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Hay NM, Windham MD, Mandáková T, Lysak MA, Hendriks KP, Mummenhoff K, Lens F, Pryer KM, Bailey CD. A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets. AMERICAN JOURNAL OF BOTANY 2023; 110:e16226. [PMID: 37561651 DOI: 10.1002/ajb2.16226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
PREMISE Although Boechera (Boechereae, Brassicaceae) has become a plant model system for both ecological genomics and evolutionary biology, all previous phylogenetic studies have had limited success in resolving species relationships within the genus. The recent effective application of sequence data from target enrichment approaches to resolve the evolutionary relationships of several other challenging plant groups prompted us to investigate their usefulness in Boechera and Boechereae. METHODS To resolve the phylogeny of Boechera and closely related genera, we utilized the Hybpiper pipeline to analyze two combined bait sets: Angiosperms353, with broad applicability across flowering plants; and a Brassicaceae-specific bait set designed for use in the mustard family. Relationships for 101 samples representing 81 currently recognized species were inferred from a total of 1114 low-copy nuclear genes using both supermatrix and species coalescence methods. RESULTS Our analyses resulted in a well-resolved and highly supported phylogeny of the tribe Boechereae. Boechereae is divided into two major clades, one comprising all western North American species of Boechera, the other encompassing the eight other genera of the tribe. Our understanding of relationships within Boechera is enhanced by the recognition of three core clades that are further subdivided into robust regional species complexes. CONCLUSIONS This study presents the first broadly sampled, well-resolved phylogeny for most known sexual diploid Boechera. This effort provides the foundation for a new phylogenetically informed taxonomy of Boechera that is crucial for its continued use as a model system.
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Affiliation(s)
- Nikolai M Hay
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - Michael D Windham
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Kasper P Hendriks
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, Osnabrück, D-49076, Germany
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands
| | - Klaus Mummenhoff
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, Osnabrück, D-49076, Germany
| | - Frederic Lens
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - C Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
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Li M, Hieno A, Motohashi K, Suga H, Kageyama K. Pythium intermedium, a species complex consisting of three phylogenetic species found in cool-temperate forest ecosystems. Fungal Biol 2021; 125:1017-1025. [PMID: 34776229 DOI: 10.1016/j.funbio.2021.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
Pythium intermedium plays a vital role in the carbon cycle of cool-temperate forests and is widely distributed in Japan's forest soils. In this study, we performed a phylogenetic analysis of the P. intermedium species complex using DNA sequences from multiple loci. The study included 35 isolates from cool-temperate forest soils, seven known P. intermedium isolates, and six known Pythium attrantheridium isolates. We also performed morphological observations and mating tests. Our results showed that all the isolates formed one large clade but were divided into three subclades. Furthermore, we observed many mating reactions between isolates from different subclades, including between P. attrantheridium and P. intermedium. Therefore, we suggest that P. intermedium, P. attrantheridium, and another phylogenetic species belong to one species complex. This is the first report of a species complex within P. intermedium and will be helpful in understanding the evolution of Pythium species in natural ecosystems.
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Affiliation(s)
- Mingzhu Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China; River Basin Research Center, Gifu University, Gifu, 501-1193, Japan.
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - Keiichi Motohashi
- Faculty of Regional Environment Science, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu, 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
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Mateo de Arias M, Gao L, Sherwood DA, Dwivedi KK, Price BJ, Jamison M, Kowallis BM, Carman JG. Whether Gametophytes are Reduced or Unreduced in Angiosperms Might Be Determined Metabolically. Genes (Basel) 2020; 11:genes11121449. [PMID: 33276690 PMCID: PMC7761559 DOI: 10.3390/genes11121449] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 02/07/2023] Open
Abstract
In angiosperms, meiotic failure coupled with the formation of genetically unreduced gametophytes in ovules (apomeiosis) constitute major components of gametophytic apomixis. These aberrant developmental events are generally thought to be caused by mutation. However, efforts to locate the responsible mutations have failed. Herein, we tested a fundamentally different hypothesis: apomeiosis is a polyphenism of meiosis, with meiosis and apomeiosis being maintained by different states of metabolic homeostasis. Microarray analyses of ovules and pistils were used to differentiate meiotic from apomeiotic processes in Boechera (Brassicaceae). Genes associated with translation, cell division, epigenetic silencing, flowering, and meiosis characterized sexual Boechera (meiotic). In contrast, genes associated with stress responses, abscisic acid signaling, reactive oxygen species production, and stress attenuation mechanisms characterized apomictic Boechera (apomeiotic). We next tested whether these metabolic differences regulate reproductive mode. Apomeiosis switched to meiosis when premeiotic ovules of apomicts were cultured on media that increased oxidative stress. These treatments included drought, starvation, and H2O2 applications. In contrast, meiosis switched to apomeiosis when premeiotic pistils of sexual plants were cultured on media that relieved oxidative stress. These treatments included antioxidants, glucose, abscisic acid, fluridone, and 5-azacytidine. High-frequency apomeiosis was initiated in all sexual species tested: Brassicaceae, Boechera stricta, Boechera exilis, and Arabidopsis thaliana; Fabaceae, Vigna unguiculata; Asteraceae, Antennaria dioica. Unreduced gametophytes formed from ameiotic female and male sporocytes, first division restitution dyads, and nucellar cells. These results are consistent with modes of reproduction and types of apomixis, in natural apomicts, being regulated metabolically.
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Affiliation(s)
- Mayelyn Mateo de Arias
- Plants, Soils, and Climate Department, Utah State University, Logan, UT 84322-4820, USA; (M.M.d.A.); (L.G.); (D.A.S.); (B.J.P.)
- Instituto Tecnológico de Santo Domingo, 10103 Santo Domingo, Dominican Republic
| | - Lei Gao
- Plants, Soils, and Climate Department, Utah State University, Logan, UT 84322-4820, USA; (M.M.d.A.); (L.G.); (D.A.S.); (B.J.P.)
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang 332000, China
| | - David A. Sherwood
- Plants, Soils, and Climate Department, Utah State University, Logan, UT 84322-4820, USA; (M.M.d.A.); (L.G.); (D.A.S.); (B.J.P.)
- Sherwood Pet Health, Logan, UT 84321, USA
| | - Krishna K. Dwivedi
- Caisson Laboratories, Inc., Smithfield, UT 84335, USA; (K.K.D.); (M.J.); (B.M.K.)
