1
|
Fleming JF, Valero‐Gracia A, Struck TH. Identifying and addressing methodological incongruence in phylogenomics: A review. Evol Appl 2023; 16:1087-1104. [PMID: 37360032 PMCID: PMC10286231 DOI: 10.1111/eva.13565] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/07/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023] Open
Abstract
The availability of phylogenetic data has greatly expanded in recent years. As a result, a new era in phylogenetic analysis is dawning-one in which the methods we use to analyse and assess our data are the bottleneck to producing valuable phylogenetic hypotheses, rather than the need to acquire more data. This makes the ability to accurately appraise and evaluate new methods of phylogenetic analysis and phylogenetic artefact identification more important than ever. Incongruence in phylogenetic reconstructions based on different datasets may be due to two major sources: biological and methodological. Biological sources comprise processes like horizontal gene transfer, hybridization and incomplete lineage sorting, while methodological ones contain falsely assigned data or violations of the assumptions of the underlying model. While the former provides interesting insights into the evolutionary history of the investigated groups, the latter should be avoided or minimized as best as possible. However, errors introduced by methodology must first be excluded or minimized to be able to conclude that biological sources are the cause. Fortunately, a variety of useful tools exist to help detect such misassignments and model violations and to apply ameliorating measurements. Still, the number of methods and their theoretical underpinning can be overwhelming and opaque. Here, we present a practical and comprehensive review of recent developments in techniques to detect artefacts arising from model violations and poorly assigned data. The advantages and disadvantages of the different methods to detect such misleading signals in phylogenetic reconstructions are also discussed. As there is no one-size-fits-all solution, this review can serve as a guide in choosing the most appropriate detection methods depending on both the actual dataset and the computational power available to the researcher. Ultimately, this informed selection will have a positive impact on the broader field, allowing us to better understand the evolutionary history of the group of interest.
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Ceriotti LF, Gatica-Soria L, Sanchez-Puerta MV. Cytonuclear coevolution in a holoparasitic plant with highly disparate organellar genomes. PLANT MOLECULAR BIOLOGY 2022; 109:673-688. [PMID: 35359176 DOI: 10.1007/s11103-022-01266-9] [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: 11/25/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Contrasting substitution rates in the organellar genomes of Lophophytum agree with the DNA repair, replication, and recombination gene content. Plastid and nuclear genes whose products form multisubunit complexes co-evolve. The organellar genomes of the holoparasitic plant Lophophytum (Balanophoraceae) show disparate evolution. In the plastid, the genome has been severely reduced and presents a > 85% AT content, while in the mitochondria most protein-coding genes have been replaced by homologs acquired by horizontal gene transfer (HGT) from their hosts (Fabaceae). Both genomes carry genes whose products form multisubunit complexes with those of nuclear genes, creating a possible hotspot of cytonuclear coevolution. In this study, we assessed the evolutionary rates of plastid, mitochondrial and nuclear genes, and their impact on cytonuclear evolution of genes involved in multisubunit complexes related to lipid biosynthesis and proteolysis in the plastid and those in charge of the oxidative phosphorylation in the mitochondria. Genes from the plastid and the mitochondria (both native and foreign) of Lophophytum showed extremely high and ordinary substitution rates, respectively. These results agree with the biased loss of plastid-targeted proteins involved in angiosperm organellar repair, replication, and recombination machinery. Consistent with the high rate of evolution of plastid genes, nuclear-encoded subunits of plastid complexes showed disproportionate increases in non-synonymous substitution rates, while those of the mitochondrial complexes did not show different rates than the control (i.e. non-organellar nuclear genes). Moreover, the increases in the nuclear-encoded subunits of plastid complexes were positively correlated with the level of physical interaction they possess with the plastid-encoded ones. Overall, these results suggest that a structurally-mediated compensatory factor may be driving plastid-nuclear coevolution in Lophophytum, and that mito-nuclear coevolution was not altered by HGT.
Collapse
Affiliation(s)
- Luis F Ceriotti
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - Leonardo Gatica-Soria
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - M Virginia Sanchez-Puerta
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina.
| |
Collapse
|
4
|
Thorogood CJ, Teixeira-Costa L, Ceccantini G, Davis C, Hiscock SJ. Endoparasitic plants and fungi show evolutionary convergence across phylogenetic divisions. THE NEW PHYTOLOGIST 2021; 232:1159-1167. [PMID: 34251722 DOI: 10.1111/nph.17556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/04/2021] [Indexed: 06/13/2023]
Abstract
Endoparasitic plants are the most reduced flowering plants, spending most of their lives as a network of filaments within the tissues of their hosts. Despite their extraordinary life form, we know little about their biology. Research into a few species has revealed unexpected insights, such as the total loss of plastome, the reduction of the vegetative phase to a proembryonic stage, and elevated information exchange between host and parasite. To consolidate our understanding, we review life history, anatomy, and molecular genetics across the four independent lineages of endoparasitic plants. We highlight convergence across these clades and a striking trans-kingdom convergence in life history among endoparasitic plants and disparate lineages of fungi at the molecular and physiological levels. We hypothesize that parasitism of woody plants preselected for the endoparasitic life history, providing parasites a stable host environment and the necessary hydraulics to enable floral gigantism and/or high reproductive output. Finally, we propose a broader view of endoparasitic plants that connects research across disciplines, for example, pollen-pistil and graft incompatibility interactions and plant associations with various fungi. We shine a light on endoparasitic plants and their hosts as under-explored ecological microcosms ripe for identifying unexpected biological processes, interactions and evolutionary convergence.
Collapse
Affiliation(s)
- Chris J Thorogood
- University of Oxford Botanic Garden, Rose Lane, Oxford, OX1 4AZ, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | | | - Gregório Ceccantini
- Dp. of Botany, University of São Paulo, IB-USP, Rua do Matão 277, São Paulo, SP 05508-090, Brazil
| | - Charles Davis
- Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Simon J Hiscock
- University of Oxford Botanic Garden, Rose Lane, Oxford, OX1 4AZ, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| |
Collapse
|
5
|
Teixeira-Costa L, Davis CC. Life history, diversity, and distribution in parasitic flowering plants. PLANT PHYSIOLOGY 2021; 187:32-51. [PMID: 35237798 PMCID: PMC8418411 DOI: 10.1093/plphys/kiab279] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 05/25/2021] [Indexed: 06/08/2023]
Abstract
A review of parasitic plant diversity and outstanding disjunct distributions according to an updated functional classification based on these plants’ life cycles.
Collapse
|
6
|
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.
Collapse
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:
| |
Collapse
|
7
|
Teixeira-Costa L, Davis CC, Ceccantini G. Striking developmental convergence in angiosperm endoparasites. AMERICAN JOURNAL OF BOTANY 2021; 108:756-768. [PMID: 33988869 DOI: 10.1002/ajb2.1658] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
PREMISE A subset of parasitic plants bear extremely reduced features and grow nearly entirely within their hosts. Until recently, most of these endoparasites were thought to represent a single clade united by their reduced morphology. Current phylogenetic understanding contradicts this assumption and indicates these plants represent distantly related clades, thus offering an opportunity to examine convergence among plants with this life history. METHODS We sampled species from Apodanthaceae, Cytinaceae, Mitrastemonaceae, and Rafflesiaceae spanning a range of developmental stages. To provide a broader comparative framework, Santalaceae mistletoes with a similar lifestyle were also analyzed. Microtomography and microscopy were used to analyze growth patterns and the ontogeny of host-parasite vascular connections. RESULTS Apodanthaceae, Cytinaceae, Mitrastemonaceae, and Rafflesiaceae species demonstrated a common development characterized by late cell differentiation. These species were also observed to form direct connections to host vessels and to cause severe alterations of host xylem development. Apodanthaceae and Rafflesiaceae species were additionally observed to form sieve elements, which connect with the host phloem. Endophytic Santalaceae species demonstrated a dramatically different developmental pattern, featuring early cell differentiation and tissue organization, and little effect on host anatomy and cambial activity. CONCLUSIONS Our results illuminate two distinct developmental trajectories in endoparasites. One involves the retention of embryonic characteristics and late connection with host vessels, as demonstrated in species of Apodanthaceae, Cytinaceae, Mitrastemonaceae, and Rafflesiaceae. The second involves tissue specialization and early connection with host xylem, as exemplified by Santalaceae species. These differences are hypothesized to be related to the absence/presence of photosynthesis in these plants.
Collapse
Affiliation(s)
- Luiza Teixeira-Costa
- Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
- Harvard University Herbaria, Cambridge, MA, 02138, USA
| | | | - Gregorio Ceccantini
- Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
| |
Collapse
|
8
|
Filip E, Skuza L. Horizontal Gene Transfer Involving Chloroplasts. Int J Mol Sci 2021; 22:ijms22094484. [PMID: 33923118 PMCID: PMC8123421 DOI: 10.3390/ijms22094484] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 02/04/2023] Open
Abstract
Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.
