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Yoo MJ, Koh J, Boatwright JL, Soltis DE, Soltis PS, Barbazuk WB, Chen S. Investigation of regulatory divergence between homoeologs in the recently formed allopolyploids, Tragopogon mirus and T. miscellus (Asteraceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1191-1205. [PMID: 37997015 DOI: 10.1111/tpj.16553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/02/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Abstract
Polyploidy is an important evolutionary process throughout eukaryotes, particularly in flowering plants. Duplicated gene pairs (homoeologs) in allopolyploids provide additional genetic resources for changes in molecular, biochemical, and physiological mechanisms that result in evolutionary novelty. Therefore, understanding how divergent genomes and their regulatory networks reconcile is vital for unraveling the role of polyploidy in plant evolution. Here, we compared the leaf transcriptomes of recently formed natural allotetraploids (Tragopogon mirus and T. miscellus) and their diploid parents (T. porrifolius X T. dubius and T. pratensis X T. dubius, respectively). Analysis of 35 400 expressed loci showed a significantly higher level of transcriptomic additivity compared to old polyploids; only 22% were non-additively expressed in the polyploids, with 5.9% exhibiting transgressive expression (lower or higher expression in the polyploids than in the diploid parents). Among approximately 7400 common orthologous regions (COREs), most loci in both allopolyploids exhibited expression patterns that were vertically inherited from their diploid parents. However, 18% and 20.3% of the loci showed novel expression bias patterns in T. mirus and T. miscellus, respectively. The expression changes of 1500 COREs were explained by cis-regulatory divergence (the condition in which the two parental subgenomes do not interact) between the diploid parents, whereas only about 423 and 461 of the gene expression changes represent trans-effects (the two parental subgenomes interact) in T. mirus and T. miscellus, respectively. The low degree of both non-additivity and trans-effects on gene expression may present the ongoing evolutionary processes of the newly formed Tragopogon polyploids (~80-90 years).
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, New York, 13699, USA
| | - Jin Koh
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, 32610, USA
| | - J Lucas Boatwright
- Plant and Environmental Science Department, Clemson University, Clemson, South Carolina, 29634, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Pamela S Soltis
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, Mississippi, 38677, USA
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2
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Hatami E, Jones KE, Kilian N. New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq). FRONTIERS IN PLANT SCIENCE 2022; 13:851716. [PMID: 35873957 PMCID: PMC9298463 DOI: 10.3389/fpls.2022.851716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Subtribe Scorzonerinae (Cichorieae, Asteraceae) contains 12 main lineages and approximately 300 species. Relationships within the subtribe, either at inter- or intrageneric levels, were largely unresolved in phylogenetic studies to date, due to the lack of phylogenetic signal provided by traditional Sanger sequencing markers. In this study, we employed a phylogenomics approach (Hyb-Seq) that targets 1,061 nuclear-conserved ortholog loci designed for Asteraceae and obtained chloroplast coding regions as a by-product of off-target reads. Our objectives were to evaluate the potential of the Hyb-Seq approach in resolving the phylogenetic relationships across the subtribe at deep and shallow nodes, investigate the relationships of major lineages at inter- and intrageneric levels, and examine the impact of the different datasets and approaches on the robustness of phylogenetic inferences. We analyzed three nuclear datasets: exon only, excluding all potentially paralogous loci; exon only, including loci that were only potentially paralogous in 1-3 samples; exon plus intron regions (supercontigs); and the plastome CDS region. Phylogenetic relationships were reconstructed using both multispecies coalescent and concatenation (Maximum Likelihood and Bayesian analyses) approaches. Overall, our phylogenetic reconstructions recovered the same monophyletic major lineages found in previous studies and were successful in fully resolving the backbone phylogeny of the subtribe, while the internal resolution of the lineages was comparatively poor. The backbone topologies were largely congruent among all inferences, but some incongruent relationships were recovered between nuclear and plastome datasets, which are discussed and assumed to represent cases of cytonuclear discordance. Considering the newly resolved phylogenies, a new infrageneric classification of Scorzonera in its revised circumscription is proposed.