- Crop Improvement Division, Indian Grassland and Fodder Research Institute, 284003 Jhansi, India
| | - Bo J. Price
- Plants, Soils, and Climate Department, Utah State University, Logan, UT 84322-4820, USA; (M.M.d.A.); (L.G.); (D.A.S.); (B.J.P.)
- Molecular Biology Program, University of Utah, Salt Lake City, UT 84112-5750, USA
| | - Michelle Jamison
- Caisson Laboratories, Inc., Smithfield, UT 84335, USA; (K.K.D.); (M.J.); (B.M.K.)
- Wescor, Inc. An Elitech Company, Logan, UT 84321, USA
| | - Becky M. Kowallis
- Caisson Laboratories, Inc., Smithfield, UT 84335, USA; (K.K.D.); (M.J.); (B.M.K.)
- Cytiva, Inc., Logan, UT 84321, USA
| | - John G. Carman
- Plants, Soils, and Climate Department, Utah State University, Logan, UT 84322-4820, USA; (M.M.d.A.); (L.G.); (D.A.S.); (B.J.P.)
- Correspondence: ; Tel.: +1-435-512-4913
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Monihan SM, Magness CA, Ryu CH, McMahon MM, Beilstein MA, Schumaker KS. Duplication and functional divergence of a calcium sensor in the Brassicaceae. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2782-2795. [PMID: 31989164 PMCID: PMC7210777 DOI: 10.1093/jxb/eraa031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/27/2020] [Indexed: 05/09/2023]
Abstract
The presence of varied numbers of CALCINEURIN B-LIKE10 (CBL10) calcium sensor genes in species across the Brassicaceae and the demonstrated role of CBL10 in salt tolerance in Arabidopsis thaliana and Eutrema salsugineum provided a unique opportunity to determine if CBL10 function is modified in different species and linked to salt tolerance. Salinity effects on species growth and cross-species complementation were used to determine the extent of conservation and divergence of CBL10 function in four species representing major lineages within the core Brassicaceae (A. thaliana, E. salsugineum, Schrenkiella parvula, and Sisymbrium irio) as well as the first diverging lineage (Aethionema arabicum). Evolutionary and functional analyses indicate that CBL10 duplicated within expanded lineage II of the Brassicaceae and that, while portions of CBL10 function are conserved across the family, there are species-specific variations in CBL10 function. Paralogous CBL10 genes within a species diverged in expression and function probably contributing to the maintenance of the duplicated gene pairs. Orthologous CBL10 genes diverged in function in a species-specific manner, suggesting that functions arose post-speciation. Multiple CBL10 genes and their functional divergence may have expanded calcium-mediated signaling responses and contributed to the ability of certain members of the Brassicaceae to maintain growth in salt-affected soils.
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Affiliation(s)
- Shea M Monihan
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | | | - Choong-Hwan Ryu
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | | | - Mark A Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Karen S Schumaker
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
- Correspondence:
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Schilling MP, Gompert Z, Li FW, Windham MD, Wolf PG. Admixture, evolution, and variation in reproductive isolation in the Boechera puberula clade. BMC Evol Biol 2018; 18:61. [PMID: 29699502 PMCID: PMC5921550 DOI: 10.1186/s12862-018-1173-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 04/04/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Hybridization is very common in plants, and the incorporation of new alleles into existing lineages (i.e. admixture) can blur species boundaries. However, admixture also has the potential to increase standing genetic variation. With new sequencing methods, we can now study admixture and reproductive isolation at a much finer scale than in the past. The genus Boechera is an extraordinary example of admixture, with over 400 hybrid derivates of varying ploidy levels. Yet, few studies have assessed admixture in this genus on a genomic scale. RESULTS In this study, we used Genotyping-by-Sequencing (GBS) to clarify the evolution of the Boechera puberula clade, whose six members are scattered across the western United States. We further assessed patterns of admixture and reproductive isolation within the group, including two additional species (B. stricta and B. retrofracta) that are widespread across North America. Based on 14,815 common genetic variants, we found evidence for some cases of hybridization. We find evidence of both recent and more ancient admixture, and that levels of admixture vary across species. CONCLUSIONS We present evidence for a monophyletic origin of the B. puberula group, and a split of B. puberula into two subspecies. Further, when inferring reproductive isolation on the basis of presence and absence of admixture, we found that the accumulation of reproductive isolation between species does not seem to occur linearly with time since divergence in this system. We discuss our results in the context of sexuality and asexuality in Boechera.
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Affiliation(s)
- Martin P Schilling
- Biology Department, Utah State University, 5305 Old Main Hill, Logan, UT, 84322, USA.,Ecology Center, Utah State University, 5205 Old Main Hill, Logan, UT, 84322, USA.,present address: Department of Ecology and Evolutionary Biology, University of Colorado, N211 Ramaley Hall, Boulder, CO, 80309, USA
| | - Zachariah Gompert
- Biology Department, Utah State University, 5305 Old Main Hill, Logan, UT, 84322, USA.,Ecology Center, Utah State University, 5205 Old Main Hill, Logan, UT, 84322, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, New York, 14853, USA.,Plant Biology Section, Cornell University, 237 Mann Dr, Ithaca, New York, 14853, USA
| | - Michael D Windham
- Department of Biology, Duke University, 266 Biological Sciences, Durham, NC, 27708, USA
| | - Paul G Wolf
- Biology Department, Utah State University, 5305 Old Main Hill, Logan, UT, 84322, USA. .,Ecology Center, Utah State University, 5205 Old Main Hill, Logan, UT, 84322, USA.
