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Klimek B, Stępniewska K, Seget B, Pandey VC, Babst-Kostecka A. Diversity and activity of soil biota at a post-mining site highly contaminated with Zn and Cd are enhanced by metallicolous compared to non-metallicolous Arabidopsis halleri ecotypes. LAND DEGRADATION & DEVELOPMENT 2023; 34:1538-1548. [PMID: 37485419 PMCID: PMC10358741 DOI: 10.1002/ldr.4551] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 11/23/2022] [Indexed: 07/25/2023]
Abstract
Hyperaccumulators' ability to take up large quantities of harmful heavy metals from contaminated soils and store them in their foliage makes them promising organisms for bioremediation. Here we demonstrate that some ecotypes of the zinc hyperaccumulator Arabidopsis halleri are more suitable for bioremediation than others, because of their distinct influence on soil biota. In a field experiment, populations originating from metal-polluted and unpolluted soils were transplanted to a highly contaminated metalliferous site in Southern Poland. Effects of plant ecotypes on soil biota were assessed by measurements of feeding activity of soil fauna (bait-lamina test) and catabolic activity and functional diversity of soil bacteria underneath A. halleri plants (Biolog® ECO plates). Chemical soil properties, plant morphological parameters, and zinc concentration in shoots and roots were additionally evaluated. Higher soil fauna feeding activity and higher bacterial community functional diversity were found in soils affected by A. halleri plants originating from metallicolous compared to non-metallicolous ecotypes. Differences in community-level physiological profiles further evidenced changes in microbial communities in response to plant ecotype. These soil characteristics were positively correlated with plant size. No differences in zinc content in shoots and roots, zinc translocation ratio, and plant morphology were observed between metallicolous and non-metallicolous plants. Our results indicate strong associations between A. halleri ecotype and soil microbial community properties. In particular, the improvement of soil biological properties by metallicolous accessions should be further explored to optimize hyperaccumulator-based bioremediation technologies.
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Affiliation(s)
- Beata Klimek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Klaudia Stępniewska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Barbara Seget
- Botany Institute, Polish Academy of Science, Kraków, Poland
| | - Vimal Chandra Pandey
- Department of Environmental Science, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
| | - Alicja Babst-Kostecka
- Department of Environmental Science, The University of Arizona, Tucson, Arizona, USA
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2
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Yoshida N, Morinaga SI, Wakamiya T, Ishii Y, Kubota S, Hikosaka K. Does selection occur at the intermediate zone of two insufficiently isolated populations? A whole-genome analysis along an altitudinal gradient. JOURNAL OF PLANT RESEARCH 2023; 136:183-199. [PMID: 36547771 DOI: 10.1007/s10265-022-01429-1] [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: 07/03/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Adaptive divergence occurs even between insufficiently isolated populations when there is a great difference in environments between their habitats. Individuals present in an intermediate zone of the two divergent populations are expected to have an admixed genetic structure due to gene flow. A selective pressure that acts on the genetically admixed individuals may limit the gene flow and maintain the adaptive divergence. Here, we addressed a question whether selection occurs in the genetically admixed individuals between two divergent populations. Arabidopsis halleri is a perennial montane plant, which has clear phenotypic dimorphisms between highland and lowland habitats in Mt. Ibuki, central Japan. We obtained the whole-genome sequences of Arabidopsis halleri plants along an altitudinal gradient of 359-1,317 m with a high spatial resolution (mean altitudinal interval of 20 m). We found a zone where the highland and lowland genes were mixing (intermediate subpopulation). In the intermediate subpopulation, we identified 5 and 13 genome regions, which included 3 and 8 genes, that had a high frequency of alleles that are accumulated in highland and lowland subpopulations, respectively. In addition, we also found that the frequency of highland alleles of these selected genome regions was smaller in the lowland subpopulation compared with that of the non-selected regions. These results suggest that the selection in the intermediate subpopulation might limit the gene flow and contribute to the adaptive divergence between altitudes. We also identified 7 genome regions that had low heterozygote frequencies in the intermediate subpopulation. We conclude that different types of selection in addition to gene flow occur at the intermediate altitude and shape the genetic structure across altitudes.
