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Koch MA, Michling F, Walther A, Huang XC, Tewes L, Müller C. Early-Mid Pleistocene genetic differentiation and range expansions as exemplified by invasive Eurasian Bunias orientalis (Brassicaceae) indicates the Caucasus as key region. Sci Rep 2017; 7:16764. [PMID: 29196646 PMCID: PMC5711908 DOI: 10.1038/s41598-017-17085-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/22/2017] [Indexed: 11/12/2022] Open
Abstract
Turkish Warty cabbage, Bunias orientalis L. (Brassicaceae) is a perennial herb known for its 250 years of invasion history into Europe and worldwide temperate regions. Putative centers of origin were debated to be located in Turkey, the Caucasus or Eastern Europe. Based on the genetic variation from the nuclear and plastid genomes, we identified two major gene pools in the Caucasian-Irano-Turanian region and close to the Northern Caucasus, respectively. These gene pools are old and started to diverge and expand approximately 930 kya in the Caucasus. Pleistocene glaciation and deglaciation cycles favoured later expansion of a European gene pool 230 kya, which was effectively separated from the Caucasian-Irano-Turanian gene pool. Although the European gene pool is genetically less diverse, it has largely served as source for colonization of Western and Northern Europe in modern times with rare observations of genetic contributions from the Caucasian-Irano-Turanian gene pool such as in North-East America. This study largely utilized herbarium material to take advantage of a biodiversity treasure trove providing biological material and also giving access to detailed collection information.
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Affiliation(s)
- Marcus A Koch
- Heidelberg University, Centre for Organismal Studies, Heidelberg, 69120, Germany.
| | - Florian Michling
- Heidelberg University, Centre for Organismal Studies, Heidelberg, 69120, Germany
| | - Andrea Walther
- Heidelberg University, Centre for Organismal Studies, Heidelberg, 69120, Germany
| | - Xiao-Chen Huang
- Heidelberg University, Centre for Organismal Studies, Heidelberg, 69120, Germany
| | - Lisa Tewes
- Bielefeld University, Chemical Ecology, Bielefeld, 33615, Germany
| | - Caroline Müller
- Bielefeld University, Chemical Ecology, Bielefeld, 33615, Germany
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152
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Sperber K, Steinbrecher T, Graeber K, Scherer G, Clausing S, Wiegand N, Hourston JE, Kurre R, Leubner-Metzger G, Mummenhoff K. Fruit fracture biomechanics and the release of Lepidium didymum pericarp-imposed mechanical dormancy by fungi. Nat Commun 2017; 8:1868. [PMID: 29192192 PMCID: PMC5709442 DOI: 10.1038/s41467-017-02051-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 11/02/2017] [Indexed: 11/15/2022] Open
Abstract
The biomechanical and ecophysiological properties of plant seed/fruit structures are fundamental to survival in distinct environments. Dispersal of fruits with hard pericarps (fruit coats) encasing seeds has evolved many times independently within taxa that have seed dispersal as their default strategy. The mechanisms by which the constraint of a hard pericarp determines germination timing in response to the environment are currently unknown. Here, we show that the hard pericarp of Lepidium didymum controls germination solely by a biomechanical mechanism. Mechanical dormancy is conferred by preventing full phase-II water uptake of the encased non-dormant seed. The lignified endocarp has biomechanically and morphologically distinct regions that serve as predetermined breaking zones. This pericarp-imposed mechanical dormancy is released by the activity of common fungi, which weaken these zones by degrading non-lignified pericarp cells. We propose that the hard pericarp with this biomechanical mechanism contributed to the global distribution of this species in distinct environments.
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Affiliation(s)
- Katja Sperber
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Tina Steinbrecher
- School of Biological Sciences, Plant Molecular Science and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Kai Graeber
- School of Biological Sciences, Plant Molecular Science and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Gwydion Scherer
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Simon Clausing
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Nils Wiegand
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - James E Hourston
- School of Biological Sciences, Plant Molecular Science and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Rainer Kurre
- Department of Biology, Center for Advanced Light Microscopy, University of Osnabrück, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Gerhard Leubner-Metzger
- School of Biological Sciences, Plant Molecular Science and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.
| | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, D-49076, Osnabrück, Germany.
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153
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Bloomer RH, Dean C. Fine-tuning timing: natural variation informs the mechanistic basis of the switch to flowering in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5439-5452. [PMID: 28992087 DOI: 10.1093/jxb/erx270] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The evolution of diverse life history strategies has allowed Arabidopsis thaliana to adapt to worldwide locations, spanning a range of latitudinal and environmental conditions. Arabidopsis thaliana accessions are either vernalization-requiring winter annuals or rapid cyclers, with extensive natural variation in vernalization requirement and response. Genetic and molecular analysis of this variation has enhanced our understanding of the mechanisms involved in life history determination, with translation to both natural and crop systems in the Brassicaceae and beyond.
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Affiliation(s)
- R H Bloomer
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - C Dean
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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154
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Mandáková T, Pouch M, Harmanová K, Zhan SH, Mayrose I, Lysak MA. Multispeed genome diploidization and diversification after an ancient allopolyploidization. Mol Ecol 2017; 26:6445-6462. [PMID: 29024107 DOI: 10.1111/mec.14379] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 01/04/2023]
Abstract
Hybridization and genome doubling (allopolyploidy) have led to evolutionary novelties as well as to the origin of new clades and species. Despite the importance of allopolyploidization, the dynamics of postpolyploid diploidization (PPD) at the genome level has been only sparsely studied. The Microlepidieae (MICR) is a crucifer tribe of 17 genera and c. 56 species endemic to Australia and New Zealand. Our phylogenetic and cytogenomic analyses revealed that MICR originated via an intertribal hybridization between ancestors of Crucihimalayeae (n = 8; maternal genome) and Smelowskieae (n = 7; paternal genome), both native to the Northern Hemisphere. The reconstructed ancestral allopolyploid genome (n = 15) originated probably in northeastern Asia or western North America during the Late Miocene (c. 10.6-7 million years ago) and reached the Australian mainland via long-distance dispersal. In Australia, the allotetraploid genome diverged into at least three main subclades exhibiting different levels of PPD and diversity: 1.25-fold descending dysploidy (DD) of n = 15 → n = 12 (autopolyploidy → 24) in perennial Arabidella (3 species), 1.5-fold DD of n = 15 → n = 10 in the perennial Pachycladon (11 spp.) and 2.1-3.75-fold DD of n = 15 → n = 7-4 in the largely annual crown-group genera (42 spp. in 15 genera). These results are among the first to demonstrate multispeed genome evolution in taxa descending from a common allopolyploid ancestor. It is suggested that clade-specific PPD can operate at different rates and efficacies and can be tentatively linked to life histories and the extent of taxonomic diversity.