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6
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Jones DC, Zheng W, Huang S, Du C, Zhao X, Yennamalli RM, Sen TZ, Nettleton D, Wurtele ES, Li L. A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence. FRONTIERS IN PLANT SCIENCE 2016; 7:983. [PMID: 27462324 PMCID: PMC4940393 DOI: 10.3389/fpls.2016.00983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/21/2016] [Indexed: 05/05/2023]
Abstract
Nearly immobile, plants have evolved new components to be able to respond to changing environments. One example is Qua Quine Starch (QQS, AT3G30720), an Arabidopsis thaliana-specific orphan gene that integrates primary metabolism with adaptation to environment changes. SAQR (Senescence-Associated and QQS-Related, AT1G64360), is unique to a clade within the family Brassicaceae; as such, the gene may have arisen about 20 million years ago. SAQR is up-regulated in QQS RNAi mutant and in the apx1 mutant under light-induced oxidative stress. SAQR plays a role in carbon allocation: overexpression lines of SAQR have significantly decreased starch content; conversely, in a saqr T-DNA knockout (KO) line, starch accumulation is increased. Meta-analysis of public microarray data indicates that SAQR expression is correlated with expression of a subset of genes involved in senescence, defense, and stress responses. SAQR promoter::GUS expression analysis reveals that SAQR expression increases after leaf expansion and photosynthetic capacity have peaked, just prior to visible natural senescence. SAQR is expressed predominantly within leaf and cotyledon vasculature, increasing in intensity as natural senescence continues, and then decreasing prior to death. In contrast, under experimentally induced senescence, SAQR expression increases in vasculature of cotyledons but not in true leaves. In SAQR KO line, the transcript level of the dirigent-like disease resistance gene (AT1G22900) is increased, while that of the Early Light Induced Protein 1 gene (ELIP1, AT3G22840) is decreased. Taken together, these data indicate that SAQR may function in the QQS network, playing a role in integration of primary metabolism with adaptation to internal and environmental changes, specifically those that affect the process of senescence.
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Affiliation(s)
- Dallas C. Jones
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
| | - Wenguang Zheng
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
| | - Sheng Huang
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
| | - Chuanlong Du
- Department of Statistics, Iowa State University, AmesIA, USA
| | - Xuefeng Zhao
- Laurence H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, AmesIA, USA
| | - Ragothaman M. Yennamalli
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture-Agriculture Research Service, AmesIA, USA
| | - Taner Z. Sen
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture-Agriculture Research Service, AmesIA, USA
| | - Dan Nettleton
- Department of Statistics, Iowa State University, AmesIA, USA
| | - Eve S. Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
- Center for Metabolic Biology, Iowa State University, AmesIA, USA
| | - Ling Li
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
- Center for Metabolic Biology, Iowa State University, AmesIA, USA
- *Correspondence: Ling Li,
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Shah JN, Kirioukhova O, Pawar P, Tayyab M, Mateo JL, Johnston AJ. Depletion of Key Meiotic Genes and Transcriptome-Wide Abiotic Stress Reprogramming Mark Early Preparatory Events Ahead of Apomeiotic Transition. FRONTIERS IN PLANT SCIENCE 2016; 7:1539. [PMID: 27833618 PMCID: PMC5080521 DOI: 10.3389/fpls.2016.01539] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/30/2016] [Indexed: 05/19/2023]
Abstract
Molecular dissection of apomixis - an asexual reproductive mode - is anticipated to solve the enigma of loss of meiotic sex, and to help fixing elite agronomic traits. The Brassicaceae genus Boechera comprises of both sexual and apomictic species, permitting comparative analyses of meiotic circumvention (apomeiosis) and parthenogenesis. Whereas previous studies reported local transcriptome changes during these events, it remained unclear whether global changes associated with hybridization, polyploidy and environmental adaptation that arose during evolution of Boechera might serve as (epi)genetic regulators of early development prior apomictic initiation. To identify these signatures during vegetative stages, we compared seedling RNA-seq transcriptomes of an obligate triploid apomict and a diploid sexual, both isolated from a drought-prone habitat. Uncovered were several genes differentially expressed between sexual and apomictic seedlings, including homologs of meiotic genes ASYNAPTIC 1 (ASY1) and MULTIPOLAR SPINDLE 1 (MPS1) that were down-regulated in apomicts. An intriguing class of apomict-specific deregulated genes included several NAC transcription factors, homologs of which are known to be transcriptionally reprogrammed during abiotic stress in other plants. Deregulation of both meiotic and stress-response genes during seedling stages might possibly be important in preparation for meiotic circumvention, as similar transcriptional alteration was discernible in apomeiotic floral buds too. Furthermore, we noted that the apomict showed better tolerance to osmotic stress in vitro than the sexual, in conjunction with significant upregulation of a subset of NAC genes. In support of the current model that DNA methylation epigenetically regulates stress, ploidy, hybridization and apomixis, we noted that ASY1, MPS1 and NAC019 homologs were deregulated in Boechera seedlings upon DNA demethylation, and ASY1 in particular seems to be repressed by global DNA methylation exclusively in the apomicts. Variability in stress and transcriptional response in a diploid apomict, which is geographically distinct from the triploid apomict, pinpoints both common and independent features of apomixis evolution. Our study provides a molecular frame-work to investigate how the adaptive traits associated with the evolutionary history of apomicts co-adapted with meiotic gene deregulation at early developmental stage, in order to predate meiotic recombination, which otherwise is thought to be favorable in stress and low-fitness conditions.
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Affiliation(s)
- Jubin N. Shah
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Olga Kirioukhova
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Pallavi Pawar
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Muhammad Tayyab
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Juan L. Mateo
- Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
- *Correspondence: Amal J. Johnston, ; Juan L. Mateo,
| | - Amal J. Johnston
- Laboratory of Germline Genetics & Evo-Devo, Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
- *Correspondence: Amal J. Johnston, ; Juan L. Mateo,
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Cano LM, Raffaele S, Haugen RH, Saunders DGO, Leonelli L, MacLean D, Hogenhout SA, Kamoun S. Major transcriptome reprogramming underlies floral mimicry induced by the rust fungus Puccinia monoica in Boechera stricta. PLoS One 2013; 8:e75293. [PMID: 24069397 PMCID: PMC3775748 DOI: 10.1371/journal.pone.0075293] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 08/12/2013] [Indexed: 01/08/2023] Open
Abstract
Pucciniamonoica is a spectacular plant parasitic rust fungus that triggers the formation of flower-like structures (pseudoflowers) in its Brassicaceae host plant Boecherastricta. Pseudoflowers mimic in shape, color, nectar and scent co-occurring and unrelated flowers such as buttercups. They act to attract insects thereby aiding spore dispersal and sexual reproduction of the rust fungus. Although much ecological research has been performed on P. monoica-induced pseudoflowers, this system has yet to be investigated at the molecular or genomic level. To date, the molecular alterations underlying the development of pseudoflowers and the genes involved have not been described. To address this, we performed gene expression profiling to reveal 256 plant biological processes that are significantly altered in pseudoflowers. Among these biological processes, plant genes involved in cell fate specification, regulation of transcription, reproduction, floral organ development, anthocyanin (major floral pigments) and terpenoid biosynthesis (major floral volatile compounds) were down-regulated in pseudoflowers. In contrast, plant genes involved in shoot, cotyledon and leaf development, carbohydrate transport, wax biosynthesis, cutin transport and L-phenylalanine metabolism (pathway that results in phenylethanol and phenylacetaldehyde volatile production) were up-regulated. These findings point to an extensive reprogramming of host genes by the rust pathogen to induce floral mimicry. We also highlight 31 differentially regulated plant genes that are enriched in the biological processes mentioned above, and are potentially involved in the formation of pseudoflowers. This work illustrates the complex perturbations induced by rust pathogens in their host plants, and provides a starting point for understanding the molecular mechanisms of pathogen-induced floral mimicry.