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Affiliation(s)
- Naofumi Yoshida
- Graduate School of Life Sciences, Tohoku University, 980-8578, Aoba, Sendai, Japan.
| | - Shin-Ichi Morinaga
- Faculty of Life and Environmental Sciences, Teikyo University of Science, 120-0045, Adachi, Tokyo, Japan
| | - Takeshi Wakamiya
- Graduate School of Integrated Sciences for Life, Hiroshima University, 739-8528, Kagamiyama, Hiroshima, Higashi, Japan
| | - Yuu Ishii
- Graduate School of Life Sciences, Tohoku University, 980-8578, Aoba, Sendai, Japan
| | | | - Kouki Hikosaka
- Graduate School of Life Sciences, Tohoku University, 980-8578, Aoba, Sendai, Japan
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Honjo MN, Kudoh H. Arabidopsis halleri: a perennial model system for studying population differentiation and local adaptation. AOB PLANTS 2019; 11:plz076. [PMID: 31832127 PMCID: PMC6899346 DOI: 10.1093/aobpla/plz076] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/26/2019] [Indexed: 05/21/2023]
Abstract
Local adaptation is assumed to occur when populations differ in a phenotypic trait or a set of traits, and such variation has a genetic basis. Here, we introduce Arabidopsis halleri and its life history as a perennial model system to study population differentiation and local adaptation. Studies on altitudinal adaptation have been conducted in two regions: Mt. Ibuki in Japan and the European Alps. Several studies have demonstrated altitudinal adaptation in ultraviolet-B (UV-B) tolerance, leaf water repellency against spring frost and anti-herbivore defences. Studies on population differentiation in A. halleri have also focused on metal hyperaccumulation and tolerance to heavy metal contamination. In these study systems, genome scans to identify candidate genes under selection have been applied. Lastly, we briefly discuss how RNA-Seq can broaden phenotypic space and serve as a link to underlying mechanisms. In conclusion, A. halleri provides us with opportunities to study population differentiation and local adaptation, and relate these to the genetic systems underlying target functional traits.
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Affiliation(s)
- Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
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Bothe H, Słomka A. Divergent biology of facultative heavy metal plants. JOURNAL OF PLANT PHYSIOLOGY 2017; 219:45-61. [PMID: 29028613 DOI: 10.1016/j.jplph.2017.08.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 05/04/2023]
Abstract
Among heavy metal plants (the metallophytes), facultative species can live both in soils contaminated by an excess of heavy metals and in non-affected sites. In contrast, obligate metallophytes are restricted to polluted areas. Metallophytes offer a fascinating biology, due to the fact that species have developed different strategies to cope with the adverse conditions of heavy metal soils. The literature distinguishes between hyperaccumulating, accumulating, tolerant and excluding metallophytes, but the borderline between these categories is blurred. Due to the fact that heavy metal soils are dry, nutrient limited and are not uniform but have a patchy distribution in many instances, drought-tolerant or low nutrient demanding species are often regarded as metallophytes in the literature. In only a few cases, the concentrations of heavy metals in soils are so toxic that only a few specifically adapted plants, the genuine metallophytes, can cope with these adverse soil conditions. Current molecular biological studies focus on the genetically amenable and hyperaccumulating Arabidopsis halleri and Noccaea (Thlaspi) caerulescens of the Brassicaceae. Armeria maritima ssp. halleri utilizes glands for the excretion of heavy metals and is, therefore, a heavy metal excluder. The two endemic zinc violets of Western Europe, Viola lutea ssp. calaminaria of the Aachen-Liège area and Viola lutea ssp. westfalica of the Pb-Cu-ditch of Blankenrode, Eastern Westphalia, as well as Viola tricolor ecotypes of Eastern Europe, keep their cells free of excess heavy metals by arbuscular mycorrhizal fungi which bind heavy metals. The Caryophyllaceae, Silene vulgaris f. humilis and Minuartia verna, apparently discard leaves when overloaded with heavy metals. All Central European metallophytes have close relatives that grow in areas outside of heavy metal soils, mainly in the Alps, and have, therefore, been considered as relicts of the glacial epoch in the past. However, the current literature favours the idea that hyperaccumulation of heavy metals serves plants as deterrent against attack by feeding animals (termed elemental defense hypothesis). The capability to hyperaccumulate heavy metals in A. halleri and N. caerulescens is achieved by duplications and alterations of the cis-regulatory properties of genes coding for heavy metal transporting/excreting proteins. Several metallophytes have developed ecotypes with a varying content of such heavy metal transporters as an adaption to the specific toxicity of a heavy metal site.