Collapse
Affiliation(s)
- Ewa Filip
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland;
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
- Correspondence:
| | - Lidia Skuza
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland;
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Cai L, Arnold BJ, Xi Z, Khost DE, Patel N, Hartmann CB, Manickam S, Sasirat S, Nikolov LA, Mathews S, Sackton TB, Davis CC. Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae). Curr Biol 2021; 31:1002-1011.e9. [DOI: 10.1016/j.cub.2020.12.045] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/11/2020] [Accepted: 12/23/2020] [Indexed: 12/18/2022]
|
11
|
Cytinus under the Microscope: Disclosing the Secrets of a Parasitic Plant. PLANTS 2021; 10:plants10010146. [PMID: 33445677 PMCID: PMC7828134 DOI: 10.3390/plants10010146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 11/17/2022]
Abstract
Well over 1% of all flowering plants are parasites, obtaining all or part of the nutrients they need from other plants. Among this extremely heterogeneous assemblage, the Cytinaceae form a small group of holoparasites, with Cytinus as the main representative genus. Despite the small number of known species and the fact that it doesn't attack crops or plants of economic importance, Cytinus is paradigmatic among parasitic plants. Recent research has indeed disclosed many aspects of host-parasite interactions and reproductive biology, the latter displaying a vast array of adaptive traits to lure a range of animal pollinators. Furthermore, analysis of biological activities of extracts of the most common species of Cytinus has provided evidence that this plant could be a valuable source of compounds with high potential in key applicative areas, namely food production (nutraceuticals) and the development of antimicrobial therapeutics. This article offers a complete overview of our current knowledge of Cytinus.
Collapse
|
12
|
Roulet ME, Garcia LE, Gandini CL, Sato H, Ponce G, Sanchez-Puerta MV. Multichromosomal structure and foreign tracts in the Ombrophytum subterraneum (Balanophoraceae) mitochondrial genome. PLANT MOLECULAR BIOLOGY 2020; 103:623-638. [PMID: 32440763 DOI: 10.1007/s11103-020-01014-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Horizontal gene transfer (HGT) is frequent in parasitic plant mitochondria as a result of vascular connections established in host-parasite relationships. Recent studies of the holoparasitic plant Lophophytum mirabile (Balanophoraceae) revealed the unprecedented acquisition of a large amount of mitochondrial sequences from its legume host. We focused on a close relative, the generalist holoparasite Ombrophytum subterraneum, to examine the incidence of HGT events in the mitochondrial genome (mtDNA). The mtDNA of O. subterraneum assembles into 54 circular chromosomes, only 34 of which contain the 51 full-length coding regions. Numerous foreign tracts (totaling almost 100 kb, ~ 14% of the mtDNA), including 12 intact genes, were acquired by HGT from the Asteraceae hosts. Nine chromosomes concentrate most of those regions and eight are almost entirely foreign. Native homologs of each foreign gene coexist in the mtDNA and are potentially functional. A large proportion of shorter regions were related to the Fabaceae (a total of ~ 110 kb, 15.4%), some of which were shared with L. mirabile. We also found evidence of foreign sequences donated by angiosperm lineages not reported as hosts (Apocynaceae, Euphorbiaceae, Lamiaceae, and Malvales). We propose an evolutionary hypothesis that involves ancient transfers from legume hosts in the common ancestor of Ombrophytum and Lophophytum followed by more recent transfer events in L. mirabile. Besides, the O. subterraneum mtDNA was also subjected to additional HGT events from diverse angiosperm lineages, including large and recent transfers from the Asteraceae, and also from Lamiaceae.
Collapse
Affiliation(s)
- M Emilia Roulet
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Laura E Garcia
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - Carolina L Gandini
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Hector Sato
- Facultad de Ciencias Agrarias, Universidad Nacional de Jujuy, Cátedra de Botánica General-Herbario JUA, Alberdi 47, 4600, San Salvador de Jujuy, Jujuy, Argentina
| | - Gabriela Ponce
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina.
| |
Collapse
|
13
|
Petersen G, Anderson B, Braun HP, Meyer EH, Møller IM. Mitochondria in parasitic plants. Mitochondrion 2020; 52:173-182. [DOI: 10.1016/j.mito.2020.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/05/2020] [Accepted: 03/23/2020] [Indexed: 02/06/2023]
|
14
|
A phylogenetic and biogeographic study of Rafflesia (Rafflesiaceae) in the Philippines: Limited dispersal and high island endemism. Mol Phylogenet Evol 2019; 139:106555. [DOI: 10.1016/j.ympev.2019.106555] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/03/2019] [Accepted: 07/04/2019] [Indexed: 01/12/2023]
|
15
|
Suetsugu K. Social wasps, crickets and cockroaches contribute to pollination of the holoparasitic plant Mitrastemon yamamotoi (Mitrastemonaceae) in southern Japan. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:176-182. [PMID: 30098096 DOI: 10.1111/plb.12889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 08/06/2018] [Indexed: 06/08/2023]
Abstract
Mitrastemon yamamotoi is completely embedded within the tissues of its hosts, except during the reproductive stage, when aboveground parts emerge from host tissues. Its highly modified appearance has attracted attention of many botanists, but very little is known about the reproductive system. Floral visitors to M. yamamotoi were observed in southern Japan. Pollination experiments were conducted to determine the plant's self-compatibility and pollen limitation, as well as the contribution of diurnal and nocturnal visitors to fruit set and outcrossing. Mitrastemon yamamotoi is mainly pollinated by social wasps, but previously unnoticed pollinators (i.e. crickets and cockroaches) are also important, based on visitation frequency and pollen loads. Results of the pollination experiments suggest that nocturnal visitors, such as crickets and cockroaches, contribute to geitonogamous pollination, whereas diurnal visitors, such as social wasps, facilitate outcrossing. The unexpected pollinator assemblage of M. yamamotoi might be influenced by multiple factors, including the highly modified flowers that are produced close to the ground in dark understorey environments, the species' winter-flowering habit and the location of the study site (i.e. near the northern limit of the species' range). Considering that M. yamamotoi occurs widely in subtropical and tropical forests in Asia, additional studies are needed to assess pollinator assemblages of M. yamamotoi at other locations.
Collapse
Affiliation(s)
- K Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| |
Collapse
|
16
|
Givnish TJ, Zuluaga A, Spalink D, Soto Gomez M, Lam VKY, Saarela JM, Sass C, Iles WJD, de Sousa DJL, Leebens-Mack J, Chris Pires J, Zomlefer WB, Gandolfo MA, Davis JI, Stevenson DW, dePamphilis C, Specht CD, Graham SW, Barrett CF, Ané C. Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots. AMERICAN JOURNAL OF BOTANY 2018; 105:1888-1910. [PMID: 30368769 DOI: 10.1002/ajb2.1178] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/03/2018] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification. METHODS We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth. KEY RESULTS Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large-scale accelerations in PACMAD-BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae-Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches. CONCLUSIONS We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome-scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).
Collapse
Affiliation(s)
- Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | | | - Daniel Spalink
- Department of Ecosystem Science, Texas A&M University, College Station, Texas, 77840, USA
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | | | - Chodon Sass
- The University and Jepson Herbarium, University of California-Berkeley, Berkeley, California, 94720, USA
| | - William J D Iles
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Danilo José Lima de Sousa
- Departamento de Ciéncias Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, 44036-900, Brazil
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, 65211, USA
| | - Wendy B Zomlefer
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Maria A Gandolfo
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Jerrold I Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | | | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Chelsea D Specht
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| |
Collapse
|
17
|
Pastore M, Rangel WDM, Giulietti AM. Flora das cangas da Serra dos Carajás, Pará, Brasil: Apodanthaceae. RODRIGUÉSIA 2018. [DOI: 10.1590/2175-7860201869311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Resumo Este estudo engloba o tratamento florístico de Apodanthaceae para as cangas da Serra dos Carajás, no estado do Pará. Inclui descrição, ilustração, fotografias, distribuição, comentários morfológicos e taxonômicos de Pilostyles blanchetii, a única espécie da família registrada na área de estudo.