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Affiliation(s)
| | - Sylvain Raffaele
- The Sainsbury Laboratory, Norwich, United Kingdom
- Laboratoire des Interactions Plantes Micro-organismes, UMR441 INRA - UMR2594 CNRS, Castanet Tolosan, France
| | - Riston H. Haugen
- Black Hills State University, Integrative Genomics Program, Spearfish, South Dakota, United States of America
| | | | - Lauriebeth Leonelli
- The Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Dan MacLean
- The Sainsbury Laboratory, Norwich, United Kingdom
| | - Saskia A. Hogenhout
- Cell and Developmental Biology, The John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich, United Kingdom
- * E-mail:
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Abstract
Ecological model systems provide a conduit to understand the ecological impact of information gained from laboratory model species. Here, I review a 2011 meeting which focused on the systematic, ecological, evolutionary and developmental biology of the ecological model genus Boechera.
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Affiliation(s)
- John T Lovell
- Department of BioAgricultural Sciences and Pest Management, C129 Plant Sciences, Colorado State University, Fort Collins, CO 80523-1177, USA.
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10
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Abstract
The selection and development of a study system for evolutionary and ecological functional genomics (EEFG) depend on a variety of factors. Here, we present the genus Boechera as an exemplary system with which to address ecological and evolutionary questions. Our focus on Boechera is based on several characteristics as follows: (i) native populations in undisturbed habitats where current environments reflect historical conditions over several thousand years; (ii) functional genomics benefitting from its close relationship to Arabidopsis thaliana; (iii) inbreeding tolerance enabling development of recombinant inbred lines, near-isogenic lines and positional cloning; (iv) interspecific crosses permitting mapping for genetic analysis of speciation; (v) apomixis (asexual reproduction by seeds) in a genetically tractable diploid; and (vi) broad geographic distribution in North America, permitting ecological genetics for a large research community. These characteristics, along with the current sequencing of three Boechera species by the Joint Genome Institute, position Boechera as a rapidly advancing system for EEFG studies.
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Affiliation(s)
- Catherine A Rushworth
- Department of Biology, Institute for Genome Sciences and Policy, Duke University, PO Box 90338, Durham, NC 27708, USA
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11
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Selection of reference genes for quantitative real-time PCR expression studies of microdissected reproductive tissues in apomictic and sexual Boechera. BMC Res Notes 2011; 4:303. [PMID: 21851639 PMCID: PMC3171723 DOI: 10.1186/1756-0500-4-303] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 08/19/2011] [Indexed: 11/26/2022] Open
Abstract
Background Apomixis, a natural form of asexual seed production in plants, is considered to have great biotechnological potential for agriculture. It has been hypothesised that de-regulation of the sexual developmental pathway could trigger apomictic reproduction. The genus Boechera represents an interesting model system for understanding apomixis, having both sexual and apomictic genotypes at the diploid level. Quantitative qRT-PCR is the most extensively used method for validating genome-wide gene expression analyses, but in order to obtain reliable results, suitable reference genes are necessary. In this work we have evaluated six potential reference genes isolated from a 454 (FLX) derived cDNA library of Boechera. RNA from live microdissected ovules and anthers at different developmental stages, as well as vegetative tissues of apomictic and sexual Boechera, were used to validate the candidates. Results Based on homologies with Arabidopsis, six genes were selected from a 454 cDNA library of Boechera: RPS18 (Ribosomal sub protein 18), Efalpha1 (Elongation factor 1 alpha), ACT 2 (Actin2), UBQ (polyubiquitin), PEX4 (Peroxisomal ubiquitin conjugating enzyme) and At1g09770.1 (Arabidopsis thaliana cell division cycle 5). Total RNA was extracted from 17 different tissues, qRT-PCRs were performed, and raw Ct values were analyzed for primer efficiencies and gene ratios. The geNorm and normFinder applications were used for selecting the most stable genes among all tissues and specific tissue groups (ovule, anthers and vegetative tissues) in both apomictic and sexual plants separately. Our results show that BoechRPS18, BoechEfα1, BoechACT2 and BoechUBQ were the most stable genes. Based on geNorm, the combinations of BoechRPS18 and BoechEfα1 or BoechUBQ and BoechEfα1 were the most stable in the apomictic plant, while BoechRPS18 and BoechACT2 or BoechUBQ and BoechACT2 performed best in the sexual plant. When subgroups of tissue samples were analyzed, different optimal combinations were identified in sexual ovules (BoechUBQ and BoechEfα1), in anthers from both reproductive systems (BoechACT2 and BoechEfα1), in apomictic vegetative tissues (BoechEfα1 and BoechACT2) and sexual vegetative tissues (BoechRPS18 and BoechEfα1). NormFinder ranked BoechACT2 as the most stable in the apomictic plant, while BoechRPS18 was the best in the sexual plant. The subgroups analysis identified the best gene for both apomictic and sexual ovules (BoechRPS18), for anthers from both reproductive system (BoechEfα1) and for apomictic and vegetative tissues (BoechACT2 and BoechRPS18 respectively) Conclusions From a total of six tested genes, BoechRPS18, BoechEfα1, BoechACT2 and BoechUBQ showed the best stability values. We furthermore provide detailed information for the accurate normalization of specific tissue gene expression analyses of apomictic and sexual Boechera.
