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Penin AA, Kasianov AS, Klepikova AV, Omelchenko DO, Makarenko MS, Logacheva MD. Origin and diversity of Capsella bursa-pastoris from the genomic point of view. BMC Biol 2024; 22:52. [PMID: 38439107 PMCID: PMC10913212 DOI: 10.1186/s12915-024-01832-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/23/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Capsella bursa-pastoris, a cosmopolitan weed of hybrid origin, is an emerging model object for the study of early consequences of polyploidy, being a fast growing annual and a close relative of Arabidopsis thaliana. The development of this model is hampered by the absence of a reference genome sequence. RESULTS We present here a subgenome-resolved chromosome-scale assembly and a genetic map of the genome of Capsella bursa-pastoris. It shows that the subgenomes are mostly colinear, with no massive deletions, insertions, or rearrangements in any of them. A subgenome-aware annotation reveals the lack of genome dominance-both subgenomes carry similar number of genes. While most chromosomes can be unambiguously recognized as derived from either paternal or maternal parent, we also found homeologous exchange between two chromosomes. It led to an emergence of two hybrid chromosomes; this event is shared between distant populations of C. bursa-pastoris. The whole-genome analysis of 119 samples belonging to C. bursa-pastoris and its parental species C. grandiflora/rubella and C. orientalis reveals introgression from C. orientalis but not from C. grandiflora/rubella. CONCLUSIONS C. bursa-pastoris does not show genome dominance. In the earliest stages of evolution of this species, a homeologous exchange occurred; its presence in all present-day populations of C. bursa-pastoris indicates on a single origin of this species. The evidence coming from whole-genome analysis challenges the current view that C. grandiflora/rubella was a direct progenitor of C. bursa-pastoris; we hypothesize that it was an extinct (or undiscovered) species sister to C. grandiflora/rubella.
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Affiliation(s)
- Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.
| | - Artem S Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Denis O Omelchenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maksim S Makarenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
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2
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Duan T, Sicard A, Glémin S, Lascoux M. Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris. eLife 2024; 12:RP88398. [PMID: 38189348 PMCID: PMC10945474 DOI: 10.7554/elife.88398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
Allopolyploidization is a frequent evolutionary transition in plants that combines whole-genome duplication (WGD) and interspecific hybridization. The genome of an allopolyploid species results from initial interactions between parental genomes and long-term evolution. Distinguishing the contributions of these two phases is essential to understanding the evolutionary trajectory of allopolyploid species. Here, we compared phenotypic and transcriptomic changes in natural and resynthesized Capsella allotetraploids with their diploid parental species. We focused on phenotypic traits associated with the selfing syndrome and on transcription-level phenomena such as expression-level dominance (ELD), transgressive expression (TRE), and homoeolog expression bias (HEB). We found that selfing syndrome, high pollen, and seed quality in natural allotetraploids likely resulted from long-term evolution. Similarly, TRE and most down-regulated ELD were only found in natural allopolyploids. Natural allotetraploids also had more ELD toward the self-fertilizing parental species than resynthesized allotetraploids, mirroring the establishment of the selfing syndrome. However, short-term changes mattered, and 40% of the cases of ELD in natural allotetraploids were already observed in resynthesized allotetraploids. Resynthesized allotetraploids showed striking variation of HEB among chromosomes and individuals. Homoeologous synapsis was its primary source and may still be a source of genetic variation in natural allotetraploids. In conclusion, both short- and long-term mechanisms contributed to transcriptomic and phenotypic changes in natural allotetraploids. However, the initial gene expression changes were largely reshaped during long-term evolution leading to further morphological changes.
