributed compared to other species. They are widely used for their medicinal and nutritional values. The information on ethnobotany, chemistry, pharmacology, and distribution of genus Hydnora was gathered using phytochemical and ethnobotanical books, electronic sources, and published articles. Preliminary phytochemical screening shows that flavonoids, phenolics, proanthocyanidins, and tannins are the main compounds in H. abyssinica and H. africana. Furthermore, 11 compounds have been isolated from H. abyssinica. The biological activities of H. abyssinica and H. africana have been reported. They include antibacterial, antiproliferative, antioxidant, antidiarrhea, and antifungal potentials. Despite the Hydnora species being practiced in ancient folkloric medicine, their traditional uses and pharmacological value are poorly documented. Based on the available information on ethnobotany, phytochemistry, pharmacology, and distribution, we aim to provide research gaps and challenges for a better understanding of this genus. This may be resourceful in the development of effective phytomedicines, and aid in conservation. The available studies on this genus on some aspects such as phytochemistry, pharmacological activities, and distribution are under-reported hence the need for further research.
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Affiliation(s)
- Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.M.M.); (M.M.M.); (E.S.M.); (M.A.O.); (V.O.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- East African Herbarium, National Museums of Kenya, P.O. Box 451660-0100 Nairobi, Kenya;
| | - Moses Mutuse Mutungi
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.M.M.); (M.M.M.); (E.S.M.); (M.A.O.); (V.O.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Elizabeth Syowai Mutinda
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.M.M.); (M.M.M.); (E.S.M.); (M.A.O.); (V.O.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Millicent Akinyi Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.M.M.); (M.M.M.); (E.S.M.); (M.A.O.); (V.O.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.M.M.); (M.M.M.); (E.S.M.); (M.A.O.); (V.O.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Geoffrey Mwachala
- East African Herbarium, National Museums of Kenya, P.O. Box 451660-0100 Nairobi, Kenya;
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (E.M.M.); (M.M.M.); (E.S.M.); (M.A.O.); (V.O.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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12
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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: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [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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13
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Plant Organelle DNA Maintenance. PLANTS 2020; 9:plants9060683. [PMID: 32481608 PMCID: PMC7356008 DOI: 10.3390/plants9060683] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023]
Abstract
Plant cells contain two double membrane bound organelles, plastids and mitochondria, that contain their own genomes. There is a very large variation in the sizes of mitochondrial genomes in higher plants, while the plastid genome remains relatively uniform across different species. One of the curious features of the organelle DNA is that it exists in a high copy number per mitochondria or chloroplast, which varies greatly in different tissues during plant development. The variations in copy number, morphology and genomic content reflect the diversity in organelle functions. The link between the metabolic needs of a cell and the capacity of mitochondria and chloroplasts to fulfill this demand is thought to act as a selective force on the number of organelles and genome copies per organelle. However, it is not yet clear how the activities of mitochondria and chloroplasts are coordinated in response to cellular and environmental cues. The relationship between genome copy number variation and the mechanism(s) by which the genomes are maintained through different developmental stages are yet to be fully understood. This Special Issue has several contributions that address current knowledge of higher plant organelle DNA. Here we briefly introduce these articles that discuss the importance of different aspects of the organelle genome in higher plants.
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