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Aliyu OM, Schranz ME, Sharbel TF. Quantitative variation for apomictic reproduction in the genus Boechera (Brassicaceae). AMERICAN JOURNAL OF BOTANY 2010; 97:1719-31. [PMID: 21616805 DOI: 10.3732/ajb.1000188] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY The evolution of asexual seed production (apomixis) from sexual relatives is a great enigma of plant biology. The genus Boechera is ideal for studying apomixis because of its close relation to Arabidopsis and the occurrence of sexual and apomictic species at low ploidy levels (diploid and triploid). Apomixis is characterized by three components: unreduced embryo-sac formation (apomeiosis), fertilization-independent embryogenesis (parthenogenesis), and functional endosperm formation (pseudogamy or autonomous endosperm formation). Understanding the variation in these traits within and between species has been hindered by the laborious histological analyses required to analyze large numbers of samples. • METHODS To quantify variability for the different components of apomictic seed development, we developed a high-throughput flow cytometric seed screen technique to measure embryo:endosperm ploidy in over 22000 single seeds derived from 71 accessions of diploid and triploid Boechera. • KEY RESULTS Three interrelated features were identified within and among Boechera species: (1) variation for most traits associated with apomictic seed formation, (2) three levels of apomeiosis expression (low, high, obligate), and (3) correlations between apomeiosis and parthenogenesis/pseudogamy. • CONCLUSIONS The data presented here provide a framework for choosing specific genotypes for correlations with large "omics" data sets being collected for Boechera to study population structure, gene flow, and evolution of specific traits. We hypothesize that low levels of apomeiosis represent an ancestral condition of Boechera, whereas high apomeiosis levels may have been induced by global gene regulatory changes associated with hybridization.
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Affiliation(s)
- Olawale M Aliyu
- Apomixis Research Group, Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany
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Hurwitz BL, Kudrna D, Yu Y, Sebastian A, Zuccolo A, Jackson SA, Ware D, Wing RA, Stein L. Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:990-1003. [PMID: 20626650 DOI: 10.1111/j.1365-313x.2010.04293.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rapid progress in comparative genomics among the grasses has revealed similar gene content and order despite exceptional differences in chromosome size and number. Large- and small-scale genomic variations are of particular interest, especially among cultivated and wild species, as they encode rapidly evolving features that may be important in adaptation to particular environments. We present a genome-wide study of intermediate-sized structural variation (SV) among rice (Oryza sativa) and three of its closest relatives in the genus Oryza (Oryza nivara, Oryza rufipogon and Oryza glaberrima). We computationally identified regional expansions, contractions and inversions in the Oryza species genomes relative to O. sativa by combining data from paired-end clone alignments to the O. sativa reference genome and physical maps. A subset of the computational predictions was validated using a new approach for BAC size determination. The result was a confirmed catalog of 674 expansions (25-38 Mb) and 611 (4-19 Mb) contractions, and 140 putative inversions (14-19 Mb) between the three Oryza species and O. sativa. In the expanded regions unique to O. sativa we found enrichment in transposable elements (TEs): long terminal repeats (LTRs) were randomly located across the chromosomes, and their insertion times corresponded to the date of the A genome radiation. Also, rice-expanded regions contained an over-representation of single-copy genes related to defense factors in the environment. This catalog of confirmed SV in reference to O. sativa provides an entry point for future research in genome evolution, speciation, domestication and novel gene discovery.
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Affiliation(s)
- Bonnie L Hurwitz
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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Dwivedi SL, Perotti E, Upadhyaya HD, Ortiz R. Sexual and apomictic plant reproduction in the genomics era: exploring the mechanisms potentially useful in crop plants. ACTA ACUST UNITED AC 2010; 23:265-79. [PMID: 20509033 DOI: 10.1007/s00497-010-0144-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Accepted: 05/11/2010] [Indexed: 11/26/2022]
Abstract
Arabidopsis, Mimulus and tomato have emerged as model plants in researching genetic and molecular basis of differences in mating systems. Variations in floral traits and loss of self-incompatibility have been associated with mating system differences in crops. Genomics research has advanced considerably, both in model and crop plants, which may provide opportunities to modify breeding systems as evidenced in Arabidopsis and tomato. Mating system, however, not recombination per se, has greater effect on the level of polymorphism. Generating targeted recombination remains one of the most important factors for crop genetic enhancement. Asexual reproduction through seeds or apomixis, by producing maternal clones, presents a tremendous potential for agriculture. Although believed to be under simple genetic control, recent research has revealed that apomixis results as a consequence of the deregulation of the timing of sexual events rather than being the product of specific apomixis genes. Further, forward genetic studies in Arabidopsis have permitted the isolation of novel genes reported to control meiosis I and II entry. Mutations in these genes trigger the production of unreduced or apomeiotic megagametes and are an important step toward understanding and engineering apomixis.
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Affiliation(s)
- Sangam L Dwivedi
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502324 AP, India.
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SIEMENS DAVIDH, HAUGEN RISTON, MATZNER STEVEN, VANASMA NICHOLAS. Plant chemical defence allocation constrains evolution of local range. Mol Ecol 2009; 18:4974-83. [DOI: 10.1111/j.1365-294x.2009.04389.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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16
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Schranz ME, Manzaneda AJ, Windsor AJ, Clauss MJ, Mitchell-Olds T. Ecological genomics of Boechera stricta: identification of a QTL controlling the allocation of methionine- vs branched-chain amino acid-derived glucosinolates and levels of insect herbivory. Heredity (Edinb) 2009; 102:465-74. [PMID: 19240753 PMCID: PMC2775550 DOI: 10.1038/hdy.2009.12] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In the Brassicaceae glucosinolates influence feeding, reproduction and development of many insect herbivores. Glucosinolate production and effects on herbivore feeding have been extensively studied in the model species Arabidopsis thaliana and Brassica crops, both of which constitutively produce leaf glucosinolates mostly derived from the amino acid methionine. Much less is known about the regulation or role in defense of glucosinolates derived from other aliphatic amino acids such as the branched-chain amino acids (BCAA) valine and isoleucine. We have identified a glucosinolate polymorphism in Boechera stricta controlling the allocation to BCAA- vs. methionine-derived glucosinolates in both leaves and seeds. Boechera stricta is a perennial species that grows in mostly undisturbed habitats of western North America. We have measured glucosinolate profiles and concentrations in 192 F2 lines that have previously been used for genetic map construction. We also performed herbivory assays on six F3 replicates per F2 line using the generalist lepidopteran Trichoplusia ni. Quantitative Trait Locus (QTL) analysis identified a single locus controlling both glucosinolate profile and levels of herbivory, the Branched Chain-Methionine Allocation or BCMA QTL. We have delimited this QTL to a small genomic region with a 1.0 LOD confidence interval just 1.9 cM wide, which in A. thaliana contains ∼100 genes. We also found that methionine-derived glucosinolates provided significantly greater defense than the BCAA-derived glucosinolates against feeding by this generalist insect herbivore. The future positional cloning of this locus will allow for testing various adaptive explanations.