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Affiliation(s)
- Terezie Mandáková
- RG Plant Cytogenomics, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Milan Pouch
- RG Plant Cytogenomics, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Klára Harmanová
- RG Plant Cytogenomics, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Shing Hei Zhan
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Martin A Lysak
- RG Plant Cytogenomics, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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155
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Hohmann N, Koch MA. An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes. BMC Genomics 2017; 18:810. [PMID: 29058582 PMCID: PMC5651623 DOI: 10.1186/s12864-017-4220-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/16/2017] [Indexed: 12/30/2022] Open
Abstract
Background Gene flow between species, across ploidal levels, and even between evolutionary lineages is a common phenomenon in the genus Arabidopsis. However, apart from two genetically fully stabilized allotetraploid species that have been investigated in detail, the extent and temporal dynamics of hybridization are not well understood. An introgression zone, with tetraploid A. arenosa introgressing into A. lyrata subsp. petraea in the Eastern Austrian Forealps and subsequent expansion towards pannonical lowlands, was described previously based on morphological observations as well as molecular data using microsatellite and plastid DNA markers. Here we investigate the spatio-temporal context of this suture zone, making use of the potential of next-generation sequencing and whole-genome data. By utilizing a combination of nuclear and plastid genomic data, the extent, direction and temporal dynamics of gene flow are elucidated in detail and Late Pleistocene evolutionary processes are resolved. Results Analysis of nuclear genomic data significantly recognizes the clinal structure of the introgression zone, but also reveals that hybridization and introgression is more common and substantial than previously thought. Also tetraploid A. lyrata and A. arenosa subsp. borbasii from outside the previously defined suture zone show genomic signals of past introgression. A. lyrata is shown to serve usually as the maternal parent in these hybridizations, but one exception is identified from plastome-based phylogenetic reconstruction. Using plastid phylogenomics with secondary time calibration, the origin of A. lyrata and A. arenosa lineages is pre-dating the last three glaciation complexes (approx. 550,000 years ago). Hybridization and introgression followed during the last two glacial-interglacial periods (since approx. 300,000 years ago) with later secondary contact at the northern and southern border of the introgression zone during the Holocene. Conclusions Footprints of adaptive introgression in the Northeastern Forealps are older than expected and predate the Last Glaciation Maximum. This correlates well with high genetic diversity found within areas that served as refuge area multiple times. Our data also provide some first hints that early introgressed and presumably preadapted populations account for successful and rapid postglacial re-colonization and range expansion. Electronic supplementary material The online version of this article (doi: 10.1186/s12864-017-4220-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nora Hohmann
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.,Present address: Department of Environmental Sciences, Botany, University of Basel, Hebelstrasse 1, CH-4056, Basel, Switzerland
| | - Marcus A Koch
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.
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156
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Lopez L, Wolf EM, Pires JC, Edger PP, Koch MA. Molecular Resources from Transcriptomes in the Brassicaceae Family. FRONTIERS IN PLANT SCIENCE 2017; 8:1488. [PMID: 28900436 PMCID: PMC5581910 DOI: 10.3389/fpls.2017.01488] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/11/2017] [Indexed: 06/07/2023]
Abstract
The rapidly falling costs and the increasing availability of large DNA sequence data sets facilitate the fast and affordable mining of large molecular markers data sets for comprehensive evolutionary studies. The Brassicaceae (mustards) are an important species-rich family in the plant kingdom with taxa distributed worldwide and a complex evolutionary history. We performed Simple Sequence Repeats (SSRs) mining using de novo assembled transcriptomes from 19 species across the Brassicaceae in order to study SSR evolution and provide comprehensive sets of molecular markers for genetic studies within the family. Moreover, we selected the genus Cochlearia to test the transferability and polymorphism of these markers among species. Additionally, we annotated Cochlearia pyrenaica transcriptome in order to identify the position of each of the mined SSRs. While we introduce a new set of tools that will further enable evolutionary studies across the Brassicaceae, we also discuss some broader aspects of SSR evolution. Overall, we developed 2012 ready-to-use SSR markers with their respective primers in 19 Brassicaceae species and a high quality annotated transcriptome for C. pyrenaica. As indicated by our transferability test with the genus Cochlearia these SSRs are transferable to species within the genus increasing exponentially the number of targeted species. Also, our polymorphism results showed substantial levels of variability for these markers. Finally, despite its complex evolutionary history, SSR evolution across the Brassicaceae family is highly conserved and we found no deviation from patterns reported in other Angiosperms.