Collapse
|
18
|
Laphitz RML, Ezcurra C, Vidal-Russell R. Cryptic species in the Andean hemiparasite Quinchamalium chilense (Schoepfiaceae: Santalales). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1404504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rita M Lopez Laphitz
- Departamento de Botánica, Instituto de Investigaciones en Biodiversidad y Medioambiente, CONICET-UNComahue, Quintral 1250, S. C. de Bariloche, 8400 Río Negro, Argentina
| | - Cecilia Ezcurra
- Departamento de Botánica, Instituto de Investigaciones en Biodiversidad y Medioambiente, CONICET-UNComahue, Quintral 1250, S. C. de Bariloche, 8400 Río Negro, Argentina
| | - Romina Vidal-Russell
- Departamento de Botánica, Instituto de Investigaciones en Biodiversidad y Medioambiente, CONICET-UNComahue, Quintral 1250, S. C. de Bariloche, 8400 Río Negro, Argentina
| |
Collapse
|
19
|
A 4000-species dataset provides new insight into the evolution of ferns. Mol Phylogenet Evol 2016; 105:200-211. [DOI: 10.1016/j.ympev.2016.09.003] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/03/2016] [Accepted: 09/07/2016] [Indexed: 01/17/2023]
|
20
|
Yang Z, Zhang Y, Wafula EK, Honaas LA, Ralph PE, Jones S, Clarke CR, Liu S, Su C, Zhang H, Altman NS, Schuster SC, Timko MP, Yoder JI, Westwood JH, dePamphilis CW. Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation. Proc Natl Acad Sci U S A 2016; 113:E7010-E7019. [PMID: 27791104 PMCID: PMC5111717 DOI: 10.1073/pnas.1608765113] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Horizontal gene transfer (HGT) is the transfer of genetic material across species boundaries and has been a driving force in prokaryotic evolution. HGT involving eukaryotes appears to be much less frequent, and the functional implications of HGT in eukaryotes are poorly understood. We test the hypothesis that parasitic plants, because of their intimate feeding contacts with host plant tissues, are especially prone to horizontal gene acquisition. We sought evidence of HGTs in transcriptomes of three parasitic members of Orobanchaceae, a plant family containing species spanning the full spectrum of parasitic capabilities, plus the free-living Lindenbergia Following initial phylogenetic detection and an extensive validation procedure, 52 high-confidence horizontal transfer events were detected, often from lineages of known host plants and with an increasing number of HGT events in species with the greatest parasitic dependence. Analyses of intron sequences in putative donor and recipient lineages provide evidence for integration of genomic fragments far more often than retro-processed RNA sequences. Purifying selection predominates in functionally transferred sequences, with a small fraction of adaptively evolving sites. HGT-acquired genes are preferentially expressed in the haustorium-the organ of parasitic plants-and are strongly biased in predicted gene functions, suggesting that expression products of horizontally acquired genes are contributing to the unique adaptive feeding structure of parasitic plants.
Collapse
Affiliation(s)
- Zhenzhen Yang
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Yeting Zhang
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Intercollege Graduate Program in Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Loren A Honaas
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Paula E Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Sam Jones
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Christopher R Clarke
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Siming Liu
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Chun Su
- Department of Biology, University of Virginia, Charlottesville, VA 22904
| | - Huiting Zhang
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Naomi S Altman
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Stephan C Schuster
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904
| | - John I Yoder
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - James H Westwood
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Claude W dePamphilis
- Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802;
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Intercollege Graduate Program in Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| |
Collapse
|
21
|
Roquet C, Coissac É, Cruaud C, Boleda M, Boyer F, Alberti A, Gielly L, Taberlet P, Thuiller W, Van Es J, Lavergne S. Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasite Cytinus hypocistis (Cytinaceae). ANNALS OF BOTANY 2016; 118:885-896. [PMID: 27443299 PMCID: PMC5055816 DOI: 10.1093/aob/mcw135] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/09/2016] [Accepted: 05/12/2016] [Indexed: 05/19/2023]
Abstract
Background and Aims Plant plastid genomes are highly conserved in size, gene content and structure; however, parasitic plants are a noticeable exception to this evolutionary stability. Although the evolution of parasites could help to better understand plastome evolution in general, complete plastomes of parasites have been sequenced only for some lineages so far. Here we contribute to filling this gap by providing and analysing the complete plastome sequence of Cytinus hypocistis, the first parasite sequenced for Malvales and a species suspected to have an extremely small genome. Methods We sequenced and assembled de novo the plastid genome of Cytinus hypocistis using a shotgun approach on genomic DNA. Phylogenomic analyses based on coding regions were performed on Malvidae. For each coding region present in Cytinus, we tested for relaxation or intensification of selective pressures in the Cytinus lineage compared with autotrophic Malvales. Key Results Cytinus hypocistis has an extremely divergent genome that is among the smallest sequenced to date (19·4 kb), with only 23 genes and no inverted repeat regions. Phylogenomic analysis confirmed the position of Cytinus within Malvales. All coding regions of Cytinus plastome presented very high substitution rates compared with non-parasitic Malvales. Conclusions Some regions were inferred to be under relaxed negative selection in Cytinus, suggesting that further plastome reduction is occurring due to relaxed purifying selection associated with the loss of photosynthetic activity. On the other hand, increased selection intensity and strong positive selection were detected for rpl22 in the Cytinus lineage, which might indicate an evolutionary role in the host-parasite arms race, a point that needs further research.
Collapse
Affiliation(s)
- Cristina Roquet
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
- *For correspondence. E-mail
| | - Éric Coissac
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Corinne Cruaud
- CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, FR-91057 Evry Cedex, France
| | - Martí Boleda
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Frédéric Boyer
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Adriana Alberti
- CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, FR-91057 Evry Cedex, France
| | - Ludovic Gielly
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Pierre Taberlet
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Wilfried Thuiller
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Jérémie Van Es
- Conservatoire Botanique National Alpin, Domaine de Charance, FR-05000 Gap, France
| | - Sébastien Lavergne
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| |
Collapse
|
22
|
Bellot S, Cusimano N, Luo S, Sun G, Zarre S, Gröger A, Temsch E, Renner SS. Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales. Genome Biol Evol 2016; 8:2214-30. [PMID: 27358425 PMCID: PMC4987112 DOI: 10.1093/gbe/evw147] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cynomoriaceae, one of the last unplaced families of flowering plants, comprise one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a
Cynomorium
specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites’ occurrence.
Cynomorium
has large genomes of 13.70–13.61 (Italy) to 13.95–13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear, plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers.
Collapse
Affiliation(s)
- Sidonie Bellot
- Department of Plant Sciences, Plant Biodiversity Research, Technical University of Munich (TUM), Freising, Germany
| | - Natalie Cusimano
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Germany
| | - Shixiao Luo
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Guangzhou, China
| | - Guiling Sun
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, China
| | - Shahin Zarre
- Department of Plant Sciences, University of Tehran, Iran
| | | | - Eva Temsch
- Department of Systematic and Evolutionary Botany, University of Vienna, Austria
| | - Susanne S Renner
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Germany
| |
Collapse
|
23
|
Wicaksono A, Mursidawati S, Sukamto LA, Teixeira da Silva JA. Rafflesia spp.: propagation and conservation. PLANTA 2016; 244:289-296. [PMID: 27059028 DOI: 10.1007/s00425-016-2512-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 03/26/2016] [Indexed: 06/05/2023]
Abstract
The propagation of Rafflesia spp. is considered to be important for future development of ornamental and other applications. Thus far, the only successful propagation technique has been grafting. This mini-review succinctly emphasizes what is known about Rafflesia species. Members of the genus Rafflesia (Rafflesiaceae), which are holoparasitic plants known to grow on a host vine, Tetrastigma sp., are widely spread from the Malayan Peninsula to various islands throughout Indonesia. The plant's geographical distribution as well as many other aspects pertaining to the basic biology of this genus have still not been studied. The young flower buds and flowers of wild Rafflesia hasseltii Suringar, Rafflesia keithii Meijer and Rafflesia cantleyi Solms-Laubach are used in local (Malaysia and Indonesia) traditional ethnomedicine as wound-healing agents, but currently no formal published research exists to validate this property. To maintain a balance between its ethnomedicinal and ornamental use, and conservation, Rafflesia spp. must be artificially cultivated to prevent overexploitation. A successful method of vegetative propagation is by host grafting using Rafflesia-impregnated Tetrastigma onto the stem of a normal Tetrastigma plant. Due to difficulties with culture contamination in vitro, callus induction was only accomplished in 2010 for the first time when picloram and 2,4-D were added to a basal Murashige and Skoog medium, and the tissue culture of holoparasitic plants continues to be extremely difficult. Seeds harvested from fertile fruit may serve as a possible method to propagate Rafflesia spp. This paper provides a brief synthesis on what is known about research related to Rafflesia spp. The objective is to further stimulate researchers to examine, through rigorous scientific discovery, the mechanisms underlying the ethnomedicinal properties, the flowering mechanisms, and suitable in vitro regeneration protocols that would allow for the fortification of germplasm conservation.