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Affiliation(s)
- Tianlin Duan
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Adrien Sicard
- Department of Plant Biology, Swedish University of Agricultural SciencesUppsalaSweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala UniversityUppsalaSweden
- UMR CNRS 6553 ECOBIO, Campus BeaulieuRennesFrance
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala UniversityUppsalaSweden
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3
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Fachrul M, Karkey A, Shakya M, Judd LM, Harshegyi T, Sim KS, Tonks S, Dongol S, Shrestha R, Salim A, Baker S, Pollard AJ, Khor CC, Dolecek C, Basnyat B, Dunstan SJ, Holt KE, Inouye M. Direct inference and control of genetic population structure from RNA sequencing data. Commun Biol 2023; 6:804. [PMID: 37532769 PMCID: PMC10397182 DOI: 10.1038/s42003-023-05171-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 07/24/2023] [Indexed: 08/04/2023] Open
Abstract
RNAseq data can be used to infer genetic variants, yet its use for estimating genetic population structure remains underexplored. Here, we construct a freely available computational tool (RGStraP) to estimate RNAseq-based genetic principal components (RG-PCs) and assess whether RG-PCs can be used to control for population structure in gene expression analyses. Using whole blood samples from understudied Nepalese populations and the Geuvadis study, we show that RG-PCs had comparable results to paired array-based genotypes, with high genotype concordance and high correlations of genetic principal components, capturing subpopulations within the dataset. In differential gene expression analysis, we found that inclusion of RG-PCs as covariates reduced test statistic inflation. Our paper demonstrates that genetic population structure can be directly inferred and controlled for using RNAseq data, thus facilitating improved retrospective and future analyses of transcriptomic data.
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Affiliation(s)
- Muhamad Fachrul
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal
| | - Mila Shakya
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Taylor Harshegyi
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Kar Seng Sim
- Genome Institute of Singapore, Singapore, Singapore
| | - Susan Tonks
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal
| | | | - Agus Salim
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, Australia
- Department of Population Health, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | | | - Christiane Dolecek
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Sarah J Dunstan
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
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Novikova PY, Kolesnikova UK, Scott AD. Ancestral self-compatibility facilitates the establishment of allopolyploids in Brassicaceae. PLANT REPRODUCTION 2023; 36:125-138. [PMID: 36282331 PMCID: PMC9957919 DOI: 10.1007/s00497-022-00451-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/20/2022] [Indexed: 05/15/2023]
Abstract
Self-incompatibility systems based on self-recognition evolved in hermaphroditic plants to maintain genetic variation of offspring and mitigate inbreeding depression. Despite these benefits in diploid plants, for polyploids who often face a scarcity of mating partners, self-incompatibility can thwart reproduction. In contrast, self-compatibility provides an immediate advantage: a route to reproductive viability. Thus, diploid selfing lineages may facilitate the formation of new allopolyploid species. Here, we describe the mechanism of establishment of at least four allopolyploid species in Brassicaceae (Arabidopsis suecica, Arabidopsis kamchatica, Capsella bursa-pastoris, and Brassica napus), in a manner dependent on the prior loss of the self-incompatibility mechanism in one of the ancestors. In each case, the degraded S-locus from one parental lineage was dominant over the functional S-locus of the outcrossing parental lineage. Such dominant loss-of-function mutations promote an immediate transition to selfing in allopolyploids and may facilitate their establishment.
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Affiliation(s)
- Polina Yu Novikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany.
| | - Uliana K Kolesnikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany
| | - Alison Dawn Scott
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany
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Li B, Gschwend AR, Hovick SM, Gutek A, McHale L, Harrison SK, Regnier EE. Evolution of weedy giant ragweed ( Ambrosia trifida): Multiple origins and gene expression variability facilitates weediness. Ecol Evol 2022; 12:e9590. [PMID: 36514541 PMCID: PMC9731915 DOI: 10.1002/ece3.9590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Agricultural weeds may originate from wild populations, but the origination patterns and genetics underlying this transition remain largely unknown. Analysis of weedy-wild paired populations from independent locations may provide evidence to identify key genetic variation contributing to this adaptive shift. We performed genetic variation and expression analyses on transcriptome data from 67 giant ragweed samples collected from different locations in Ohio, Iowa, and Minnesota and found geographically separated weedy populations likely originated independently from their adjacent wild populations, but subsequent spreading of weedy populations also occurred locally. By using eight closely related weedy-wild paired populations, we identified thousands of unique transcripts in weedy populations that reflect shared or specific functions corresponding, respectively, to both convergently evolved and population-specific weediness processes. In addition, differential expression of specific groups of genes was detected between weedy and wild giant ragweed populations using gene expression diversity and gene co-expression network analyses. Our study suggests an integrated route of weedy giant ragweed origination, consisting of independent origination combined with the subsequent spreading of certain weedy populations, and provides several lines of evidence to support the hypothesis that gene expression variability plays a key role in the evolution of weedy species.