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Affiliation(s)
- Lua Lopez
- Biodiversity and Plant Systematics, Centre of Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Eva M. Wolf
- Biodiversity and Plant Systematics, Centre of Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - J. Chris Pires
- Division of Biological Sciences, University of MissouriColumbia, MO, United States
| | - Patrick P. Edger
- Department of Horticulture, Michigan State UniversityEast Lansing, MI, United States
- Ecology, Evolutionary Biology and Behavior, Michigan State UniversityEast Lansing, MI, United States
| | - Marcus A. Koch
- Biodiversity and Plant Systematics, Centre of Organismal Studies, University of HeidelbergHeidelberg, Germany
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157
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Mandáková T, Hloušková P, German DA, Lysak MA. Monophyletic Origin and Evolution of the Largest Crucifer Genomes. PLANT PHYSIOLOGY 2017; 174:2062-2071. [PMID: 28667048 PMCID: PMC5543974 DOI: 10.1104/pp.17.00457] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/26/2017] [Indexed: 05/04/2023]
Abstract
Clade E, or the Hesperis clade, is one of the major Brassicaceae (Crucifereae) clades, comprising some 48 genera and 351 species classified into seven tribes and is distributed predominantly across arid and montane regions of Asia. Several taxa have socioeconomic significance, being important ornamental but also weedy and invasive species. From the comparative genomic perspective, the clade is noteworthy as it harbors species with the largest crucifer genomes but low numbers of chromosomes (n = 5-7). By applying comparative cytogenetic analysis and whole-chloroplast phylogenetics, we constructed, to our knowledge, the first partial and complete cytogenetic maps for selected representatives of clade E tribes and investigated their relationships in a family-wide context. The Hesperis clade is a well-supported monophyletic lineage comprising seven tribes: Anchonieae, Buniadeae, Chorisporeae, Dontostemoneae, Euclidieae, Hesperideae, and Shehbazieae. The clade diverged from other Brassicaceae crown-group clades during the Oligocene, followed by subsequent Miocene tribal diversifications in central/southwestern Asia. The inferred ancestral karyotype of clade E (CEK; n = 7) originated from an older n = 8 genome, which also was the purported progenitor of tribe Arabideae (KAA genome). In most taxa of clade E, the seven linkage groups of CEK either remained conserved (Chorisporeae) or were reshuffled by chromosomal translocations (Euclidieae). In 50% of Anchonieae and Hesperideae species, the CEK genome has undergone descending dysploidy toward n = 6 (-5). These genomic data elucidate early genome evolution in Brassicaceae and pave the way for future whole-genome sequencing and assembly efforts in this as yet genomically neglected group of crucifer plants.
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Affiliation(s)
- Terezie Mandáková
- Plant Cytogenomics Research Group, Central European Institute of Technology, and Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Petra Hloušková
- Plant Cytogenomics Research Group, Central European Institute of Technology, and Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Dmitry A German
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- South-Siberian Botanical Garden, Altai State University, 656049 Barnaul, Russia
| | - Martin A Lysak
- Plant Cytogenomics Research Group, Central European Institute of Technology, and Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
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158
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Mandáková T, Li Z, Barker MS, Lysak MA. Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:3-21. [PMID: 28370611 DOI: 10.1111/tpj.13553] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/17/2017] [Accepted: 03/23/2017] [Indexed: 05/10/2023]
Abstract
Hybridization and polyploidy followed by genome-wide diploidization had a significant impact on the diversification of land plants. The ancient At-α whole-genome duplication (WGD) preceded the diversification of crucifers (Brassicaceae). Some genera and tribes also experienced younger, mesopolyploid WGDs concealed by subsequent genome diploidization. Here we tested if multiple base chromosome numbers originated due to genome diploidization after independent mesopolyploid WGDs and how diploidization affected post-polyploid gene retention. Sixteen species representing 10 Brassicaceae tribes were analyzed by comparative chromosome painting and/or whole-transcriptome analysis of gene age distributions and phylogenetic analyses of gene duplications. Overall, we found evidence for at least 13 independent mesopolyploidies followed by different degrees of diploidization across the Brassicaceae. New mesotetraploid events were uncovered for the tribes Anastaticeae, Iberideae and Schizopetaleae, and mesohexaploid WGDs for Cochlearieae and Physarieae. In contrast, we found convergent patterns of gene retention and loss among these independent WGDs. Our combined analyses of genomic data for Brassicaceae indicate that extant chromosome number variation in many plant groups, and especially monophyletic taxa with multiple base chromosome numbers, can result from clade-specific genome duplications followed by diploidization. Our observation of parallel gene retention and loss across multiple independent WGDs provides one of the first multi-species tests of the predictability of patterns of post-polyploid genome evolution.
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Affiliation(s)
- Terezie Mandáková
- Plant Cytogenomics Research Group, CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Martin A Lysak
- Plant Cytogenomics Research Group, CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
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159
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Xiang Y, Huang CH, Hu Y, Wen J, Li S, Yi T, Chen H, Xiang J, Ma H. Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication. Mol Biol Evol 2017; 34:262-281. [PMID: 27856652 PMCID: PMC5400374 DOI: 10.1093/molbev/msw242] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ∼3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptomic and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ∼101.6 Ma for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit evolution. Phylogenomic analysis yielded strong evidence for numerous whole genome duplications (WGDs), supporting the hypothesis that the apple tribe had a WGD and revealing another one shared by fleshy fruit-bearing members of this tribe, with moderate support for WGDs in the peach tribe and other groups. Ancestral character reconstruction for fruit types supports independent origins of fleshy fruits from dry-fruit ancestors, including the evolution of drupes (e.g., peach) and pomes (e.g., apple) from follicetum, and drupetum (raspberry and blackberry) from achenetum. We propose that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution.