Collapse
Affiliation(s)
- Adhityo Wicaksono
- Laboratory of Plant Breeding and Genetics, Faculty of Agriculture, Universitas Gadjah Mada, Jl. Agro, Bulaksumur, Yogyakarta, 55281, Indonesia
- Laboratory of Paper Coating and Converting, Centre for Functional Material, Åbo Akademi University, Porthaninkatu 3, 20500, Turku, Finland
| | - Sofi Mursidawati
- Center for Plant Conservation, Bogor Botanical Garden, Indonesian Institute of Sciences (LIPI), Jl. Ir. Juanda no. 13, Bogor, 16003, Indonesia
| | - Lazarus A Sukamto
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor Km 46, Cibinong, 16911, Indonesia
| | | |
Collapse
|
24
|
Park S, Grewe F, Zhu A, Ruhlman TA, Sabir J, Mower JP, Jansen RK. Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers. THE NEW PHYTOLOGIST 2015; 208:570-83. [PMID: 25989702 DOI: 10.1111/nph.13467] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/15/2015] [Indexed: 05/20/2023]
Abstract
The exchange of genetic material between cellular organelles through intracellular gene transfer (IGT) or between species by horizontal gene transfer (HGT) has played an important role in plant mitochondrial genome evolution. The mitochondrial genomes of Geraniaceae display a number of unusual phenomena including highly accelerated rates of synonymous substitutions, extensive gene loss and reduction in RNA editing. Mitochondrial DNA sequences assembled for 17 species of Geranium revealed substantial reduction in gene and intron content relative to the ancestor of the Geranium lineage. Comparative analyses of nuclear transcriptome data suggest that a number of these sequences have been functionally relocated to the nucleus via IGT. Evidence for rampant HGT was detected in several Geranium species containing foreign organellar DNA from diverse eudicots, including many transfers from parasitic plants. One lineage has experienced multiple, independent HGT episodes, many of which occurred within the past 5.5 Myr. Both duplicative and recapture HGT were documented in Geranium lineages. The mitochondrial genome of Geranium brycei contains at least four independent HGT tracts that are absent in its nearest relative. Furthermore, G. brycei mitochondria carry two copies of the cox1 gene that differ in intron content, providing insight into contrasting hypotheses on cox1 intron evolution.
Collapse
Affiliation(s)
- Seongjun Park
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
| | - Felix Grewe
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA
| | - Andan Zhu
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
| | - Jamal Sabir
- Department of Biological Science, Biotechnology Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
- Department of Biological Science, Biotechnology Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| |
Collapse
|
25
|
Davis CC, Xi Z. Horizontal gene transfer in parasitic plants. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:14-19. [PMID: 26051213 DOI: 10.1016/j.pbi.2015.05.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/08/2015] [Accepted: 05/12/2015] [Indexed: 06/04/2023]
Abstract
Horizontal gene transfer (HGT) between species has been a major focus of plant evolutionary research during the past decade. Parasitic plants, which establish a direct connection with their hosts, have provided excellent examples of how these transfers are facilitated via the intimacy of this symbiosis. In particular, phylogenetic studies from diverse clades indicate that parasitic plants represent a rich system for studying this phenomenon. Here, HGT has been shown to be astonishingly high in the mitochondrial genome, and appreciable in the nuclear genome. Although explicit tests remain to be performed, some transgenes have been hypothesized to be functional in their recipient species, thus providing a new perspective on the evolution of novelty in parasitic plants.
Collapse
Affiliation(s)
- Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA.
| | - Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA
| |
Collapse
|
26
|
Lam VKY, Soto Gomez M, Graham SW. The Highly Reduced Plastome of Mycoheterotrophic Sciaphila (Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection. Genome Biol Evol 2015; 105:480-494. [PMID: 26170229 DOI: 10.1002/ajb2.1070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/02/2018] [Indexed: 05/03/2023] Open
Abstract
The enigmatic monocot family Triuridaceae provides a potentially useful model system for studying the effects of an ancient loss of photosynthesis on the plant plastid genome, as all of its members are mycoheterotrophic and achlorophyllous. However, few studies have placed the family in a comparative context, and its phylogenetic placement is only partly resolved. It was also unclear whether any taxa in this family have retained a plastid genome. Here, we used genome survey sequencing to retrieve plastid genome data for Sciaphila densiflora (Triuridaceae) and ten autotrophic relatives in the orders Dioscoreales and Pandanales. We recovered a highly reduced plastome for Sciaphila that is nearly colinear with Carludovica palmata, a photosynthetic relative that belongs to its sister group in Pandanales, Cyclanthaceae-Pandanaceae. This phylogenetic placement is well supported and robust to a broad range of analytical assumptions in maximum-likelihood inference, and is congruent with recent findings based on nuclear and mitochondrial evidence. The 28 genes retained in the S. densiflora plastid genome are involved in translation and other nonphotosynthetic functions, and we demonstrate that nearly all of the 18 protein-coding genes are under strong purifying selection. Our study confirms the utility of whole plastid genome data in phylogenetic studies of highly modified heterotrophic plants, even when they have substantially elevated rates of substitution.
Collapse
Affiliation(s)
- Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
27
|
Kannan S, Rogozin IB, Koonin EV. MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes. BMC Evol Biol 2014; 14:237. [PMID: 25421434 PMCID: PMC4256733 DOI: 10.1186/s12862-014-0237-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 11/07/2014] [Indexed: 01/19/2023] Open
Abstract
Background Mitochondria are ubiquitous membranous organelles of eukaryotic cells that evolved from an alpha-proteobacterial endosymbiont and possess a small genome that encompasses from 3 to 106 genes. Accumulation of thousands of mitochondrial genomes from diverse groups of eukaryotes provides an opportunity for a comprehensive reconstruction of the evolution of the mitochondrial gene repertoire. Results Clusters of orthologous mitochondrial protein-coding genes (MitoCOGs) were constructed from all available mitochondrial genomes and complemented with nuclear orthologs of mitochondrial genes. With minimal exceptions, the mitochondrial gene complements of eukaryotes are subsets of the superset of 66 genes found in jakobids. Reconstruction of the evolution of mitochondrial genomes indicates that the mitochondrial gene set of the last common ancestor of the extant eukaryotes was slightly larger than that of jakobids. This superset of mitochondrial genes likely represents an intermediate stage following the loss and transfer to the nucleus of most of the endosymbiont genes early in eukaryote evolution. Subsequent evolution in different lineages involved largely parallel transfer of ancestral endosymbiont genes to the nuclear genome. The intron density in nuclear orthologs of mitochondrial genes typically is nearly the same as in the rest of the genes in the respective genomes. However, in land plants, the intron density in nuclear orthologs of mitochondrial genes is almost 1.5-fold lower than the genomic mean, suggestive of ongoing transfer of functional genes from mitochondria to the nucleus. Conclusions The MitoCOGs are expected to become an important resource for the study of mitochondrial evolution. The nearly complete superset of mitochondrial genes in jakobids likely represents an intermediate stage in the evolution of eukaryotes after the initial, extensive loss and transfer of the endosymbiont genes. In addition, the bacterial multi-subunit RNA polymerase that is encoded in the jakobid mitochondrial genomes was replaced by a single-subunit phage-type RNA polymerase in the rest of the eukaryotes. These results are best compatible with the rooting of the eukaryotic tree between jakobids and the rest of the eukaryotes. The land plants are the only eukaryotic branch in which the gene transfer from the mitochondrial to the nuclear genome appears to be an active, ongoing process. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0237-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sivakumar Kannan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| |
Collapse
|
28
|
Nikolov LA, Tomlinson PB, Manickam S, Endress PK, Kramer EM, Davis CC. Holoparasitic Rafflesiaceae possess the most reduced endophytes and yet give rise to the world's largest flowers. ANNALS OF BOTANY 2014; 114:233-42. [PMID: 24942001 PMCID: PMC4111398 DOI: 10.1093/aob/mcu114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 05/02/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Species in the holoparasitic plant family Rafflesiaceae exhibit one of the most highly modified vegetative bodies in flowering plants. Apart from the flower shoot and associated bracts, the parasite is a mycelium-like endophyte living inside their grapevine hosts. This study provides a comprehensive treatment of the endophytic vegetative body for all three genera of Rafflesiaceae (Rafflesia, Rhizanthes and Sapria), and reports on the cytology and development of the endophyte, including its structural connection to the host, shedding light on the poorly understood nature of this symbiosis. METHODS Serial sectioning and staining with non-specific dyes, periodic-Schiff's reagent and aniline blue were employed in order to characterize the structure of the endophyte across a phylogenetically diverse sampling. KEY RESULTS A previously identified difference in the nuclear size between Rafflesiaceae endophytes and their hosts was used to investigate the morphology and development of the endophytic body. The endophytes generally comprise uniseriate filaments oriented radially within the host root. The emergence of the parasite from the host during floral development is arrested in some cases by an apparent host response, but otherwise vegetative growth does not appear to elicit suppression by the host. CONCLUSIONS Rafflesiaceae produce greatly reduced and modified vegetative bodies even when compared with the other holoparasitic angiosperms once grouped with Rafflesiaceae, which possess some vegetative differentiation. Based on previous studies of seeds together with these findings, it is concluded that the endophyte probably develops directly from a proembryo, and not from an embryo proper. Similarly, the flowering shoot arises directly from the undifferentiated endophyte. These filaments produce a protocorm in which a shoot apex originates endogenously by formation of a secondary morphological surface. This degree of modification to the vegetative body is exceptional within angiosperms and warrants additional investigation. Furthermore, the study highlights a mechanical isolation mechanism by which the host may defend itself from the parasite.