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Affiliation(s)
- Bo Li
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Andrea R. Gschwend
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Stephen M. Hovick
- Department of Evolution, Ecology and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA
| | - Amanda Gutek
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Leah McHale
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - S. Kent Harrison
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Emilie E. Regnier
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
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Mikula O, Macholán M, Ďureje Ľ, Hiadlovská Z, Daniszová K, Janotová K, Vošlajerová Bímová B. House mouse subspecies do differ in their social structure. Ecol Evol 2022; 12:e9683. [PMID: 36590341 PMCID: PMC9797468 DOI: 10.1002/ece3.9683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/17/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022] Open
Abstract
It is widely acknowledged that population structure can have a substantial impact on evolutionary trajectories. In social animals, this structure is strongly influenced by relationships among the population members, so studies of differences in social structure between diverging populations or nascent species are of prime interest. Ideal models for such a study are two house mouse subspecies, Mus musculus musculus and M. m. domesticus, meeting in Europe along a secondary contact zone. Though the latter subspecies has usually been supposed to form tighter and more isolated social units than the former, the evidence is still inconclusive. Here, we carried out a series of radiofrequency identification experiments in semi-natural enclosures to gather large longitudinal data sets on individual mouse movements. The data were summarized in the form of uni- and multi-layer social networks. Within them, we could delimit and describe the social units ("modules"). While the number of estimated units was similar in both subspecies, domesticus revealed a more "modular" structure. This subspecies also showed more intramodular social interactions, higher spatial module separation, higher intramodular persistence of parent-offspring contacts, and lower multiple paternity, suggesting more effective control of dominant males over reproduction. We also demonstrate that long-lasting modules can be identified with basic reproductive units or demes. We thus provide the first robust evidence that the two subspecies differ in their social structure and dynamics of the structure formation.
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Affiliation(s)
- Ondřej Mikula
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and GeneticsCzech Academy of SciencesBrnoCzech Republic
- Institute of Vertebrate BiologyCzech Academy of SciencesResearch Facility StudenecBrnoCzech Republic
| | - Miloš Macholán
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and GeneticsCzech Academy of SciencesBrnoCzech Republic
- Department of Botany and Zoology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Ľudovít Ďureje
- Institute of Vertebrate BiologyCzech Academy of SciencesResearch Facility StudenecBrnoCzech Republic
| | - Zuzana Hiadlovská
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and GeneticsCzech Academy of SciencesBrnoCzech Republic
| | - Kristina Daniszová
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and GeneticsCzech Academy of SciencesBrnoCzech Republic
| | - Kateřina Janotová
- Institute of Vertebrate BiologyCzech Academy of SciencesResearch Facility StudenecBrnoCzech Republic
| | - Barbora Vošlajerová Bímová
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and GeneticsCzech Academy of SciencesBrnoCzech Republic
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7
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Cornille A, Tiret M, Salcedo A, Huang HR, Orsucci M, Milesi P, Kryvokhyzha D, Holm K, Ge XJ, Stinchcombe JR, Glémin S, Wright SI, Lascoux M. The relative role of plasticity and demographic history in Capsella bursa-pastoris: a common garden experiment in Asia and Europe. AOB PLANTS 2022; 14:plac011. [PMID: 35669442 PMCID: PMC9162126 DOI: 10.1093/aobpla/plac011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/28/2022] [Indexed: 05/15/2023]
Abstract