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Affiliation(s)
- Yezi Xiang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA
| | - Jun Wen
- The Smithsonian Institution, Washington, DC
| | - Shisheng Li
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, School of Life Sciences, Huanggang Normal College, Huanggang, Hubei, China
| | - Tingshuang Yi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hongyi Chen
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, School of Life Sciences, Huanggang Normal College, Huanggang, Hubei, China
| | - Jun Xiang
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, School of Life Sciences, Huanggang Normal College, Huanggang, Hubei, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
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160
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Zeng L, Zhang N, Zhang Q, Endress PK, Huang J, Ma H. Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets. THE NEW PHYTOLOGIST 2017; 214:1338-1354. [PMID: 28294342 DOI: 10.1111/nph.14503] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/25/2016] [Indexed: 05/21/2023]
Abstract
Explosive diversification is widespread in eukaryotes, making it difficult to resolve phylogenetic relationships. Eudicots contain c. 75% of extant flowering plants, are important for human livelihood and terrestrial ecosystems, and have probably experienced explosive diversifications. The eudicot phylogenetic relationships, especially among those of the Pentapetalae, remain unresolved. Here, we present a highly supported eudicot phylogeny and diversification rate shifts using 31 newly generated transcriptomes and 88 other datasets covering 70% of eudicot orders. A highly supported eudicot phylogeny divided Pentapetalae into two groups: one with rosids, Saxifragales, Vitales and Santalales; the other containing asterids, Caryophyllales and Dilleniaceae, with uncertainty for Berberidopsidales. Molecular clock analysis estimated that crown eudicots originated c. 146 Ma, considerably earlier than earliest tricolpate pollen fossils and most other molecular clock estimates, and Pentapetalae sequentially diverged into eight major lineages within c. 15 Myr. Two identified increases of diversification rate are located in the stems leading to Pentapetalae and asterids, and lagged behind the gamma hexaploidization. The nuclear genes from newly generated transcriptomes revealed a well-resolved eudicot phylogeny, sequential separation of major core eudicot lineages and temporal mode of diversifications, providing new insights into the evolutionary trend of morphologies and contributions to the diversification of eudicots.
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Affiliation(s)
- Liping Zeng
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA
| | - Ning Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013, USA
| | - Qiang Zhang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Guilin, 541006, China
| | - Peter K Endress
- Institute of Systematic Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Jie Huang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Guilin, 541006, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
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161
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Lee CR, Wang B, Mojica JP, Mandáková T, Prasad KVSK, Goicoechea JL, Perera N, Hellsten U, Hundley HN, Johnson J, Grimwood J, Barry K, Fairclough S, Jenkins JW, Yu Y, Kudrna D, Zhang J, Talag J, Golser W, Ghattas K, Schranz ME, Wing R, Lysak MA, Schmutz J, Rokhsar DS, Mitchell-Olds T. Young inversion with multiple linked QTLs under selection in a hybrid zone. Nat Ecol Evol 2017; 1:119. [PMID: 28812690 PMCID: PMC5607633 DOI: 10.1038/s41559-017-0119] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/16/2017] [Indexed: 12/23/2022]
Abstract
Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.
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Affiliation(s)
- Cheng-Ruei Lee
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
- Institute of Ecology and Evolutionary Biology and Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan ROC
| | - Baosheng Wang
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
- Department of Plant Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Julius P Mojica
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
| | - Terezie Mandáková
- Plant Cytogenomics Group, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno CZ-62500, Czech Republic
| | | | - Jose Luis Goicoechea
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Nadeesha Perera
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
| | - Uffe Hellsten
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Hope N Hundley
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jenifer Johnson
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Stephen Fairclough
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jerry W Jenkins
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Yeisoo Yu
- Phyzen Genomics Institute, Phyzen Inc., Seoul 151-836, South Korea
| | - Dave Kudrna
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Jianwei Zhang
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Wolfgang Golser
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Kathryn Ghattas
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Rod Wing
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Martin A Lysak
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Thomas Mitchell-Olds
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
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162
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Feng G, Burleigh JG, Braun EL, Mei W, Barbazuk WB. Evolution of the 3R-MYB Gene Family in Plants. Genome Biol Evol 2017; 9:1013-1029. [PMID: 28444194 PMCID: PMC5405339 DOI: 10.1093/gbe/evx056] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2017] [Indexed: 12/13/2022] Open
Abstract
Plant 3R-MYB transcription factors are an important subgroup of the MYB super family in plants; however, their evolutionary history and functions remain poorly understood. We identified 225 3R-MYB proteins from 65 plant species, including algae and all major lineages of land plants. Two segmental duplication events preceding the common ancestor of angiosperms have given rise to three subgroups of the 3R-MYB proteins. Five conserved introns in the domain region of the 3R-MYB genes were identified, which arose through a step-wise pattern of intron gain during plant evolution. Alternative splicing (AS) analysis of selected species revealed that transcripts from more than 60% of 3R-MYB genes undergo AS. AS could regulate transcriptional activity for some of the plant 3R-MYBs by generating different regulatory motifs. The 3R-MYB genes of all subgroups appear to be enriched for Mitosis-Specific Activator element core sequences within their upstream promoter region, which suggests a functional involvement in cell cycle. Notably, expression of 3R-MYB genes from different species exhibits differential regulation under various abiotic stresses. These data suggest that the plant 3R-MYBs function in both cell cycle regulation and abiotic stress response, which may contribute to the adaptation of plants to a sessile lifestyle.
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Affiliation(s)
- Guanqiao Feng
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL
| | - John Gordon Burleigh
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL.,Department of Biology, University of Florida, Gainesville, FL.,Genetics Institute, University of Florida, Gainesville, FL
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL.,Genetics Institute, University of Florida, Gainesville, FL
| | - Wenbin Mei
- Department of Biology, University of Florida, Gainesville, FL
| | - William Bradley Barbazuk
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL.,Department of Biology, University of Florida, Gainesville, FL.,Genetics Institute, University of Florida, Gainesville, FL
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163
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Kreiner JM, Kron P, Husband BC. Frequency and maintenance of unreduced gametes in natural plant populations: associations with reproductive mode, life history and genome size. THE NEW PHYTOLOGIST 2017; 214:879-889. [PMID: 28134436 DOI: 10.1111/nph.14423] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 12/03/2016] [Indexed: 05/20/2023]
Abstract
Fertilization involving unreduced (2n) gametes is considered the dominant mechanism of polyploid formation in angiosperms; however, our knowledge of the prevalence of and evolutionary mechanisms maintaining 2n gametes in natural populations is limited. We hypothesize that 2n gametes are deleterious consequences of meiotic errors maintained by mutation-selection balance and should increase in species with relaxed opportunities for selection on sexual processes (asexuality), reduced efficacy of selection (asexuality, selfing) and increased genome instability (high chromosome number). We used flow cytometry to estimate male 2n gamete production in 60 populations from 24 species of Brassicaceae. We quantified variation in 2n gamete production within and among species, and examined associations with life history, reproductive mode, genome size and chromosomal number while accounting for phylogeny. Most individuals produced < 2% 2n male gametes, whereas a small number had > 5% (up to 85%) production. Variation in 2n gamete production was significant among species and related to reproductive system; asexual species produced significantly more 2n gametes than mixed-mating and outcrossing species. Our results, unique in their multi-species perspective, are consistent with 2n gametes being deleterious but maintained when opportunities for selection are limited. Rare individuals with elevated 2n gamete production may be key contributors to polyploid formation.