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Affiliation(s)
- Elham Hatami
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Katy E. Jones
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Norbert Kilian
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany
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Mavrodiev EV, Gómez JP, Mavrodiev NE, Melton AE, Martínez‐Azorín M, Crespo MB, Robinson SK, Steadman DW. On biodiversity and conservation of the
Iris hexagona
complex (
Phaeiris
, Iridaceae). Ecosphere 2021. [DOI: 10.1002/ecs2.3331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Evgeny V. Mavrodiev
- Florida Museum of Natural History University of Florida PO Box 117800 Gainesville Florida32611USA
| | - Juan P. Gómez
- Departamento de Química y Biología Universidad del Norte Km 5 Vía a Pto. Colombia Barranquilla Colombia
| | | | - Anthony E. Melton
- Florida Museum of Natural History University of Florida PO Box 117800 Gainesville Florida32611USA
| | - Mario Martínez‐Azorín
- Departamento de Ciencias Ambientales y Recursos Naturales (Botánica) Universidad de Alicante Apartado 99 AlicanteE‐03080Spain
| | - Manuel B. Crespo
- Departamento de Ciencias Ambientales y Recursos Naturales (Botánica) Universidad de Alicante Apartado 99 AlicanteE‐03080Spain
| | - Scott K. Robinson
- Florida Museum of Natural History University of Florida PO Box 117800 Gainesville Florida32611USA
| | - David W. Steadman
- Florida Museum of Natural History University of Florida PO Box 117800 Gainesville Florida32611USA
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Zaika MA, Kilian N, Jones K, Krinitsina AA, Nilova MV, Speranskaya AS, Sukhorukov AP. Scorzonera sensu lato (Asteraceae, Cichorieae) - taxonomic reassessment in the light of new molecular phylogenetic and carpological analyses. PHYTOKEYS 2020; 137:1-85. [PMID: 31969792 PMCID: PMC6962254 DOI: 10.3897/phytokeys.137.46544] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/24/2019] [Indexed: 05/22/2023]
Abstract
Scorzonera comprises 180-190 species and belongs to the subtribe Scorzonerinae. Its circumscription has long been the subject of debate and available molecular phylogenetic analyses affirmed the polyphyly of Scorzonera in its wide sense. We provide a re-evaluation of Scorzonera and other related genera, based on carpological (including anatomical) and extended molecular phylogenetic analyses. We present, for the first time, a comprehensive sampling, including Scorzonera in its widest sense and all other genera recognised in the Scorzonerinae. We conducted phylogenetic analyses using Maximum Parsimony, Maximum Likelihood and Bayesian analyses, based on sequences of the nuclear ribosomal ITS and of two plastid markers (partial rbcL and matK) and Maximum Parsimony for reconstructing the carpological character states at ancestral nodes. Achene characters, especially related to pericarp anatomy, such as general topography of the tissue types, disposition of the mechanical tissue and direction of its fibres, presence or absence of air cavities, provide, in certain cases, support for the phylogenetic lineages revealed. Confirming the polyphyly of Scorzonera, we propose a revised classification of the subtribe, accepting the genera Scorzonera (including four major clades: Scorzonera s. str., S. purpurea, S. albicaulis and Podospermum), Gelasia, Lipschitzia gen. nov. (for the Scorzonera divaricata clade), Pseudopodospermum, Pterachaenia (also including Scorzonera codringtonii), Ramaliella gen. nov. (for the S. polyclada clade) and Takhtajaniantha. A key to the revised genera and a characterisation of the genera and major clades are provided.