The colonization success of a species depends on the interplay between its phenotypic plasticity, adaptive potential and demographic history. Assessing their relative contributions during the different phases of a species range expansion is challenging, and requires large-scale experiments. Here, we investigated the relative contributions of plasticity, performance and demographic history to the worldwide expansion of the shepherd's purse, Capsella bursa-pastoris. We installed two large common gardens of the shepherd's purse, a young, self-fertilizing, allopolyploid weed with a worldwide distribution. One common garden was located in Europe, the other in Asia. We used accessions from three distinct genetic clusters (Middle East, Europe and Asia) that reflect the demographic history of the species. Several life-history traits were measured. To explain the phenotypic variation between and within genetic clusters, we analysed the effects of (i) the genetic clusters, (ii) the phenotypic plasticity and its association to fitness and (iii) the distance in terms of bioclimatic variables between the sampling site of an accession and the common garden, i.e. the environmental distance. Our experiment showed that (i) the performance of C. bursa-pastoris is closely related to its high phenotypic plasticity; (ii) within a common garden, genetic cluster was a main determinant of phenotypic differences; and (iii) at the scale of the experiment, the effect of environmental distance to the common garden could not be distinguished from that of genetic clusters. Phenotypic plasticity and demographic history both play important role at different stages of range expansion. The success of the worldwide expansion of C. bursa-pastoris was undoubtedly influenced by its strong phenotypic plasticity.
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Affiliation(s)
| | | | | | | | - Marion Orsucci
- Department of Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
- Science for Life Laboratory, 752 37 Uppsala, Sweden
| | - Dmytro Kryvokhyzha
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Karl Holm
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, M5S 3B2 Toronto, ON, Canada
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Orsucci M, Yang X, Vanikiotis T, Guerrina M, Duan T, Lascoux M, Glémin S. Competitive ability depends on mating system and ploidy level across Capsella species. ANNALS OF BOTANY 2022; 129:697-708. [PMID: 35325927 PMCID: PMC9113120 DOI: 10.1093/aob/mcac044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 10/14/2021] [Accepted: 03/23/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Self-fertilization is often associated with ecological traits corresponding to the ruderal strategy, and selfers are expected to be less competitive than outcrossers, either because of a colonization/competition trade-off or because of the deleterious genetic effects of selfing. Range expansion could reduce further competitive ability while polyploidy could mitigate the effects of selfing. If pollinators are not limited, individual fitness is thus expected to be higher in outcrossers than in selfers and, within selfers, in polyploids than in diploids. Although often proposed in the botanical literature and also suggested by meta-analyses, these predictions have not been directly tested yet. METHODS In order to compare fitness and the competitive ability of four Capsella species with a different mating system and ploidy level, we combined two complementary experiments. First, we carried out an experiment outdoors in north-west Greece, i.e. within the range of the obligate outcrossing species, C. grandiflora, where several life history traits were measured under two different disturbance treatments, weeded plots vs. unweeded plots. To better control competition and to remove potential effects of local adaptation of the outcrosser, we also performed a similar competition experiment but under growth chamber conditions. KEY RESULTS In the outdoor experiment, disturbance of the environment did not affect the phenotype in any of the four species. For most traits, the obligate outcrossing species performed better than all selfing species. In contrast, polyploids did not survive or reproduce better than diploids. Under controlled conditions, as in the field experiment, the outcrosser had a higher fitness than selfing species and was less affected by competition. Finally, contrary to the outdoor experiment where the two behaved identically, polyploid selfers were less affected by competition than diploid selfes. CONCLUSIONS In the Capsella genus, selfing induces lower fitness than outcrossing and can also reduce competitive ability. The effect of polyploidy is, however, unclear. These results highlight the possible roles of ecological context in the evolution of selfing species.