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Affiliation(s)
- Julia M Kreiner
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Paul Kron
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
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164
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Nikolov LA, Tsiantis M. Using mustard genomes to explore the genetic basis of evolutionary change. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:119-128. [PMID: 28285128 DOI: 10.1016/j.pbi.2017.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 02/16/2017] [Accepted: 02/21/2017] [Indexed: 06/06/2023]
Abstract
Recent advances in sequencing technologies and gene manipulation tools have driven mustard species into the spotlight of comparative research and have offered powerful insight how phenotypic space is explored during evolution. Evidence emerged for genome-wide signal of transcription factors and gene duplication contributing to trait divergence, e.g., PLETHORA5/7 in leaf complexity. Trait divergence is often manifested in differential expression due to cis-regulatory divergence, as in KNOX genes and REDUCED COMPLEXITY, and can be coupled with protein divergence. Fruit shape in Capsella rubella results from anisotropic growth during three distinct phases. Brassicaceae exhibit novel fruit dispersal strategy, explosive pod shatter, where the rapid movement depends on slow build-up of tension and its rapid release facilitated by asymmetric cell wall thickenings.
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Affiliation(s)
- Lachezar A Nikolov
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany.
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165
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Guo X, Liu J, Hao G, Zhang L, Mao K, Wang X, Zhang D, Ma T, Hu Q, Al-Shehbaz IA, Koch MA. Plastome phylogeny and early diversification of Brassicaceae. BMC Genomics 2017; 18:176. [PMID: 28209119 PMCID: PMC5312533 DOI: 10.1186/s12864-017-3555-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 02/03/2017] [Indexed: 12/19/2022] Open
Abstract
Background The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. Results Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family. Conclusions Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3555-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xinyi Guo
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | - Jianquan Liu
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China.
| | - Guoqian Hao
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China.,Biodiversity Institute of Mount Emei, Mount Emei Scenic Area Management Committee, 614200, Leshan, Sichuan, People's Republic of China
| | - Lei Zhang
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | - Kangshan Mao
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | - Xiaojuan Wang
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | - Dan Zhang
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | - Tao Ma
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | - Quanjun Hu
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | | | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Im Neuenheimer Feld 345, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, 69120, Heidelberg, Germany
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166
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Guo X, Liu J, Hao G, Zhang L, Mao K, Wang X, Zhang D, Ma T, Hu Q, Al-Shehbaz IA, Koch MA. Plastome phylogeny and early diversification of Brassicaceae. BMC Genomics 2017. [PMID: 28209119 DOI: 10.1186/s12864-017-3555-3553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. RESULTS Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family. CONCLUSIONS Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.
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Affiliation(s)
- Xinyi Guo
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | - Jianquan Liu
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China.
| | - Guoqian Hao
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
- Biodiversity Institute of Mount Emei, Mount Emei Scenic Area Management Committee, 614200, Leshan, Sichuan, People's Republic of China
| | - Lei Zhang
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | - Kangshan Mao
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | - Xiaojuan Wang
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | - Dan Zhang
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | - Tao Ma
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | - Quanjun Hu
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China
| | | | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Im Neuenheimer Feld 345, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, 69120, Heidelberg, Germany
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167
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Eshel G, Shaked R, Kazachkova Y, Khan A, Eppel A, Cisneros A, Acuna T, Gutterman Y, Tel-Zur N, Rachmilevitch S, Fait A, Barak S. Anastatica hierochuntica, an Arabidopsis Desert Relative, Is Tolerant to Multiple Abiotic Stresses and Exhibits Species-Specific and Common Stress Tolerance Strategies with Its Halophytic Relative, Eutrema ( Thellungiella) salsugineum. FRONTIERS IN PLANT SCIENCE 2017; 7:1992. [PMID: 28144244 PMCID: PMC5239783 DOI: 10.3389/fpls.2016.01992] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/15/2016] [Indexed: 05/08/2023]
Abstract
The search for novel stress tolerance determinants has led to increasing interest in plants native to extreme environments - so called "extremophytes." One successful strategy has been comparative studies between Arabidopsis thaliana and extremophyte Brassicaceae relatives such as the halophyte Eutrema salsugineum located in areas including cold, salty coastal regions of China. Here, we investigate stress tolerance in the desert species, Anastatica hierochuntica (True Rose of Jericho), a member of the poorly investigated lineage III Brassicaceae. We show that A. hierochuntica has a genome approximately 4.5-fold larger than Arabidopsis, divided into 22 diploid chromosomes, and demonstrate that A. hierochuntica exhibits tolerance to heat, low N and salt stresses that are characteristic of its habitat. Taking salt tolerance as a case study, we show that A. hierochuntica shares common salt tolerance mechanisms with E. salsugineum such as tight control of shoot Na+ accumulation and resilient photochemistry features. Furthermore, metabolic profiling of E. salsugineum and A. hierochuntica shoots demonstrates that the extremophytes exhibit both species-specific and common metabolic strategies to cope with salt stress including constitutive up-regulation (under control and salt stress conditions) of ascorbate and dehydroascorbate, two metabolites involved in ROS scavenging. Accordingly, A. hierochuntica displays tolerance to methyl viologen-induced oxidative stress suggesting that a highly active antioxidant system is essential to cope with multiple abiotic stresses. We suggest that A. hierochuntica presents an excellent extremophyte Arabidopsis relative model system for understanding plant survival in harsh desert conditions.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Simon Barak