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Affiliation(s)
- M E Schranz
- Department of Experimental Plant Systematics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
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Multilocus patterns of nucleotide diversity, population structure and linkage disequilibrium in Boechera stricta, a wild relative of Arabidopsis. Genetics 2008; 181:1021-33. [PMID: 19104077 DOI: 10.1534/genetics.108.095364] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Information about polymorphism, population structure, and linkage disequilibrium (LD) is crucial for association studies of complex trait variation. However, most genomewide studies have focused on model systems, with very few analyses of undisturbed natural populations. Here, we sequenced 86 mapped nuclear loci for a sample of 46 genotypes of Boechera stricta and two individuals of B. holboellii, both wild relatives of Arabidopsis. Isolation by distance was significant across the species range of B. stricta, and three geographic groups were identified by structure analysis, principal coordinates analysis, and distance-based phylogeny analyses. The allele frequency spectrum indicated a genomewide deviation from an equilibrium neutral model, with silent nucleotide diversity averaging 0.004. LD decayed rapidly, declining to background levels in approximately 10 kb or less. For tightly linked SNPs separated by <1 kb, LD was dependent on the reference population. LD was lower in the specieswide sample than within populations, suggesting that low levels of LD found in inbreeding species such as B. stricta, Arabidopsis thaliana, and barley may result from broad geographic sampling that spans heterogeneous genetic groups. Finally, analyses also showed that inbreeding B. stricta and A. thaliana have approximately 45% higher recombination per kilobase than outcrossing A. lyrata.
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McGarry RC, Ayre BG. A DNA element between At4g28630 and At4g28640 confers companion-cell specific expression following the sink-to-source transition in mature minor vein phloem. PLANTA 2008; 228:839-49. [PMID: 18682980 DOI: 10.1007/s00425-008-0786-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2008] [Accepted: 07/04/2008] [Indexed: 05/05/2023]
Abstract
The collection phloem in minor veins is distinct from other vein classes in that the minor veins mature during the sink to source transition and are the primary sites of phloem loading. After maturation, minor vein phloem maintains its character in part through minor-vein specific regulatory cascades; however despite its physiological significance, little of these developmental programs is understood. From an Arabidopsis enhancer trap screen, we identified MATURE MINOR VEIN ELEMENT1 (MMVE1) in the intergenic region between two oppositely oriented genes, the ABC transporter ATM1 (At4g28630) and IAA11 (At4g28640). MMVE1 promotes reporter gene activity in minor vein phloem in a pattern resembling the sink to source transition. Promoter truncation experiments and phylogenetic footprinting demonstrate sequences proximal to ATM1 promote minor vein expression whereas sequences closer to IAA11 repress it. Both orientations of the promoter were used to drive expression of CONSTANS to generate a phloem mobile signal conferring early flowering under non-inductive conditions. Tandem copies of MMVE1 increase minor vein expression strength and specificity. MMVE1 is the first minor vein enhancer characterized from a species that loads from the apoplast, and supports the presence of unique regulatory cascades operating in minor vein phloem.
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Affiliation(s)
- Roisin C McGarry
- Department of Biological Sciences, University of North Texas, 1504 W. Mulberry, SRB Rm 120, P.O. Box 305220, Denton, TX 76203 5220, USA.
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Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4. Nature 2008; 453:391-5. [PMID: 18425111 DOI: 10.1038/nature06877] [Citation(s) in RCA: 627] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Accepted: 02/28/2008] [Indexed: 11/08/2022]
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ANSELL SW, GRUNDMANN M, RUSSELL SJ, SCHNEIDER H, VOGEL JC. Genetic discontinuity, breeding-system change and population history ofArabis alpinain the Italian Peninsula and adjacent Alps. Mol Ecol 2008; 17:2245-57. [DOI: 10.1111/j.1365-294x.2008.03739.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zeller G, Clark RM, Schneeberger K, Bohlen A, Weigel D, Rätsch G. Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays. Genome Res 2008; 18:918-29. [PMID: 18323538 DOI: 10.1101/gr.070169.107] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Whole-genome oligonucleotide resequencing arrays have allowed the comprehensive discovery of single nucleotide polymorphisms (SNPs) in eukaryotic genomes of moderate to large size. With this technology, the detection rate for isolated SNPs is typically high. However, it is greatly reduced when other polymorphisms are located near a SNP as multiple mismatches inhibit hybridization to arrayed oligonucleotides. Contiguous tracts of suppressed hybridization therefore typify polymorphic regions (PRs) such as clusters of SNPs or deletions. We developed a machine learning method, designated margin-based prediction of polymorphic regions (mPPR), to predict PRs from resequencing array data. Conceptually similar to hidden Markov models, the method is trained with discriminative learning techniques related to support vector machines, and accurately identifies even very short polymorphic tracts (<10 bp). We applied this method to resequencing array data previously generated for the euchromatic genomes of 20 strains (accessions) of the best-characterized plant, Arabidopsis thaliana. Nonredundantly, 27% of the genome was included within the boundaries of PRs predicted at high specificity ( approximately 97%). The resulting data set provides a fine-scale view of polymorphic sequences in A. thaliana; patterns of polymorphism not apparent in SNP data were readily detected, especially for noncoding regions. Our predictions provide a valuable resource for evolutionary genetic and functional studies in A. thaliana, and our method is applicable to similar data sets in other species. More broadly, our computational approach can be applied to other segmentation tasks related to the analysis of genomic variation.