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Affiliation(s)
- Maxim A. Zaika
- Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, 119234, Moscow, RussiaLomonosov Moscow State UniversityMoscowRussia
| | - Norbert Kilian
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Str. 6–8, 14195 Berlin, GermanyFreie Universität BerlinBerlinGermany
| | - Katy Jones
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Str. 6–8, 14195 Berlin, GermanyFreie Universität BerlinBerlinGermany
| | - Anastasiya A. Krinitsina
- Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, 119234, Moscow, RussiaLomonosov Moscow State UniversityMoscowRussia
- I.M. Sechenov First Moscow State Medical University, Pharmaceutical Natural Science Department, Izmailovsky Boulevard, 8, 105043, Moscow, RussiaI.M. Sechenov First Moscow State Medical UniversityMoscowRussia
| | - Maya V. Nilova
- Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, 119234, Moscow, RussiaLomonosov Moscow State UniversityMoscowRussia
| | - Anna S. Speranskaya
- Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, 119234, Moscow, RussiaLomonosov Moscow State UniversityMoscowRussia
| | - Alexander P. Sukhorukov
- Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, 119234, Moscow, RussiaLomonosov Moscow State UniversityMoscowRussia
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Matthews A, Emelianova K, Hatimy AA, Chester M, Pellicer J, Ahmad KS, Guignard MS, Rouhan G, Soltis DE, Soltis PS, Leitch IJ, Leitch AR, Mavrodiev EV, Buggs RJA. 250 years of hybridization between two biennial herb species without speciation. AOB PLANTS 2015; 7:plv081. [PMID: 26187604 PMCID: PMC4571729 DOI: 10.1093/aobpla/plv081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/04/2015] [Indexed: 05/23/2023]
Abstract
Hybridization between plant species can generate novel morphological diversity and lead to speciation at homoploid or polyploid levels. Hybrids between biennial herbs Tragopogon pratensis and T. porrifolius have been studied in experimental and natural populations for over 250 years. Here we examine their current status in natural populations in southeast England. All hybrids found were diploid; they tended to grow taller and with more buds than their parental species; many showed partial fertility; a few showed evidence of backcrossing. However, we found no evidence to suggest that the hybrids are establishing as a new species, nor can we find literature documenting speciation of these hybrids elsewhere. This lack of speciation despite at least 250 years of hybridization contrasts with the fact that both parental species have formed new allopolyploid species through hybridization with another diploid, T. dubius. Understanding why hybrids often do not speciate, despite repeated opportunities, would enhance our understanding of both the evolutionary process and risk assessments of invasive species.
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Affiliation(s)
- Andrew Matthews
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK Present address: Division of Ecology and Evolution, Imperial College London, Silwood Park Campus, Ascot, UK
| | - Katie Emelianova
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Abubakar A Hatimy
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Michael Chester
- Department of Biology, University of Florida, Gainesville, FL 32611, USA Department of Plant Science, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Khawaja Shafique Ahmad
- Lab of Plant Taxonomy, Department of Botany, University of Agriculture, Faisalabad 38040, Pakistan
| | - Maité S Guignard
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Germinal Rouhan
- Museum national d'Histoire naturelle, UMR CNRS 7205, Herbier National, CP3916 rue Buffon, F-75231 Paris, France
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Evgeny V Mavrodiev
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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Mavrodiev EV, Chester M, Suárez-Santiago VN, Visger CJ, Rodriguez R, Susanna A, Baldini RM, Soltis PS, Soltis DE. Multiple origins and chromosomal novelty in the allotetraploid Tragopogon castellanus (Asteraceae). THE NEW PHYTOLOGIST 2015; 206:1172-1183. [PMID: 25557021 DOI: 10.1111/nph.13227] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 11/10/2014] [Indexed: 06/04/2023]
Abstract
Tragopogon includes two classic examples of recently formed allopolyploid species in North America: T. mirus and T. miscellus. Older Tragopogon allotetraploids from Eurasia offer ideal taxa for comparing the longer term outcomes of allopolyploidy. To help resolve the ancestry of one of these older polyploids, phylogenetic analyses of multiple populations of the allotetraploid T. castellanus (2n = 24) and its putative diploid parents, T. crocifolius and T. lamottei, were conducted using sequences from nuclear (internal transcribed spacer, ITS; and alcohol dehydrogenase 1A, Adh) and plastid (trnT-trnL spacer, trnL intron, trnL-trnF spacer and rpl16 intron) loci. Fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used to investigate the chromosomal constitution of T. castellanus. Our data confirm that the widely distributed T. crocifolius and the Iberian endemic, T. lamottei, are the diploid parents of T. castellanus, and that this polyploid formed at least three times. One group of populations of T. castellanus is distinct in exhibiting two pairs of rearranged chromosomes. These data suggest that some of the chromosomal variants that originate in young polyploids (here, an intergenomic translocation) may become fixed in populations, contributing to novelty in older polyploid lineages. The geographical distributions of the allopolyploids and parents are also complex, with allotetraploid populations being disjunct from one or both of the most closely related diploid parental populations.
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Affiliation(s)
- Evgeny V Mavrodiev
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Michael Chester
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | | | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Roseana Rodriguez
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB-CSIC-ICUB), Pg. del Migdia, s.n., ES-08038, Barcelona, Spain
| | - Riccardo M Baldini
- Dipartimento di Biologia & Centro Studi Erbario Tropicale, Università degli Studi, Via G. La Pira 4, I-50121, Firenze, Italy
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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