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Affiliation(s)
- Hermann Bothe
- Botanical Institute, The University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany.
| | - Aneta Słomka
- Department of Plant Cytology and Embryology, Jagiellonian University, Gronostajowa 9 Str., 30-387 Cracow, Poland.
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Asaf S, Khan AL, Khan MA, Waqas M, Kang SM, Yun BW, Lee IJ. Chloroplast genomes of Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea: Structures and comparative analysis. Sci Rep 2017; 7:7556. [PMID: 28790364 PMCID: PMC5548756 DOI: 10.1038/s41598-017-07891-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 07/05/2017] [Indexed: 11/26/2022] Open
Abstract
We investigated the complete chloroplast (cp) genomes of non-model Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea using Illumina paired-end sequencing to understand their genetic organization and structure. Detailed bioinformatics analysis revealed genome sizes of both subspecies ranging between 154.4~154.5 kbp, with a large single-copy region (84,197~84,158 bp), a small single-copy region (17,738~17,813 bp) and pair of inverted repeats (IRa/IRb; 26,264~26,259 bp). Both cp genomes encode 130 genes, including 85 protein-coding genes, eight ribosomal RNA genes and 37 transfer RNA genes. Whole cp genome comparison of A. halleri ssp. gemmifera and A. lyrata ssp. petraea, along with ten other Arabidopsis species, showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. The location and distribution of repeat sequences were determined, and sequence divergences of shared genes were calculated among related species. Comparative phylogenetic analysis of the entire genomic data set and 70 shared genes between both cp genomes confirmed the previous phylogeny and generated phylogenetic trees with the same topologies. The sister species of A. halleri ssp. gemmifera is A. umezawana, whereas the closest relative of A. lyrata spp. petraea is A. arenicola.
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Affiliation(s)
- Sajjad Asaf
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Abdul Latif Khan
- Chair of Oman's Medicinal Plants & Marine Natural Products, University of Nizwa, Nizwa, 616, Oman
| | - Muhammad Aaqil Khan
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Muhammad Waqas
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sang-Mo Kang
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Byung-Wook Yun
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Briskine RV, Paape T, Shimizu-Inatsugi R, Nishiyama T, Akama S, Sese J, Shimizu KK. Genome assembly and annotation ofArabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology. Mol Ecol Resour 2016; 17:1025-1036. [DOI: 10.1111/1755-0998.12604] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 08/04/2016] [Accepted: 09/16/2016] [Indexed: 01/30/2023]
Affiliation(s)
- Roman V. Briskine
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 Zurich CH-8057 Switzerland
| | - Timothy Paape
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 Zurich CH-8057 Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 Zurich CH-8057 Switzerland
| | - Tomoaki Nishiyama
- Advanced Science Research Center; Kanazawa University; 13-1 Takara-machi Kanazawa 920-0934 Japan
| | - Satoru Akama
- Biotechnology Research Institute for Drug Discovery; National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7 Aomi Koto-ku Tokyo 135-0064 Japan
| | - Jun Sese
- Biotechnology Research Institute for Drug Discovery; National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7 Aomi Koto-ku Tokyo 135-0064 Japan
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 Zurich CH-8057 Switzerland
- Kihara Institute for Biological Research; Yokohama City University; 642-12 Maioka Totsuka-ward Yokohama 244-0813 Japan
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Wasowicz P, Pauwels M, Pasierbinski A, Przedpelska-Wasowicz EM, Babst-Kostecka AA, Saumitou-Laprade P, Rostanski A. Phylogeography of Arabidopsis halleri (Brassicaceae) in mountain regions of Central Europe inferred from cpDNA variation and ecological niche modelling. PeerJ 2016; 4:e1645. [PMID: 26835186 PMCID: PMC4734066 DOI: 10.7717/peerj.1645] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 01/11/2016] [Indexed: 11/20/2022] Open