Collapse
Affiliation(s)
- Lachezar A Nikolov
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
| | - P B Tomlinson
- The Kampong, National Tropical Botanical Garden, 4013 Douglas Road, Miami, FL 33133, USA
| | - Sugumaran Manickam
- Rimba Ilmu Botanic Garden, Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia and
| | - Peter K Endress
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
| |
Collapse
|
29
|
Nikolov LA, Staedler YM, Manickam S, Schönenberger J, Endress PK, Kramer EM, Davis CC. Floral structure and development in Rafflesiaceae with emphasis on their exceptional gynoecia. AMERICAN JOURNAL OF BOTANY 2014; 101:225-243. [PMID: 24509798 DOI: 10.3732/ajb.1400009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY The holoparasitic plant family Rafflesiaceae include the world's largest flowers. Despite their iconic status, relatively little is known about the morphology and development of their flowers. A recent study clarified the organization of the outer (sterile) floral organs, surprisingly revealing that their distinctive floral chambers arose via different developmental pathways in the two major genera of the family. Here, we expand that research to investigate the structure and development of the reproductive organs of Rafflesiaceae. METHODS Serial sectioning, scanning electron microscopy, and x-ray tomography of floral buds were employed to reconstruct the structure and development of all three Rafflesiaceae genera. KEY RESULTS Unlike most angiosperms, which form their shoot apex from the primary morphological surface, the shoot apex of Rafflesiaceae instead forms secondarily via internal cell separation (schizogeny) along the distal boundary of the host-parasite interface. Similarly, the radially directed ovarial clefts of the gynoecium forms via schizogeny within solid tissue, and no carpels are initiated from the floral apex. CONCLUSIONS The development of the shoot apex and gynoecium of Rafflesiaceae are highly unusual. Although secondary formation of the morphological surface from the shoot apex has been documented in other plant groups, secondary derivation of the inner gynoecium surface is otherwise unknown. Both features are likely synapomorphies of Rafflesiaceae. The secondary derivation of the shoot apex may protect the developing floral shoot as it emerges from within dense host tissue. The secondary formation of the ovarial clefts may generate the extensive placental area necessary to produce hundreds of thousands of ovules.
Collapse
Affiliation(s)
- Lachezar A Nikolov
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, Massachusetts 02138 USA
| | | | | | | | | | | | | |
Collapse
|
30
|
Molina J, Hazzouri KM, Nickrent D, Geisler M, Meyer RS, Pentony MM, Flowers JM, Pelser P, Barcelona J, Inovejas SA, Uy I, Yuan W, Wilkins O, Michel CI, LockLear S, Concepcion GP, Purugganan MD. Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae). Mol Biol Evol 2014; 31:793-803. [PMID: 24458431 PMCID: PMC3969568 DOI: 10.1093/molbev/msu051] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability to undertake photosynthesis. With short-read sequencing technology, we assembled a draft sequence of the mitochondrial genome of Rafflesia lagascae Blanco, a species endemic to the Philippine island of Luzon, with ∼350× sequencing depth coverage. Using multiple approaches, however, we were only able to identify small fragments of plastid sequences at low coverage depth (<2×) and could not recover any substantial portion of a chloroplast genome. The gene fragments we identified included photosynthesis and energy production genes (atp, ndh, pet, psa, psb, rbcL), ribosomal RNA genes (rrn16, rrn23), ribosomal protein genes (rps7, rps11, rps16), transfer RNA genes, as well as matK, accD, ycf2, and multiple nongenic regions from the inverted repeats. None of the identified plastid gene sequences had intact reading frames. Phylogenetic analysis suggests that ∼33% of these remnant plastid genes may have been horizontally transferred from the host plant genus Tetrastigma with the rest having ambiguous phylogenetic positions (<50% bootstrap support), except for psaB that was strongly allied with the plastid homolog in Nicotiana. Our inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches—despite success in identifying and developing a draft assembly of the much larger mitochondrial genome—suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastid genome, or if present is found in cryptic form at very low levels.
Collapse
Affiliation(s)
- Jeanmaire Molina
- Department of Biology, Long Island University, Brooklyn
- Center for Genomics and Systems Biology, New York University
- *Corresponding author: E-mail: ;
| | - Khaled M. Hazzouri
- Center for Genomics and Systems Biology, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Daniel Nickrent
- Department of Plant Biology, Southern Illinois University, Carbondale
| | - Matthew Geisler
- Department of Plant Biology, Southern Illinois University, Carbondale
| | - Rachel S. Meyer
- Center for Genomics and Systems Biology, New York University
| | - Melissa M. Pentony
- Computational Genomics Core, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Jonathan M. Flowers
- Center for Genomics and Systems Biology, New York University
- Center for Genomics and Systems Biology, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Pieter Pelser
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Julie Barcelona
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Samuel Alan Inovejas
- Electron Microscope Facility, St. Luke’s Medical Center, Quezon City, Philippines
| | - Iris Uy
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City, Philippines
| | - Wei Yuan
- Center for Genomics and Systems Biology, New York University
| | - Olivia Wilkins
- Center for Genomics and Systems Biology, New York University
| | | | | | - Gisela P. Concepcion
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City, Philippines
| | - Michael D. Purugganan
- Center for Genomics and Systems Biology, New York University
- Center for Genomics and Systems Biology, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates
- *Corresponding author: E-mail: ;
| |
Collapse
|
31
|
Le Péchon T, Gigord LDB. On the relevance of molecular tools for taxonomic revision in Malvales, Malvaceae s.l., and Dombeyoideae. Methods Mol Biol 2014; 1115:337-363. [PMID: 24415483 DOI: 10.1007/978-1-62703-767-9_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this article, we present an overview of changes to the taxonomy of Malvales. In traditional classifications, this order was variously circumscribed as including four main families (i.e., Malvaceae, Bombacaceae, Sterculiaceae, and Tiliaceae, also known now as "Core Malvales"), but major disagreements existed between different taxonomic treatments. Contributions from molecular data, new morpho-anatomical data, and progress in methodological approaches have recently led to a new broader concept of this order (namely, "expanded Malvales"). Now, expanded Malvales includes ten families (Neuradaceae, Thymelaeaceae, Sphaerosepalaceae, Bixaceae, Cistaceae, Sarcolaenaceae, Dipterocarpaceae, Cytinaceae, Muntingiaceae, Malvaceae s.l.) distributed among seven monophyletic lineages. All these families were previously considered to have malvalean affinities in some traditional treatments, except the holoparasitic and highly modified Cytinaceae. Although molecular evidence has clarified the Malvales taxonomy, the phylogenetic positions of Sarcolaenaceae, Thymelaeaceae, and Sphaerosepalaceae are still controversial and need new analyses focusing specifically on these families to assess their phylogenetic placement and their morphological evolution.In a phylogenetic context, molecular data combined with recent examination of morphological characters supported the hypothesis of a common origin of "core Malvales." However, these analyses also showed that the former families but Malvaceae s.s. were paraphyletic or polyphyletic. As a consequence, recent taxonomic treatments grouped taxa formerly included in "Core Malvales" in a broader concept of Malvaceae s.l. Additionally, the intrafamilial taxonomy has been deeply modified, and in its present circumscription, Malvaceae includes nine subfamilies (Grewioideae, Byttnerioideae, Sterculioideae, Dombeyoideae, Brownlowioideae, Tilioideae, Bombacoideae, Malvoideae, Helicteroideae) in two main lineages. Phylogenetic studies on subfamilial rearrangements have focused on the relationships between emblematic taxa such as Bombacoideae and Malvoideae (which form together the /Malvatheca lineage). However, our understanding of the phylogenetic relationships among and within taxa of the other subfamilies (e.g., Dombeyoideae, Tilioideae, and Sterculioideae) has not followed at the same pace. Despite recent investigations, the relationships between the subfamilies of Malvaceae s.l. remain controversial. As an example of these taxonomic issues, we review the systematic studies on Dombeyoideae, with special emphasis on taxa endemic to the Mascarene archipelago (Indian Ocean). Recent investigations have shown that several island endemic genera such as Trochetia, Ruizia, and Astiria (endemic to the Mascarenes) are nested within the mega-genus Dombeya. Consequently, the current taxonomy of this genus does not match the phylogeny and should be modified. Therefore, we propose three possible taxonomic schemes as part of an ongoing revision of the Mascarene Dombeyoideae. However, these taxonomic rearrangements should only be made after a broader study of the diversity in Madagascar and adjacent areas. This broader approach shall avoid possibly multiple and contradictory taxonomic revisions of restricted regions if they were each studied in isolation.
Collapse
Affiliation(s)
- Timothée Le Péchon
- Chinese Academy of Sciences, Chengdu Institute of Biology, Chengdu, Sichuan, China
| | | |
Collapse
|
32
|
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] [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.