- French Associates Institute for Biotechnology and Agriculture of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the NegevSde Boker, Israel
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168
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Olsen CE, Huang XC, Hansen CIC, Cipollini D, Ørgaard M, Matthes A, Geu-Flores F, Koch MA, Agerbirk N. Glucosinolate diversity within a phylogenetic framework of the tribe Cardamineae (Brassicaceae) unraveled with HPLC-MS/MS and NMR-based analytical distinction of 70 desulfoglucosinolates. PHYTOCHEMISTRY 2016; 132:33-56. [PMID: 27743600 DOI: 10.1016/j.phytochem.2016.09.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/29/2016] [Accepted: 09/29/2016] [Indexed: 05/22/2023]
Abstract
As a basis for future investigations of evolutionary trajectories and biosynthetic mechanisms underlying variations in glucosinolate structures, we screened members of the crucifer tribe Cardamineae by HPLC-MS/MS, isolated and identified glucosinolates by NMR, searched the literature for previous data for the tribe, and collected HPLC-MS/MS data for nearly all glucosinolates known from the tribe as well as some related structures (70 in total). This is a considerable proportion of the approximately 142 currently documented natural glucosinolates. Calibration with authentic references allowed distinction (or elucidation) of isomers in many cases, such as distinction of β-hydroxyls, methylthios, methylsulfinyls and methylsulfonyls. A mechanism for fragmentation of secondary β-hydroxyls in MS was elucidated, and two novel glucosinolates were discovered: 2-hydroxy-3-methylpentylglucosinolate in roots of Cardamine pratensis and 2-hydroxy-8-(methylsulfinyl)octylglucosinolate in seeds of Rorippa amphibia. A large number of glucosinolates (ca. 54 with high structural certainty and a further 28 or more suggested from tandem MS), representing a wide structural variation, is documented from the tribe. This included glucosinolates apparently derived from Met, Phe, Trp, Val/Leu, Ile and higher homologues. Normal side chain elongation and side chain decoration by oxidation or methylation was observed, as well as rare abnormal side chain decoration (hydroxylation of aliphatics at the δ rather than β-position). Some species had diverse profiles, e.g. R. amphibia and C. pratensis (19 and 16 individual glucosinolates, respectively), comparable to total diversity in literature reports of Armoracia rusticana (17?), Barbarea vulgaris (20-24), and Rorippa indica (>20?). The ancestor or the tribe would appear to have used Trp, Met, and homoPhe as glucosinolate precursor amino acids, and to exhibit oxidation of thio to sulfinyl, formation of alkenyls, β-hydroxylation of aliphatic chains and hydroxylation and methylation of indole glucosinolates. Two hotspots of apparent biochemical innovation and loss were identified: C. pratensis and the genus Barbarea. Diversity in other species mainly included structures also known from other crucifers. In addition to a role of gene duplication, two contrasting genetic/biochemical mechanisms for evolution of such combined diversity and redundancy are discussed: (i) involvement of widespread genes with expression varying during evolution, and (ii) mutational changes in substrate specificities of CYP79F and GS-OH enzymes.
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Affiliation(s)
- Carl Erik Olsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Xiao-Chen Huang
- Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Cecilie I C Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Don Cipollini
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA
| | - Marian Ørgaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Annemarie Matthes
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Fernando Geu-Flores
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Marcus A Koch
- Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Niels Agerbirk
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
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169
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Huang CH, Zhang C, Liu M, Hu Y, Gao T, Qi J, Ma H. Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics. Mol Biol Evol 2016; 33:2820-2835. [PMID: 27604225 PMCID: PMC5062320 DOI: 10.1093/molbev/msw157] [Citation(s) in RCA: 100] [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: 01/23/2023] Open
Abstract
Biodiversity results from multiple evolutionary mechanisms, including genetic variation and natural selection. Whole-genome duplications (WGDs), or polyploidizations, provide opportunities for large-scale genetic modifications. Many evolutionarily successful lineages, including angiosperms and vertebrates, are ancient polyploids, suggesting that WGDs are a driving force in evolution. However, this hypothesis is challenged by the observed lower speciation and higher extinction rates of recently formed polyploids than diploids. Asteraceae includes about 10% of angiosperm species, is thus undoubtedly one of the most successful lineages and paleopolyploidization was suggested early in this family using a small number of datasets. Here, we used genes from 64 new transcriptome datasets and others to reconstruct a robust Asteraceae phylogeny, covering 73 species from 18 tribes in six subfamilies. We estimated their divergence times and further identified multiple potential ancient WGDs within several tribes and shared by the Heliantheae alliance, core Asteraceae (Asteroideae-Mutisioideae), and also with the sister family Calyceraceae. For two of the WGD events, there were subsequent great increases in biodiversity; the older one proceeded the divergence of at least 10 subfamilies within 10 My, with great variation in morphology and physiology, whereas the other was followed by extremely high species richness in the Heliantheae alliance clade. Our results provide different evidence for several WGDs in Asteraceae and reveal distinct association among WGD events, dramatic changes in environment and species radiations, providing a possible scenario for polyploids to overcome the disadvantages of WGDs and to evolve into lineages with high biodiversity.
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Affiliation(s)
- Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Caifei Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Mian Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA
| | - Tiangang Gao
- State Key Laboratory of Evolutionary and Systematic Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
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170
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Gan X, Hay A, Kwantes M, Haberer G, Hallab A, Ioio RD, Hofhuis H, Pieper B, Cartolano M, Neumann U, Nikolov LA, Song B, Hajheidari M, Briskine R, Kougioumoutzi E, Vlad D, Broholm S, Hein J, Meksem K, Lightfoot D, Shimizu KK, Shimizu-Inatsugi R, Imprialou M, Kudrna D, Wing R, Sato S, Huijser P, Filatov D, Mayer KFX, Mott R, Tsiantis M. The Cardamine hirsuta genome offers insight into the evolution of morphological diversity. NATURE PLANTS 2016; 2:16167. [PMID: 27797353 PMCID: PMC8826541 DOI: 10.1038/nplants.2016.167] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 09/30/2016] [Indexed: 05/18/2023]
Abstract
Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.