Abstract
The present study aimed to investigate phylogeographical patterns present within A. halleri in Central Europe. 1,281 accessions sampled from 52 populations within the investigated area were used in the study of genetic variation based on chloroplast DNA. Over 500 high-quality species occurrence records were used in ecological niche modelling experiments. We evidenced the presence of a clear phylogeographic structure within A. halleri in Central Europe. Our results showed that two genetically different groups of populations are present in western and eastern part of the Carpathians. The hypothesis of the existence of a glacial refugium in the Western Carpathians adn the Bohemian Forest cannot be rejected from our data. It seems, however, that the evidence collected during the present study is not conclusive. The area of Sudetes was colonised after LGM probably by migrants from the Bohemian Forest.
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Affiliation(s)
- Pawel Wasowicz
- Icelandic Institute of Natural History, Iceland
- Faculty of Biology and Environmental Protection, Department of Botany and Nature Protection, University of Silesia, Katowice, Poland
| | - Maxime Pauwels
- Unité Evo-Eco-Paléo (EEP)—UMR 8198, Université de Lille—Sciences et Technologies, CNRS, Villeneuve d’Ascq, France
| | - Andrzej Pasierbinski
- Faculty of Biology and Environmental Protection, Department of Botany and Nature Protection, University of Silesia, Katowice, Poland
| | | | | | - Pierre Saumitou-Laprade
- Unité Evo-Eco-Paléo (EEP)—UMR 8198, Université des Sciences et Technologies de Lille (Lille I), Villeneuve d’Ascq, France
| | - Adam Rostanski
- Faculty of Biology and Environmental Protection, Department of Botany and Nature Protection, University of Silesia, Katowice, Poland
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Hohmann N, Schmickl R, Chiang TY, Lučanová M, Kolář F, Marhold K, Koch MA. Taming the wild: resolving the gene pools of non-model Arabidopsis lineages. BMC Evol Biol 2014; 14:224. [PMID: 25344686 PMCID: PMC4216345 DOI: 10.1186/s12862-014-0224-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 10/15/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of the Arabidopsis supra-groups and hypothesized evolutionary lineages and none include sampling at a world-wide scale. Here we explore the gene pools of these various taxa using various molecular markers and cytological analyses. RESULTS Based on ITS, microsatellite, chloroplast and nuclear DNA content data we demonstrate the presence of three major evolutionary groups broadly characterized as A. lyrata group, A. halleri group and A. arenosa group. All are composed of further species and sub-species forming larger aggregates. Depending on the resolution of the marker, a few closely related taxa such as A. pedemontana, A. cebennensis and A. croatica are also clearly distinct evolutionary lineages. ITS sequences and a population-based screen based on microsatellites were highly concordant. The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry. The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins. CONCLUSIONS Our study provides a comprehensive overview of the genetic variation within and among the various taxa of the genus Arabidopsis. The resolved gene pools and evolutionary lineages will set the framework for future comparative studies on genetic diversity. Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.
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Affiliation(s)
- Nora Hohmann
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany.
| | - Roswitha Schmickl
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany.
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, Cheng-Kung University, Tainan, Taiwan.
| | - Magdalena Lučanová
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic.
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic.
| | - Filip Kolář
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic.