Collapse
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)
| |
Collapse
|
33
|
Wijayawardena BK, Minchella DJ, DeWoody JA. Hosts, parasites, and horizontal gene transfer. Trends Parasitol 2013; 29:329-38. [DOI: 10.1016/j.pt.2013.05.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 12/16/2022]
|
34
|
Bromham L, Cowman PF, Lanfear R. Parasitic plants have increased rates of molecular evolution across all three genomes. BMC Evol Biol 2013; 13:126. [PMID: 23782527 PMCID: PMC3694452 DOI: 10.1186/1471-2148-13-126] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/05/2013] [Indexed: 11/26/2022] Open
Abstract
Background Theoretical models and experimental evidence suggest that rates of molecular evolution could be raised in parasitic organisms compared to non-parasitic taxa. Parasitic plants provide an ideal test for these predictions, as there are at least a dozen independent origins of the parasitic lifestyle in angiosperms. Studies of a number of parasitic plant lineages have suggested faster rates of molecular evolution, but the results of some studies have been mixed. Comparative analysis of all parasitic plant lineages, including sequences from all three genomes, is needed to examine the generality of the relationship between rates of molecular evolution and parasitism in plants. Results We analysed DNA sequence data from the mitochondrial, nuclear and chloroplast genomes for 12 independent evolutionary origins of parasitism in angiosperms. We demonstrated that parasitic lineages have a faster rate of molecular evolution than their non-parasitic relatives in sequences for all three genomes, for both synonymous and nonsynonymous substitutions. Conclusions Our results prove that raised rates of molecular evolution are a general feature of parasitic plants, not confined to a few taxa or specific genes. We discuss possible causes for this relationship, including increased positive selection associated with host-parasite arms races, relaxed selection, reduced population size or repeated bottlenecks, increased mutation rates, and indirect causal links with generation time and body size. We find no evidence that faster rates are due to smaller effective populations sizes or changes in selection pressure. Instead, our results suggest that parasitic plants have a higher mutation rate than their close non-parasitic relatives. This may be due to a direct connection, where some aspect of the parasitic lifestyle drives the evolution of raised mutation rates. Alternatively, this pattern may be driven by an indirect connection between rates and parasitism: for example, parasitic plants tend to be smaller than their non-parasitic relatives, which may result in more cell generations per year, thus a higher rate of mutations arising from DNA copy errors per unit time. Demonstration that adoption of a parasitic lifestyle influences the rate of genomic evolution is relevant to attempts to infer molecular phylogenies of parasitic plants and to estimate their evolutionary divergence times using sequence data.
Collapse
Affiliation(s)
- Lindell Bromham
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, A.C.T. 0200, Australia.
| | | | | |
Collapse
|
35
|
Xi Z, Wang Y, Bradley RK, Sugumaran M, Marx CJ, Rest JS, Davis CC. Massive mitochondrial gene transfer in a parasitic flowering plant clade. PLoS Genet 2013; 9:e1003265. [PMID: 23459037 PMCID: PMC3573108 DOI: 10.1371/journal.pgen.1003265] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/07/2012] [Indexed: 11/18/2022] Open
Abstract
Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Parasitic plants have provided the strongest evidence of HGT, which appears to be facilitated by the intimate physical association between the parasites and their hosts. A recent phylogenomic study demonstrated that in the holoparasite Rafflesia cantleyi (Rafflesiaceae), whose close relatives possess the world's largest flowers, about 2.1% of nuclear gene transcripts were likely acquired from its obligate host. Here, we used next-generation sequencing to obtain the 38 protein-coding and ribosomal RNA genes common to the mitochondrial genomes of angiosperms from R. cantleyi and five additional species, including two of its closest relatives and two host species. Strikingly, our phylogenetic analyses conservatively indicate that 24%–41% of these gene sequences show evidence of HGT in Rafflesiaceae, depending on the species. Most of these transgenic sequences possess intact reading frames and are actively transcribed, indicating that they are potentially functional. Additionally, some of these transgenes maintain synteny with their donor and recipient lineages, suggesting that native genes have likely been displaced via homologous recombination. Our study is the first to comprehensively assess the magnitude of HGT in plants involving a genome (i.e., mitochondria) and a species interaction (i.e., parasitism) where it has been hypothesized to be potentially rampant. Our results establish for the first time that, although the magnitude of HGT involving nuclear genes is appreciable in these parasitic plants, HGT involving mitochondrial genes is substantially higher. This may represent a more general pattern for other parasitic plant clades and perhaps more broadly for angiosperms. Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Here, using phylogenomic approaches, we demonstrate that as much as ∼40% of the mitochondrial genes in the parasitic plant species Rafflesiaceae are acquired from their hosts via HGT. These transgenes are likely functional in their recipient species and in some cases appear to have displaced native copies in the same genomic location. These results establish for the first time that, although the magnitude of HGT involving nuclear genes is appreciable in parasitic plants, HGT involving mitochondrial genes is substantially higher.
Collapse
Affiliation(s)
- Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
- Department of Ecology and Evolutionary Biology, School of Life Science, Fudan University, Shanghai, China
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - M. Sugumaran
- Rimba Ilmu Botanic Garden, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Christopher J. Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Joshua S. Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
36
|
Braukmann T, Kuzmina M, Stefanovic S. Plastid genome evolution across the genus Cuscuta (Convolvulaceae): two clades within subgenus Grammica exhibit extensive gene loss. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:977-89. [PMID: 23349139 PMCID: PMC3580819 DOI: 10.1093/jxb/ers391] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The genus Cuscuta (Convolvulaceae, the morning glory family) is one of the most intensely studied lineages of parasitic plants. Whole plastome sequencing of four Cuscuta species has demonstrated changes to both plastid gene content and structure. The presence of photosynthetic genes under purifying selection indicates that Cuscuta is cryptically photosynthetic. However, the tempo and mode of plastid genome evolution across the diversity of this group (~200 species) remain largely unknown. A comparative investigation of plastid genome content, grounded within a phylogenetic framework, was conducted using a slot-blot Southern hybridization approach. Cuscuta was extensively sampled (~56% of species), including groups previously suggested to possess more altered plastomes compared with other members of this genus. A total of 56 probes derived from all categories of protein-coding genes, typically found within the plastomes of flowering plants, were used. The results indicate that two clades within subgenus Grammica (clades 'O' and 'K') exhibit substantially more plastid gene loss relative to other members of Cuscuta. All surveyed members of the 'O' clade show extensive losses of plastid genes from every category of genes typically found in the plastome, including otherwise highly conserved small and large ribosomal subunits. The extent of plastid gene losses within this clade is similar in magnitude to that observed previously in some non-asterid holoparasites, in which the very presence of a plastome has been questioned. The 'K' clade also exhibits considerable loss of plastid genes. Unlike in the 'O' clade, in which all species seem to be affected, the losses in clade 'K' progress phylogenetically, following a pattern consistent with the Evolutionary Transition Series hypothesis. This clade presents an ideal opportunity to study the reduction of the plastome of parasites 'in action'. The widespread plastid gene loss in these two clades is hypothesized to be a consequence of the complete loss of photosynthesis. Additionally, taxa that would be the best candidates for entire plastome sequencing are identified in order to investigate further the loss of photosynthesis and reduction of the plastome within Cuscuta.
Collapse
Affiliation(s)
- Thomas Braukmann
- Department of Biology, University of Toronto-Mississauga, 3359 Mississauga Rd. N, Mississauga, Ontario, Canada.
| | | | | |
Collapse
|
37
|
Hardy NB, Cook LG. Testing for Ecological Limitation of Diversification: A Case Study Using Parasitic Plants. Am Nat 2012; 180:438-49. [DOI: 10.1086/667588] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
38
|
Xi Z, Bradley RK, Wurdack KJ, Wong K, Sugumaran M, Bomblies K, Rest JS, Davis CC. Horizontal transfer of expressed genes in a parasitic flowering plant. BMC Genomics 2012; 13:227. [PMID: 22681756 PMCID: PMC3460754 DOI: 10.1186/1471-2164-13-227] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/08/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent studies have shown that plant genomes have potentially undergone rampant horizontal gene transfer (HGT). In plant parasitic systems HGT appears to be facilitated by the intimate physical association between the parasite and its host. HGT in these systems has been invoked when a DNA sequence obtained from a parasite is placed phylogenetically very near to its host rather than with its closest relatives. Studies of HGT in parasitic plants have relied largely on the fortuitous discovery of gene phylogenies that indicate HGT, and no broad systematic search for HGT has been undertaken in parasitic systems where it is most expected to occur. RESULTS We analyzed the transcriptomes of the holoparasite Rafflesia cantleyi Solms-Laubach and its obligate host Tetrastigma rafflesiae Miq. using phylogenomic approaches. Our analyses show that several dozen actively transcribed genes, most of which appear to be encoded in the nuclear genome, are likely of host origin. We also find that hundreds of vertically inherited genes (VGT) in this parasitic plant exhibit codon usage properties that are more similar to its host than to its closest relatives. CONCLUSIONS Our results establish for the first time a substantive number of HGTs in a plant host-parasite system. The elevated rate of unidirectional host-to- parasite gene transfer raises the possibility that HGTs may provide a fitness benefit to Rafflesia for maintaining these genes. Finally, a similar convergence in codon usage of VGTs has been shown in microbes with high HGT rates, which may help to explain the increase of HGTs in these parasitic plants.