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Affiliation(s)
- Georg Zeller
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen 72070, Germany
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Affiliation(s)
- Peggy Ozias-Akins
- Department of Horticulture, University of Georgia Tifton Campus, Tifton, Georgia;
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Armstead I, Huang L, King J, Ougham H, Thomas H, King I. Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation. BMC Genomics 2007; 8:283. [PMID: 17708759 PMCID: PMC2041955 DOI: 10.1186/1471-2164-8-283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Accepted: 08/20/2007] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Various methods have been developed to explore inter-genomic relationships among plant species. Here, we present a sequence similarity analysis based upon comparison of transcript-assembly and methylation-filtered databases from five plant species and physically anchored rice coding sequences. RESULTS A comparison of the frequency of sequence alignments, determined by MegaBLAST, between rice coding sequences in TIGR pseudomolecules and annotations vs 4.0 and comprehensive transcript-assembly and methylation-filtered databases from Lolium perenne (ryegrass), Zea mays (maize), Hordeum vulgare (barley), Glycine max (soybean) and Arabidopsis thaliana (thale cress) was undertaken. Each rice pseudomolecule was divided into 10 segments, each containing 10% of the functionally annotated, expressed genes. This indicated a correlation between relative segment position in the rice genome and numbers of alignments with all the queried monocot and dicot plant databases. Colour-coded moving windows of 100 functionally annotated, expressed genes along each pseudomolecule were used to generate 'heat-maps'. These revealed consistent intra- and inter-pseudomolecule variation in the relative concentrations of significant alignments with the tested plant databases. Analysis of the annotations and derived putative expression patterns of rice genes from 'hot-spots' and 'cold-spots' within the heat maps indicated possible functional differences. A similar comparison relating to ancestral duplications of the rice genome indicated that duplications were often associated with 'hot-spots'. CONCLUSION Physical positions of expressed genes in the rice genome are correlated with the degree of conservation of similar sequences in the transcriptomes of other plant species. This relative conservation is associated with the distribution of different sized gene families and segmentally duplicated loci and may have functional and evolutionary implications.
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Affiliation(s)
- Ian Armstead
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Lin Huang
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Julie King
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Helen Ougham
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Howard Thomas
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Ian King
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
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Holub EB. Natural variation in innate immunity of a pioneer species. CURRENT OPINION IN PLANT BIOLOGY 2007; 10:415-24. [PMID: 17631039 DOI: 10.1016/j.pbi.2007.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 05/21/2007] [Accepted: 05/23/2007] [Indexed: 05/05/2023]
Abstract
By 2010, we will have detailed knowledge about the genome of Arabidopsis thaliana from a Linnean-like effort by an international research community to identify nearly all of the genes in the species and to classify the products that these genes encode according to a primary function in a generic plant cell. To know the wild species, however, we will require knowledge of which genes provide the raw material for phenotypic variation and natural selection, and consequently affect the adaptability of individual plants and local populations across their geographic range, and ultimately survival of the species. Natural variation in innate immunity will be at the forefront of this exciting research frontier as a model for the molecular ecology of plant-microbe interactions.
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Affiliation(s)
- Eric B Holub
- Warwick-HRI, University of Warwick, Wellesbourne, UK.
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Schranz ME, Windsor AJ, Song BH, Lawton-Rauh A, Mitchell-Olds T. Comparative genetic mapping in Boechera stricta, a close relative of Arabidopsis. PLANT PHYSIOLOGY 2007; 144:286-98. [PMID: 17369426 PMCID: PMC1913784 DOI: 10.1104/pp.107.096685] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Accepted: 02/28/2007] [Indexed: 05/14/2023]
Abstract
The angiosperm family Brassicaceae contains both the research model Arabidopsis (Arabidopsis thaliana) and the agricultural genus Brassica. Comparative genomics in the Brassicaceae has largely focused on direct comparisons between Arabidopsis and the species of interest. However, the reduced genome size and chromosome number (n = 5) of Arabidopsis complicates comparisons. Arabidopsis shows extensive genome and chromosome reshuffling compared to its close relatives Arabidopsis lyrata and Capsella rubella, both with n = 8. To facilitate comparative genomics across the Brassicaceae we recently outlined a system of 24 conserved chromosomal blocks based on their positions in an ancestral karyotype of n = 8, rather than by their position in Arabidopsis. In this report we use this system as a tool to understand genome structure and evolution in Boechera stricta (n = 7). B. stricta is a diploid, sexual, and highly self-fertilizing species occurring in mostly montane regions of western North America. We have created an F(2) genetic map of B. stricta based on 192 individuals scored at 196 microsatellite and candidate gene loci. Single-nucleotide polymorphism genotyping of 94 of the loci was done simultaneously using an Illumina bead array. The total map length is 725.8 cM, with an average marker spacing of 3.9 cM. There are no gaps greater than 19.3 cM. The chromosomal reduction from n = 8 to n = 7 and other genomic changes in B. stricta likely involved a pericentric inversion, a chromosomal fusion, and two reciprocal translocations that are easily visualized using the genomic blocks. Our genetic map will facilitate the analysis of ecologically relevant quantitative variation in Boechera. Sequence data from this article can be found in the GenBank/EMBL data libraries under accession numbers DU 667459 to DU 708532.
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Affiliation(s)
- M Eric Schranz
- Department of Biology, Duke University, Durham, NC 27708, USA.
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Stinchcombe JR, Hoekstra HE. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity (Edinb) 2007; 100:158-70. [PMID: 17314923 DOI: 10.1038/sj.hdy.6800937] [Citation(s) in RCA: 380] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A central challenge in evolutionary biology is to identify genes underlying ecologically important traits and describe the fitness consequences of naturally occurring variation at these loci. To address this goal, several novel approaches have been developed, including 'population genomics,' where a large number of molecular markers are scored in individuals from different environments with the goal of identifying markers showing unusual patterns of variation, potentially due to selection at linked sites. Such approaches are appealing because of (1) the increasing ease of generating large numbers of genetic markers, (2) the ability to scan the genome without measuring phenotypes and (3) the simplicity of sampling individuals without knowledge of their breeding history. Although such approaches are inherently applicable to non-model systems, to date these studies have been limited in their ability to uncover functionally relevant genes. By contrast, quantitative genetics has a rich history, and more recently, quantitative trait locus (QTL) mapping has had some success in identifying genes underlying ecologically relevant variation even in novel systems. QTL mapping, however, requires (1) genetic markers that specifically differentiate parental forms, (2) a focus on a particular measurable phenotype and (3) controlled breeding and maintenance of large numbers of progeny. Here we present current advances and suggest future directions that take advantage of population genomics and quantitative genetic approaches - in both model and non-model systems. Specifically, we discuss advantages and limitations of each method and argue that a combination of the two provides a powerful approach to uncovering the molecular mechanisms responsible for adaptation.