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Affiliation(s)
- Xiangchao Gan
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Angela Hay
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Michiel Kwantes
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Georg Haberer
- Plant Genome and Systems Biology, Helmholtz Zentrum Munich, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Asis Hallab
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Raffaele Dello Ioio
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
- Present Address: †Present address: Department of Biology and Biotechnology, Università La Sapienza, P.le Aldo Moro, 5, 00185 Rome, Italy (R.D.I.). The Global Food Security, BBSRC, Polaris House, North Star Avenue, Swindon SN2 1UH, UK (E.K.). Institute of Biotechnology, Viikinkaari 1, 00014 University of Helsinki, Finland (S.B.),
| | - Hugo Hofhuis
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Bjorn Pieper
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Maria Cartolano
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Ulla Neumann
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Lachezar A. Nikolov
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Baoxing Song
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Mohsen Hajheidari
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Roman Briskine
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Evangelia Kougioumoutzi
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford UK
- Present Address: †Present address: Department of Biology and Biotechnology, Università La Sapienza, P.le Aldo Moro, 5, 00185 Rome, Italy (R.D.I.). The Global Food Security, BBSRC, Polaris House, North Star Avenue, Swindon SN2 1UH, UK (E.K.). Institute of Biotechnology, Viikinkaari 1, 00014 University of Helsinki, Finland (S.B.),
| | - Daniela Vlad
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford UK
| | - Suvi Broholm
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford UK
- Present Address: †Present address: Department of Biology and Biotechnology, Università La Sapienza, P.le Aldo Moro, 5, 00185 Rome, Italy (R.D.I.). The Global Food Security, BBSRC, Polaris House, North Star Avenue, Swindon SN2 1UH, UK (E.K.). Institute of Biotechnology, Viikinkaari 1, 00014 University of Helsinki, Finland (S.B.),
| | - Jotun Hein
- Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG Oxford UK
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, 62901 Illinois USA
| | - David Lightfoot
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, 62901 Illinois USA
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Martha Imprialou
- Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG Oxford UK
| | - David Kudrna
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, 85721 Arizona USA
| | - Rod Wing
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, 85721 Arizona USA
| | - Shusei Sato
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford UK
| | - Peter Huijser
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford UK
| | - Klaus F. X. Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum Munich, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Richard Mott
- UCL Genetics Institute, University College London, Gower Street, WC1E 6BT London UK
| | - Miltos Tsiantis
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
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171
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Braverman JM, Hamilton MB, Johnson BA. Patterns of Substitution Rate Variation at Many Nuclear Loci in Two Species Trios in the Brassicaceae Partitioned with ANOVA. J Mol Evol 2016; 83:97-109. [PMID: 27592229 DOI: 10.1007/s00239-016-9752-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 07/14/2016] [Indexed: 01/09/2023]
Abstract
There are marked variations among loci and among lineages in rates of nucleotide substitution. The generation time hypothesis (GTH) is a neutral explanation for substitution rate heterogeneity that has genomewide application, predicting that species with shorter generation times accumulate DNA sequence substitutions faster than species with longer generation times do since faster genome replication provides more opportunities for mutations to occur and reach fixation by genetic drift. Relatively few studies have rigorously evaluated the GTH in plants, and there are numerous alternative hypotheses for plant substitution rate variation. One major challenge has been finding pairs of closely related plant species with contrasting generation times and appropriate outgroup taxa that all also have DNA sequence data for numerous loci. To test for causes of rate variation, we obtained sequence data for 256 genes for Arabidopsis thaliana, normally reproducing every year, and the biennial Arabidopsis lyrata with three closely related outgroup taxa (Brassica rapa, Capsella grandiflora, and Neslia paniculata) as well as the biennial Brassica oleracea and the annual B. rapa lineage with the outgroup N. paniculata. A sign test indicated that more loci than expected by chance have faster rates of substitution on the branch leading to the annual than to the perennial for one three-species trio but not another. Tajima's 1D and 2D tests, and a likelihood ratio test that incorporated saturation correction, rejected rate homogeneity for up to 26 genes (up to 14 genes when correcting for multiple tests), consistently showing faster rates for the annual lineage in the Arabidopsis species trio. ANOVA showed significant rate heterogeneity between the Arabidopsis and Brassica species trios (about 6 % of rate variation) and among loci (about 26-32 % of rate variation). The lineage-by-locus interaction which would be caused by locus- and lineage-specific natural selection explained about 13 % of substitution rate variation in one ANOVA model using substitution rates from genes partitioned into odd and even codons but was not a significant effect without partitioned genes. Annual/perennial lineage and species trio by annual/perennial lineage each explained about 1 % of substitution rate variation.
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Affiliation(s)
- John M Braverman
- Department of Biology, Saint Joseph's University, Philadelphia, PA, USA.
| | | | - Brent A Johnson
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, USA
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172
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Chen H, Deng T, Yue J, Al-Shehbaz IA, Sun H. Molecular phylogeny reveals the non-monophyly of tribe Yinshanieae (Brassicaceae) and description of a new tribe, Hillielleae. PLANT DIVERSITY 2016; 38:171-182. [PMID: 30159462 PMCID: PMC6112204 DOI: 10.1016/j.pld.2016.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 04/14/2016] [Indexed: 05/14/2023]
Abstract
The taxonomic treatment within the unigeneric tribe Yinshanieae (Brassicaceae) is controversial, owing to differences in generic delimitation applied to its species. In this study, sequences from nuclear ITS and chloroplast trnL-F regions were used to test the monophyly of Yinshanieae, while two nuclear markers (ITS, ETS) and four chloroplast markers (trnL-F, trnH-psbA, rps16, rpL32-trnL) were used to elucidate the phylogenetic relationships within the tribe. Using maximum parsimony, maximum likelihood, and Bayesian inference methods, we reconstructed the phylogeny of Brassicaceae and Yinshanieae. The results show that Yinshanieae is not a monophyletic group, with the taxa splitting into two distantly related clades: one clade contains four taxa and falls in Lineage I, whereas the other includes all species previously placed in Hilliella and is embedded in the Expanded Lineage II. The tribe Yinshanieae is redefined, and a new tribe, Hillielleae, is proposed based on combined evidence from molecular phylogeny, morphology, and cytology.