Collapse
Affiliation(s)
- Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Braukmann T, Stefanović S. Plastid genome evolution in mycoheterotrophic Ericaceae. PLANT MOLECULAR BIOLOGY 2012; 79:5-20. [PMID: 22442035 DOI: 10.1007/s11103-012-9884-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2011] [Accepted: 01/12/2012] [Indexed: 05/09/2023]
Abstract
Unlike parasitic plants, which are linked to their hosts directly through haustoria, mycoheterotrophic (MHT) plants derive all or part of their water and nutrients from autothrophs via fungal mycorrhizal intermediaries. Ericaceae, the heather family, are a large and diverse group of plants known to form elaborate symbiotic relationships with mycorrhizal fungi. Using PHYA sequence data, we first investigated relationships among mycoheterotrophic Ericaceae and their close autotrophic relatives. Phylogenetic results suggest a minimum of two independent origins of MHT within this family. Additionally, a comparative investigation of plastid genomes (plastomes) grounded within this phylogenetic framework was conducted using a slot-blot Southern hybridization approach. This survey encompassed numerous lineages of Ericaceae with different life histories and trophic levels, including multiple representatives from mixotrophic Pyroleae and fully heterotrophic Monotropeae and Pterosporeae. Fifty-four probes derived from all categories of protein coding genes typically found within the plastomes of flowering plants were used. Our results indicate that the holo-mycoheterotrophic Ericaceae exhibit extensive loss of genes relating to photosynthetic function and expression of the plastome but retain genes with possible functions outside photosynthesis. Mixotrophic taxa tend to retain most genes relating to photosynthetic functions but are varied regarding the plastid ndh gene content. This investigation extends previous inferences that the loss of the NDH complex occurs prior to becoming holo-heterotrophic and it shows that the pattern of gene losses among mycoheterotrophic Ericaceae is similar to that of haustorial parasites. Additionally, we identify the most desirable candidate species for entire plastome sequencing.
Collapse
Affiliation(s)
- Thomas Braukmann
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada.
| | | |
Collapse
|
40
|
Su HJ, Murata J, Hu JM. Morphology and phylogenetics of two holoparasitic plants, Balanophora japonica and Balanophora yakushimensis (Balanophoraceae), and their hosts in Taiwan and Japan. JOURNAL OF PLANT RESEARCH 2012; 125:317-326. [PMID: 21894574 DOI: 10.1007/s10265-011-0447-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 08/02/2011] [Indexed: 05/31/2023]
Abstract
Balanophora japonica and B. yakushimensis are two putatively agamospermic taxa previously reported from southern Japan. Their inflorescences superficially represent those of B. laxiflora and B. fungosa. In this study we confirmed their presence in Taiwan by morphological and phylogenetic analysis using nuclear 18S rDNA and nrITS sequences with related taxa. B. japonica, B. yakushimensis, and B. laxiflora formed a well-supported clade that is distinct from other Balanophora. All three taxa also show considerable differences on morphological and nucleotide sequence differences, therefore the name of B. yakushimensis is retained. The results provide new insights on the intrageneric classification of Balanophora and suggest the positioning of female flowers should be down-weighted. We also successfully identify the hosts of B. japonica and B. yakushimensis by amplifying chloroplast matK sequences from the connected root tissues. The results showed that B. japonica parasitizes on Symplocos species, and that B. yakushimensis parasitizes on Distylium racemosum in Japan and Schima superba in Taiwan's population.
Collapse
Affiliation(s)
- Huei-Jiun Su
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Rm 1227, Life Science Building, 1 Sec. 4, Roosevelt Road, Taipei 106, Taiwan
| | | | | |
Collapse
|
41
|
Rothfels CJ, Larsson A, Kuo LY, Korall P, Chiou WL, Pryer KM. Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns. Syst Biol 2012; 61:490-509. [DOI: 10.1093/sysbio/sys001] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Carl J. Rothfels
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Anders Larsson
- Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Li-Yaung Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Petra Korall
- Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Wen-Liang Chiou
- Botanical Garden Division, Taiwan Forestry Research Institute, 53 Nan-hai Road, Taipei 10066, Taiwan
| | - Kathleen M. Pryer
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| |
Collapse
|
42
|
Horizontal Gene Transfer in Eukaryotes: Fungi-to-Plant and Plant-to-Plant Transfers of Organellar DNA. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2012. [DOI: 10.1007/978-94-007-2920-9_10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
43
|
Sanchez-Puerta MV, Abbona CC, Zhuo S, Tepe EJ, Bohs L, Olmstead RG, Palmer JD. Multiple recent horizontal transfers of the cox1 intron in Solanaceae and extended co-conversion of flanking exons. BMC Evol Biol 2011; 11:277. [PMID: 21943226 PMCID: PMC3192709 DOI: 10.1186/1471-2148-11-277] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 09/27/2011] [Indexed: 12/02/2022] Open
Abstract
Background The most frequent case of horizontal transfer in plants involves a group I intron in the mitochondrial gene cox1, which has been acquired via some 80 separate plant-to-plant transfer events among 833 diverse angiosperms examined. This homing intron encodes an endonuclease thought to promote the intron's promiscuous behavior. A promising experimental approach to study endonuclease activity and intron transmission involves somatic cell hybridization, which in plants leads to mitochondrial fusion and genome recombination. However, the cox1 intron has not yet been found in the ideal group for plant somatic genetics - the Solanaceae. We therefore undertook an extensive survey of this family to find members with the intron and to learn more about the evolutionary history of this exceptionally mobile genetic element. Results Although 409 of the 426 species of Solanaceae examined lack the cox1 intron, it is uniformly present in three phylogenetically disjunct clades. Despite strong overall incongruence of cox1 intron phylogeny with angiosperm phylogeny, two of these clades possess nearly identical intron sequences and are monophyletic in intron phylogeny. These two clades, and possibly the third also, contain a co-conversion tract (CCT) downstream of the intron that is extended relative to all previously recognized CCTs in angiosperm cox1. Re-examination of all published cox1 genes uncovered additional cases of extended co-conversion and identified a rare case of putative intron loss, accompanied by full retention of the CCT. Conclusions We infer that the cox1 intron was separately and recently acquired by at least three different lineages of Solanaceae. The striking identity of the intron and CCT from two of these lineages suggests that one of these three intron captures may have occurred by a within-family transfer event. This is consistent with previous evidence that horizontal transfer in plants is biased towards phylogenetically local events. The discovery of extended co-conversion suggests that other cox1 conversions may be longer than realized but obscured by the exceptional conservation of plant mitochondrial sequences. Our findings provide further support for the rampant-transfer model of cox1 intron evolution and recommend the Solanaceae as a model system for the experimental analysis of cox1 intron transfer in plants.
Collapse
|
44
|
Yang Y, Maruyama S, Sekimoto H, Sakayama H, Nozaki H. An extended phylogenetic analysis reveals ancient origin of "non-green" phosphoribulokinase genes from two lineages of "green" secondary photosynthetic eukaryotes: Euglenophyta and Chlorarachniophyta. BMC Res Notes 2011; 4:330. [PMID: 21899749 PMCID: PMC3224528 DOI: 10.1186/1756-0500-4-330] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 09/07/2011] [Indexed: 01/29/2023] Open
Abstract
Background Euglenophyta and Chlorarachniophyta are groups of photosynthetic eukaryotes harboring secondary plastids of distinct green algal origins. Although previous phylogenetic analyses of genes encoding Calvin cycle enzymes demonstrated the presence of genes apparently not derived from green algal endosymbionts in the nuclear genomes of Euglena gracilis (Euglenophyta) and Bigelowiella natans (Chlorarachniophyta), the origins of these "non-green" genes in "green" secondary phototrophs were unclear due to the limited taxon sampling. Results Here, we sequenced five new phosphoribulokinase (PRK) genes (from one euglenophyte, two chlorarachniophytes, and two glaucophytes) and performed an extended phylogenetic analysis of the genes based on a phylum-wide taxon sampling from various photosynthetic eukaryotes. Our phylogenetic analyses demonstrated that the PRK sequences form two genera of Euglenophyta formed a robust monophyletic group within a large clade including stramenopiles, haptophytes and a cryptophyte, and three genera of Chlorarachniophyta were placed within the red algal clade. These "non-green" affiliations were supported by the taxon-specific insertion/deletion sequences in the PRK alignment, especially between euglenophytes and stramenopiles. In addition, phylogenetic analysis of another Calvin cycle enzyme, plastid-targeted sedoheptulose-bisphosphatase (SBP), showed that the SBP sequences from two genera of Chlorarachniophyta were positioned within a red algal clade. Conclusions Our results suggest that PRK genes may have been transferred from a "stramenopile" ancestor to Euglenophyta and from a "red algal" ancestor to Chlorarachniophyta before radiation of extant taxa of these two "green" secondary phototrophs. The presence of two of key Calvin cycle enzymes, PRK and SBP, of red algal origins in Chlorarachniophyta indicate that the contribution of "non-green" algae to the plastid proteome in the "green" secondary phototrophs is more significant than ever thought. These "non-green" putative plastid-targeted enzymes from Chlorarachniophyta are likely to have originated from an ancestral red alga via horizontal gene transfer, or from a cryptic red algal endosymbiosis in the common ancestor of the extant chlorarachniophytes.