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Affiliation(s)
- Marion Orsucci
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Xuyue Yang
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Theofilos Vanikiotis
- Department of Biological Applications & Technology, University of Ioannina, Leof. S. Niarchou GR-451 10, Ioannina, Greece
| | - Maria Guerrina
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Tianlin Duan
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
- UMR CNRS 6553 ECOBIO, Campus Beaulieu, bât 14a, CS 74205, 35042 Rennes, France
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9
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López-Baucells A, Yoh N, Rocha R, Bobrowiec PED, Palmeirim JM, Meyer CFJ. Optimizing bat bioacoustic surveys in human-modified Neotropical landscapes. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02366. [PMID: 33938592 DOI: 10.1002/eap.2366] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
During the last decades, the use of bioacoustics as a non-invasive and cost-effective sampling method has greatly increased worldwide. For bats, acoustic surveys have long been known to complement traditional mist-netting, however, appropriate protocol guidelines are still lacking for tropical regions. Establishing the minimum sampling effort needed to detect ecological changes in bat assemblages (e.g., activity, composition, and richness) is crucial in view of workload and project cost constraints, and because detecting such changes must be reliable enough to support effective conservation management. Using one of the most comprehensive tropical bat acoustic data sets, collected in the Amazon, we assessed the minimum survey effort required to accurately assess the completeness of assemblage inventories and habitat selection in fragmented forest landscapes for aerial insectivorous bats. We evaluated a combination of 20 different temporal sampling schemes, which differed regarding number of hours per night, number of nights per site, and sampling only during the wet or dry season, or both. This was assessed under two different landscape scenarios: in primary forest fragments embedded in a matrix of secondary forest and in the same forest fragments, but after they had been re-isolated through clearing of the secondary forest. We found that the sampling effort required to achieve 90% inventory completeness varied considerably depending on the research aim and the landscape scenario evaluated, averaging ~80 and 10 nights before and after fragment re-isolation, respectively. Recording for more than 4 h per night did not result in a substantial reduction in the required number of sampling nights. Regarding the effects of habitat selection, except for assemblage composition, bat responses in terms of richness, diversity, and activity were similar across all sampling schemes after fragment re-isolation. However, before re-isolation, a minimum of four to six sampling hours per night after dusk and three to five nights of sampling per site were needed to detect significant effects that could otherwise go unnoticed. Based on our results, we propose guidelines that will aid to optimize sampling protocols for bat acoustic surveys in the Neotropics.
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Affiliation(s)
- Adrià López-Baucells
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisbon, 1749-016, Portugal
- Natural Sciences Museum of Granollers, Av/Francesc Macià 51, Granollers, Catalonia, 08402, Spain
- Biological Dynamics of Forest Fragments Project (PDBFF), National Institute for Amazonian Research and Smithsonian Tropical Research Institute, Manaus, AM, 69011-970, Brazil
| | - Natalie Yoh
- Ecosystems and Environment Research Centre (EERC), School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT, United Kingdom
- Durrell Institute of Conservation & Ecology (DICE), University of Kent, Canterbury, CT2 7NZ, United Kingdom
| | - Ricardo Rocha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisbon, 1749-016, Portugal
- Biological Dynamics of Forest Fragments Project (PDBFF), National Institute for Amazonian Research and Smithsonian Tropical Research Institute, Manaus, AM, 69011-970, Brazil
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Portugal
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, Institute of Agronomy, University of Lisbon, Lisbon, 1349-017, Portugal
| | - Paulo E D Bobrowiec
- Biological Dynamics of Forest Fragments Project (PDBFF), National Institute for Amazonian Research and Smithsonian Tropical Research Institute, Manaus, AM, 69011-970, Brazil
| | - Jorge M Palmeirim
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisbon, 1749-016, Portugal
| | - Christoph F J Meyer
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisbon, 1749-016, Portugal
- Biological Dynamics of Forest Fragments Project (PDBFF), National Institute for Amazonian Research and Smithsonian Tropical Research Institute, Manaus, AM, 69011-970, Brazil