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic.
| | - Karol Marhold
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic.
- Institute of Botany Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, SK-845 23, Slovakia.
| | - Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany.
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Koch MA, German DA. Taxonomy and systematics are key to biological information: Arabidopsis, Eutrema (Thellungiella), Noccaea and Schrenkiella (Brassicaceae) as examples. FRONTIERS IN PLANT SCIENCE 2013; 4:267. [PMID: 23914192 PMCID: PMC3728732 DOI: 10.3389/fpls.2013.00267] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/02/2013] [Indexed: 05/20/2023]
Abstract
Taxonomy and systematics provide the names and evolutionary framework for any biological study. Without these names there is no access to a biological context of the evolutionary processes which gave rise to a given taxon: close relatives and sister species (hybridization), more distantly related taxa (ancestral states), for example. This is not only true for the single species a research project is focusing on, but also for its relatives, which might be selected for comparative approaches and future research. Nevertheless, taxonomical and systematic knowledge is rarely fully explored and considered across biological disciplines. One would expect the situation to be more developed with model organisms such as Noccaea, Arabidopsis, Schrenkiella and Eutrema (Thellungiella). However, we show the reverse. Using Arabidopsis halleri and Noccaea caerulescens, two model species among metal accumulating taxa, we summarize and reflect past taxonomy and systematics of Arabidopsis and Noccaea and provide a modern synthesis of taxonomic, systematic and evolutionary perspectives. The same is presented for several species of Eutrema s. l. and Schrenkiella recently appeared as models for studying stress tolerance in plants and widely known under the name Thellungiella.
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Affiliation(s)
- Marcus A. Koch
- Department of Biodiversity and Plant Systematics, Center for Organismal Studies Heidelberg, Heidelberg UniversityHeidelberg, Germany
| | - Dmitry A. German
- Department of Biodiversity and Plant Systematics, Center for Organismal Studies Heidelberg, Heidelberg UniversityHeidelberg, Germany
- South-Siberian Botanical Garden, Altai State UniversityBarnaul, Russia
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Pauwels M, Vekemans X, Godé C, Frérot H, Castric V, Saumitou-Laprade P. Nuclear and chloroplast DNA phylogeography reveals vicariance among European populations of the model species for the study of metal tolerance, Arabidopsis halleri (Brassicaceae). THE NEW PHYTOLOGIST 2012; 193:916-928. [PMID: 22225532 DOI: 10.1111/j.1469-8137.2011.04003.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Arabidopsis halleri is a pseudometallophyte involved in numerous molecular studies of the adaptation to anthropogenic metal stress. In order to test the representativeness of genetic accessions commonly used in these studies, we investigated the A. halleri population genetic structure in Europe. Microsatellite and nucleotide polymorphisms from the nuclear and chloroplast genomes, respectively, were used to genotype 65 populations scattered over Europe. The large-scale population structure was characterized by a significant phylogeographic signal between two major genetic units. The localization of the phylogeographic break was assumed to result from vicariance between large populations isolated in southern and central Europe, on either side of ice sheets covering the Alps during the Quaternary ice ages. Genetic isolation was shown to be maintained in western Europe by the high summits of the Alps, whereas admixture was detected in the Carpathians. Considering the phylogeographic literature, our results suggest a distinct phylogeographic pattern for European species occurring in both mountain and lowland habitats. Considering the evolution of metal adaptation in A. halleri, it appears that recent adaptations to anthropogenic metal stress that have occurred within either phylogeographic unit should be regarded as independent events that potentially have involved the evolution of a variety of genetic mechanisms.