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Affiliation(s)
- J R Stinchcombe
- Department of Ecology and Evolutionary Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.
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Haberer G, Mader MT, Kosarev P, Spannagl M, Yang L, Mayer KFX. Large-scale cis-element detection by analysis of correlated expression and sequence conservation between Arabidopsis and Brassica oleracea. PLANT PHYSIOLOGY 2006; 142:1589-602. [PMID: 17028152 PMCID: PMC1676041 DOI: 10.1104/pp.106.085639] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The rapidly increasing amount of plant genomic sequences allows for the detection of cis-elements through comparative methods. In addition, large-scale gene expression data for Arabidopsis (Arabidopsis thaliana) have recently become available. Coexpression and evolutionarily conserved sequences are criteria widely used to identify shared cis-regulatory elements. In our study, we employ an integrated approach to combine two sources of information, coexpression and sequence conservation. Best-candidate orthologous promoter sequences were identified by a bidirectional best blast hit strategy in genome survey sequences from Brassica oleracea. The analysis of 779 microarrays from 81 different experiments provided detailed expression information for Arabidopsis genes coexpressed in multiple tissues and under various conditions and developmental stages. We discovered candidate transcription factor binding sites in 64% of the Arabidopsis genes analyzed. Among them, we detected experimentally verified binding sites and showed strong enrichment of shared cis-elements within functionally related genes. This study demonstrates the value of partially shotgun sequenced genomes and their combinatorial use with functional genomics data to address complex questions in comparative genomics.
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Affiliation(s)
- Georg Haberer
- Munich Information Center for Protein Sequences, Institute for Bioinformatics, GSF National Research Center for Environment and Health, 85764 Neuherberg, Germany
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Benderoth M, Textor S, Windsor AJ, Mitchell-Olds T, Gershenzon J, Kroymann J. Positive selection driving diversification in plant secondary metabolism. Proc Natl Acad Sci U S A 2006; 103:9118-23. [PMID: 16754868 PMCID: PMC1482576 DOI: 10.1073/pnas.0601738103] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Indexed: 11/18/2022] Open
Abstract
In Arabidopsis thaliana and related plants, glucosinolates are a major component in the blend of secondary metabolites and contribute to resistance against herbivorous insects. Methylthioalkylmalate synthases (MAM) encoded at the MAM gene cluster control an early step in the biosynthesis of glucosinolates and, therefore, are central to the diversification of glucosinolate metabolism. We sequenced bacterial artificial chromosomes containing the MAM cluster from several Arabidopsis relatives, conducted enzyme assays with heterologously expressed MAM genes, and analyzed MAM nucleotide variation patterns. Our results show that gene duplication, neofunctionalization, and positive selection provide the mechanism for biochemical adaptation in plant defense. These processes occur repeatedly in the history of the MAM gene family, indicating their fundamental importance for the evolution of plant metabolic diversity both within and among species.
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Affiliation(s)
| | - Susanne Textor
- Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany
| | | | | | - Jonathan Gershenzon
- Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany
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Schranz ME, Mitchell-Olds T. Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. THE PLANT CELL 2006; 18:1152-65. [PMID: 16617098 PMCID: PMC1456871 DOI: 10.1105/tpc.106.041111] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Recent studies have elucidated the ancient polyploid history of the Arabidopsis thaliana (Brassicaceae) genome. The studies concur that there was at least one polyploidy event occurring some 14.5 to 86 million years ago (Mya), possibly near the divergence of the Brassicaceae from its sister family, Cleomaceae. Using a comparative genomics approach, we asked whether this polyploidy event was unique to members of the Brassicaceae, shared with the Cleomaceae, or an independent polyploidy event in each lineage. We isolated and sequenced three genomic regions from diploid Cleome spinosa (Cleomaceae) that are each homoeologous to a duplicated region shared between At3 and At5, centered on the paralogs of SEPALLATA (SEP) and CONSTANS (CO). Phylogenetic reconstructions and analysis of synonymous substitution rates support the hypothesis that a genomic triplication in Cleome occurred independently of and more recently than the duplication event in the Brassicaceae. There is a strong correlation in the copy number (single versus duplicate) of individual genes, suggesting functionally consistent influences operating on gene copy number in these two independently evolving lineages. However, the amount of gene loss in Cleome is greater than in Arabidopsis. The genome of C. spinosa is only 1.9 times the size of A. thaliana, enabling comparative genome analysis of separate but related polyploidy events.
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Affiliation(s)
- M Eric Schranz
- Department of Genetics and Evolution, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany.
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Schranz ME, Mitchell-Olds T. Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. THE PLANT CELL 2006; 18:1152-1165. [PMID: 16617098 DOI: 10.1105/tpc.106.041111.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Recent studies have elucidated the ancient polyploid history of the Arabidopsis thaliana (Brassicaceae) genome. The studies concur that there was at least one polyploidy event occurring some 14.5 to 86 million years ago (Mya), possibly near the divergence of the Brassicaceae from its sister family, Cleomaceae. Using a comparative genomics approach, we asked whether this polyploidy event was unique to members of the Brassicaceae, shared with the Cleomaceae, or an independent polyploidy event in each lineage. We isolated and sequenced three genomic regions from diploid Cleome spinosa (Cleomaceae) that are each homoeologous to a duplicated region shared between At3 and At5, centered on the paralogs of SEPALLATA (SEP) and CONSTANS (CO). Phylogenetic reconstructions and analysis of synonymous substitution rates support the hypothesis that a genomic triplication in Cleome occurred independently of and more recently than the duplication event in the Brassicaceae. There is a strong correlation in the copy number (single versus duplicate) of individual genes, suggesting functionally consistent influences operating on gene copy number in these two independently evolving lineages. However, the amount of gene loss in Cleome is greater than in Arabidopsis. The genome of C. spinosa is only 1.9 times the size of A. thaliana, enabling comparative genome analysis of separate but related polyploidy events.
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Affiliation(s)
- M Eric Schranz
- Department of Genetics and Evolution, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany.
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