Collapse
Affiliation(s)
- Yi Yang
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan.
| | | | | | | | | |
Collapse
|
45
|
Lemaire B, Huysmans S, Smets E, Merckx V. Rate accelerations in nuclear 18S rDNA of mycoheterotrophic and parasitic angiosperms. JOURNAL OF PLANT RESEARCH 2011; 124:561-76. [PMID: 21188459 PMCID: PMC3159761 DOI: 10.1007/s10265-010-0395-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 10/25/2010] [Indexed: 05/08/2023]
Abstract
Rate variation in genes from all three genomes has been observed frequently in plant lineages with a parasitic and mycoheterotrophic mode of life. While the loss of photosynthetic ability leads to a relaxation of evolutionary constraints in genes involved in the photosynthetic apparatus, it remains to be determined how prevalent increased substitution rates are in nuclear DNA of non-photosynthetic angiosperms. In this study we infer rates of molecular evolution of 18S rDNA of all parasitic and mycoheterotorphic plant families (except Lauraceae and Polygalaceae) using relative rate tests. In several holoparasitic and mycoheterotrophic plant lineages extremely high substitution rates are observed compared to other photosynthetic angiosperms. The position and frequency of these substitutions have been identified to understand the mutation dynamics of 18S rRNA in achlorophyllous plants. Despite the presence of significantly elevated substitution rates, very few mutations occur in major functional and structural regions of the small ribosomal molecule, providing evidence that the efficiency of the translational apparatus in non-photosynthetic plants has not been affected.
Collapse
Affiliation(s)
- Benny Lemaire
- Laboratory of Plant Systematics, Institute of Botany and Microbiology, K.U. Leuven, Kasteelpark Arenberg, Belgium.
| | | | | | | |
Collapse
|
46
|
Talianova M, Janousek B. What can we learn from tobacco and other Solanaceae about horizontal DNA transfer? AMERICAN JOURNAL OF BOTANY 2011; 98:1231-42. [PMID: 21795732 DOI: 10.3732/ajb.1000370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In eukaryotic organisms, horizontal gene transfer (HGT) is regarded as an important though infrequent source of reticulate evolution. Many confirmed instances of natural HGT involving multicellular eukaryotes come from flowering plants. This review intends to provide a synthesis of present knowledge regarding HGT in higher plants, with an emphasis on tobacco and other species in the Solanaceae family because there are numerous detailed reports concerning natural HGT events, involving various donors, in this family. Moreover, in-depth experimental studies using transgenic tobacco are of great importance for understanding this process. Valuable insights are offered concerning the mechanisms of HGT, the adaptive role and regulation of natural transgenes, and new routes for gene trafficking. With an increasing amount of data on HGT, a synthetic view is beginning to emerge.
Collapse
Affiliation(s)
- Martina Talianova
- Department of Plant Developmental Genetics, Institute of Biophysics AS CR, Kralovopolska 135, 612 65, Brno, Czech Republic.
| | | |
Collapse
|
47
|
Soltis DE, Smith SA, Cellinese N, Wurdack KJ, Tank DC, Brockington SF, Refulio-Rodriguez NF, Walker JB, Moore MJ, Carlsward BS, Bell CD, Latvis M, Crawley S, Black C, Diouf D, Xi Z, Rushworth CA, Gitzendanner MA, Sytsma KJ, Qiu YL, Hilu KW, Davis CC, Sanderson MJ, Beaman RS, Olmstead RG, Judd WS, Donoghue MJ, Soltis PS. Angiosperm phylogeny: 17 genes, 640 taxa. AMERICAN JOURNAL OF BOTANY 2011; 98:704-30. [PMID: 21613169 DOI: 10.3732/ajb.1000404] [Citation(s) in RCA: 351] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
PREMISE OF THE STUDY Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. METHODS We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid). KEY RESULTS Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae]. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, Caryophyllales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support. CONCLUSIONS Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.
Collapse
Affiliation(s)
- Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida 32611-8525, USA. .edu
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Mower JP, Stefanović S, Hao W, Gummow JS, Jain K, Ahmed D, Palmer JD. Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes. BMC Biol 2010; 8:150. [PMID: 21176201 PMCID: PMC3022774 DOI: 10.1186/1741-7007-8-150] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 12/22/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. Previous results indicate that parasitic plants are often involved as either transfer donors or recipients, suggesting that direct contact between parasite and host facilitates genetic transfer among plants. RESULTS In order to uncover the mechanistic details of plant-to-plant HGT, the extent and evolutionary fate of transfer was investigated between two groups: the parasitic genus Cuscuta and a small clade of Plantago species. A broad polymerase chain reaction (PCR) survey of mitochondrial genes revealed that at least three genes (atp1, atp6 and matR) were recently transferred from Cuscuta to Plantago. Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. Patterns of sequence evolution suggest that these foreign genes degraded into pseudogenes shortly after transfer and reverse transcription (RT)-PCR analyses demonstrate that none are detectably transcribed. Three cases of gene conversion were detected between native and foreign copies of the atp1 gene. The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. However, samplings of multiple individuals from two of the three species in the recipient Plantago clade revealed complex and perplexing phylogenetic discrepancies and patterns of sequence divergence for all three of the foreign genes. CONCLUSIONS This study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. The discovery of gene conversion between co-resident foreign and native mitochondrial copies suggests that transferred genes may be evolutionarily important in generating mitochondrial genetic diversity. Finally, the complex relationships within each lineage of transferred genes imply a surprisingly complicated history of these genes in Plantago subsequent to their acquisition via HGT and this history probably involves some combination of additional transfers (including intracellular transfer), gene duplication, differential loss and mutation-rate variation. Unravelling this history will probably require sequencing multiple mitochondrial and nuclear genomes from Plantago. See Commentary: http://www.biomedcentral.com/1741-7007/8/147.
Collapse
Affiliation(s)
- Jeffrey P Mower
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana 47403, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Saša Stefanović
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana 47403, USA
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Weilong Hao
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana 47403, USA
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5G 1L5, Canada
| | - Julie S Gummow
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana 47403, USA
| | - Kanika Jain
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Dana Ahmed
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Jeffrey D Palmer
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana 47403, USA
| |
Collapse
|
49
|
Bendiksby M, Schumacher T, Gussarova G, Nais J, Mat-Salleh K, Sofiyanti N, Madulid D, Smith SA, Barkman T. Elucidating the evolutionary history of the Southeast Asian, holoparasitic, giant-flowered Rafflesiaceae: Pliocene vicariance, morphological convergence and character displacement. Mol Phylogenet Evol 2010; 57:620-33. [DOI: 10.1016/j.ympev.2010.08.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 07/31/2010] [Accepted: 08/09/2010] [Indexed: 11/30/2022]
|
50
|
Filipowicz N, Renner SS. The worldwide holoparasitic Apodanthaceae confidently placed in the Cucurbitales by nuclear and mitochondrial gene trees. BMC Evol Biol 2010; 10:219. [PMID: 20663122 PMCID: PMC3055242 DOI: 10.1186/1471-2148-10-219] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 07/21/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Of the c. 450 families of flowering plants, only two are left "unplaced" in the most recent APG classification of angiosperms. One of these is the Apodanthaceae, a clade of c. 19 holoparasitic species in two or three genera occurring in North and South America, Africa, the Near East, and Australia. Because of lateral gene transfer between Apodanthaceae and their hosts it has been difficult to infer the family's true closest relatives. RESULTS Here we report a phylogenetic analysis of 16 accessions representing six species of Apodanthaceae from the United States, Chile, Iran, and Australia, using the mitochondrial matR gene and the nuclear 18S gene. Data matrices include 190 matR sequences from up to 95 families in 39 orders of flowering plants and 197 18S sequences from 101 families representing the 16 orders of rosids. Analyses were performed at the nucleotide and at the amino acid level. Both gene trees agree with angiosperm phylogenies found in other studies using more genes. Apodanthaceae and the seven families of the order Cucurbitales form a clade with 100% bootstrap support from matR and 56% from 18 S. In addition, the Apodanthaceae and Cucurbitales matR gene sequences uniquely share two non-synonymous codon changes and one synonymous change, as well as a codon insertion, already found by Barkman et al. (2007). CONCLUSIONS Apodanthaceae belong in the Cucurbitales with which they share inferior ovaries, parietal placentation and a dioecious mating system, traits that are ancestral in Cucurbitales and which can now be interpreted as possible synapomorphies of an enlarged order Cucurbitales. The occurrence of Apodanthaceae in the Americas, Africa, the Near East, and Australia, and their adaptation to distantly related host species in the Fabaceae and Salicaceae suggest a long evolutionary history.
Collapse
Affiliation(s)
- Natalia Filipowicz
- Systematic Botany and Mycology, University of Munich LMU, Menzinger Strasse 67, Munich, Germany
| | | |
Collapse
|