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Affiliation(s)
- Maxime Pauwels
- Laboratoire de Génétique et Evolution des Populations Végétales, FRE CNRS 3268, Université de Lille-Lille1, F-59655 Villeneuve d'Ascq, France
| | - Xavier Vekemans
- Laboratoire de Génétique et Evolution des Populations Végétales, FRE CNRS 3268, Université de Lille-Lille1, F-59655 Villeneuve d'Ascq, France
| | - Cécile Godé
- Laboratoire de Génétique et Evolution des Populations Végétales, FRE CNRS 3268, Université de Lille-Lille1, F-59655 Villeneuve d'Ascq, France
| | - Hélène Frérot
- Laboratoire de Génétique et Evolution des Populations Végétales, FRE CNRS 3268, Université de Lille-Lille1, F-59655 Villeneuve d'Ascq, France
| | - Vincent Castric
- Laboratoire de Génétique et Evolution des Populations Végétales, FRE CNRS 3268, Université de Lille-Lille1, F-59655 Villeneuve d'Ascq, France
| | - Pierre Saumitou-Laprade
- Laboratoire de Génétique et Evolution des Populations Végétales, FRE CNRS 3268, Université de Lille-Lille1, F-59655 Villeneuve d'Ascq, France
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Hunter B, Bomblies K. Progress and Promise in using Arabidopsis to Study Adaptation, Divergence, and Speciation. THE ARABIDOPSIS BOOK 2010; 8:e0138. [PMID: 22303263 PMCID: PMC3244966 DOI: 10.1199/tab.0138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Fundamental questions remain to be answered on how lineages split and new species form. The Arabidopsis genus, with several increasingly well characterized species closely related to the model system A. thaliana, provides a rare opportunity to address key questions in speciation research. Arabidopsis species, and in some cases populations within a species, vary considerably in their habitat preferences, adaptations to local environments, mating system, life history strategy, genome structure and chromosome number. These differences provide numerous open doors for understanding the role these factors play in population divergence and how they may cause barriers to arise among nascent species. Molecular tools available in A. thaliana are widely applicable to its relatives, and together with modern comparative genomic approaches they will provide new and increasingly mechanistic insights into the processes underpinning lineage divergence and speciation. We will discuss recent progress in understanding the molecular basis of local adaptation, reproductive isolation and genetic incompatibility, focusing on work utilizing the Arabidopsis genus, and will highlight several areas in which additional research will provide meaningful insights into adaptation and speciation processes in this genus.
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Affiliation(s)
- Ben Hunter
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave., Cambridge, MA, USA
| | - Kirsten Bomblies
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave., Cambridge, MA, USA
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Shimizu-Inatsugi R, Lihová J, Iwanaga H, Kudoh H, Marhold K, Savolainen O, Watanabe K, Yakubov VV, Shimizu KK. The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri. Mol Ecol 2009; 18:4024-48. [PMID: 19754506 DOI: 10.1111/j.1365-294x.2009.04329.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyploidization, or genome duplication, has played a critical role in the diversification of animals, fungi and plants. Little is known about the population structure and multiple origins of polyploid species because of the difficulty in identifying multiple homeologous nuclear genes. The allotetraploid species Arabidopsis kamchatica is closely related to the model species Arabidopsis thaliana and is distributed in a broader climatic niche than its parental species. Here, we performed direct sequencing of homeologous pairs of the low-copy nuclear genes WER and CHS by designing homeolog-specific primers, and obtained also chloroplast and ribosomal internal transcribed spacer sequences. Phylogenetic analysis showed that 50 individuals covering the distribution range including North America are allopolyploids derived from Arabidopsis lyrata and Arabidopsis halleri. Three major clusters within A. kamchatica were detected using Bayesian clustering. One cluster has widespread distribution. The other two are restricted to the southern part of the distribution range including Japan, where the parent A. lyrata is not currently distributed. This suggests that the mountains in Central Honshu and surrounding areas in Japan served as refugia during glacial-interglacial cycles and retained this diversity. We also found that multiple haplotypes of nuclear and chloroplast sequences of A. kamchatica are identical to those of their parental species. This indicates that multiple diploid individuals contributed to the origin of A. kamchatica. The haplotypes of low-copy nuclear genes in Japan suggest independent polyploidization events rather than introgression. Our findings suggest that self-compatibility and gene silencing occurred independently in different origins.
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