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Affiliation(s)
- Hongliang Chen
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jipei Yue
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | | | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Corresponding author.
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173
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Lysak MA, Mandáková T, Schranz ME. Comparative paleogenomics of crucifers: ancestral genomic blocks revisited. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:108-15. [PMID: 26945766 DOI: 10.1016/j.pbi.2016.02.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/29/2016] [Accepted: 02/01/2016] [Indexed: 05/03/2023]
Abstract
A decade ago the concept of the Ancestral Crucifer Karyotype (ACK) and the definition of 24 conserved genomic blocks was presented. Subsequently, 35 cytogenetic reconstructions and/or draft genome sequences of crucifer species (members of the Brassicaceae family) have been analyzed in the context of this system; placing crucifers at the forefront of plant phylogenomics. In this review, we highlight how the ACK and genomic blocks have facilitated and guided genomic analysis of crucifers in the last 10 years and provide an update of this robust model.
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Affiliation(s)
- Martin A Lysak
- Plant Cytogenomics Group, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, Brno CZ-62500, Czech Republic
| | - Terezie Mandáková
- Plant Cytogenomics Group, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, Brno CZ-62500, Czech Republic
| | - M Eric Schranz
- Biosystematics Group, Wageningen University (WU), Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands.
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174
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Biogeography and diversification of Brassicales: A 103million year tale. Mol Phylogenet Evol 2016; 99:204-224. [PMID: 26993763 DOI: 10.1016/j.ympev.2016.02.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 11/23/2022]
Abstract
Brassicales is a diverse order perhaps most famous because it houses Brassicaceae and, its premier member, Arabidopsis thaliana. This widely distributed and species-rich lineage has been overlooked as a promising system to investigate patterns of disjunct distributions and diversification rates. We analyzed plastid and mitochondrial sequence data from five gene regions (>8000bp) across 151 taxa to: (1) produce a chronogram for major lineages in Brassicales, including Brassicaceae and Arabidopsis, based on greater taxon sampling across the order and previously overlooked fossil evidence, (2) examine biogeographical ancestral range estimations and disjunct distributions in BioGeoBEARS, and (3) determine where shifts in species diversification occur using BAMM. The evolution and radiation of the Brassicales began 103Mya and was linked to a series of inter-continental vicariant, long-distance dispersal, and land bridge migration events. North America appears to be a significant area for early stem lineages in the order. Shifts to Australia then African are evident at nodes near the core Brassicales, which diverged 68.5Mya (HPD=75.6-62.0). This estimated age combined with fossil evidence, indicates that some New World clades embedded amongst Old World relatives (e.g., New World capparoids) are the result of different long distance dispersal events, whereas others may be best explained by land bridge migration (e.g., Forchhammeria). Based on these analyses, the Brassicaceae crown group diverged in Europe/Northern Africa in the Eocene, circa 43.4Mya (HPD=46.6-40.3) and Arabidopsis separated from close congeners circa 10.4Mya. These ages fall between divergent dates that were previously published, suggesting we are slowly converging on a robust age estimate for the family. Three significant shifts in species diversification are observed in the order: (1) 58Mya at the crown of Capparaceae, Cleomaceae and Brassicaceae, (2) 38Mya at the crown of Resedaceae+Stixis clade, and (3) 21Mya at the crown of the tribes Brassiceae and Sisymbrieae within Brassicaceae.
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175
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Niu B, Wang L, Zhang L, Ren D, Ren R, Copenhaver GP, Ma H, Wang Y. Arabidopsis Cell Division Cycle 20.1 Is Required for Normal Meiotic Spindle Assembly and Chromosome Segregation. THE PLANT CELL 2015; 27:3367-82. [PMID: 26672070 PMCID: PMC4707457 DOI: 10.1105/tpc.15.00834] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/16/2015] [Accepted: 11/22/2015] [Indexed: 05/18/2023]
Abstract
Cell division requires proper spindle assembly; a surveillance pathway, the spindle assembly checkpoint (SAC), monitors whether the spindle is normal and correctly attached to kinetochores. The SAC proteins regulate mitotic chromosome segregation by affecting CDC20 (Cell Division Cycle 20) function. However, it is unclear whether CDC20 regulates meiotic spindle assembly and proper homolog segregation. Here, we show that the Arabidopsis thaliana CDC20.1 gene is indispensable for meiosis and male fertility. We demonstrate that cdc20.1 meiotic chromosomes align asynchronously and segregate unequally and the metaphase I spindle has aberrant morphology. Comparison of the distribution of meiotic stages at different time points between the wild type and cdc20.1 reveals a delay of meiotic progression from diakinesis to anaphase I. Furthermore, cdc20.1 meiocytes exhibit an abnormal distribution of a histone H3 phosphorylation mark mediated by the Aurora kinase, providing evidence that CDC20.1 regulates Aurora localization for meiotic chromosome segregation. Further evidence that CDC20.1 and Aurora are functionally related was provided by meiosis-specific knockdown of At-Aurora1 expression, resulting in meiotic chromosome segregation defects similar to those of cdc20.1. Taken together, these results suggest a critical role for CDC20.1 in SAC-dependent meiotic chromosome segregation.
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Affiliation(s)
- Baixiao Niu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Liudan Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ding Ren
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ren Ren
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Gregory P Copenhaver
- Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280 Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-3280
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China Center for Evolutionary Biology, Institutes of Biomedical Sciences School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
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