- Ecosystems and Environment Research Centre (EERC), School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT, United Kingdom
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Wang X, Rao H, Ma J, Chen X, Li G, Zhao G. Genomic Variation Landscape of the Model Salt Cress Eutrema salsugineum. FRONTIERS IN PLANT SCIENCE 2021; 12:700161. [PMID: 34484264 PMCID: PMC8416042 DOI: 10.3389/fpls.2021.700161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/22/2021] [Indexed: 05/13/2023]
Abstract
Eutrema salsugineum has long been used as the model for examining salt and other abiotic stress in plants. In addition to the forward genetics approaches widely used in the lab, natural variations undoubtedly will provide a rich genetic resource for studying molecular mechanisms underlying the stress tolerance and local adaptation of this species. We used 90 resequencing whole genomes of natural populations of this species across its Asian and North American distributions to detect the selection signals for genes involved in salt and other stresses at the species-range level and local distribution. We detected selection signals for genes involved in salt and other abiotic tolerance at the species level. In addition, several cold-induced and defense genes showed selection signals due to local adaptation in North America-NE Russia or northern China, respectively. These variations and findings provide valuable resources for further deciphering genetic mechanisms underlying the stress tolerance and local adaptations of this model species.
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Affiliation(s)
- Xiaojuan Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Hua Rao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
- Special Economic Zone for Science and Technology Synergy, China State-Level Xixian New Area, Xi'an, China
| | - Jianxiang Ma
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaodan Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Guanglin Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
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11
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Dixon A, Comont D, Slavov GT, Neve P. Population genomics of selectively neutral genetic structure and herbicide resistance in UK populations of Alopecurus myosuroides. PEST MANAGEMENT SCIENCE 2021; 77:1520-1529. [PMID: 33155426 DOI: 10.1002/ps.6174] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/22/2020] [Accepted: 11/06/2020] [Indexed: 06/07/2023]
Abstract
BACKGROUND Alopecurus myosuroides (blackgrass) is a major weed in Europe with known resistance to multiple herbicide modes of action. In the UK, there is evidence that blackgrass has undergone a range expansion. In this paper, genotyping-by-sequencing and population-level herbicide resistance phenotypes are used to explore spatial patterns of selectively neutral genetic variation and resistance. We also perform a preliminary genome-wide association study (GWAS) and genomic prediction analysis to evaluate the potential of these approaches for investigating nontarget site herbicide resistance. RESULTS Blackgrass was collected from 47 fields across the British Isles and up to eight plants per field population (n = 369) were genotyped by Restriction site-associated DNA (RAD)-sequencing. A total of 20 426 polymorphic loci were identified and used for population genetic analyses. Phenotypic assays revealed significant variation in herbicide resistance between populations. Population structure was weak (FST = 0.024-0.048), but spatial patterns were consistent with an ongoing westward and northward range expansion. We detected strong and consistent Wahlund effects (FIS = 0.30). There were no spatial patterns of herbicide resistance or evidence for confounding with population structure. Using a combination of population-level GWAS and genomic prediction we found that the top 20, 200, and 2000 GWAS loci had higher predictive abilities for fenoxaprop resistance compared to all markers. CONCLUSION There is likely extensive human-mediated gene flow between field populations of the weed blackgrass at a national scale. The lack of confounding of adaptive and neutral genetic variation can enable future, more extensive GWAS analyses to identify the genetic architecture of evolved herbicide resistance. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Andrea Dixon
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - David Comont
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
| | - Gancho T Slavov
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
- Scion, Rotorua, New Zealand
| | - Paul Neve
- Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
- Agriculture & Horticulture Development Board, Warwickshire, UK
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12
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Kost MA, Perales H, Wijeratne S, Wijeratne AJ, Stockinger EJ, Mercer KL. Transcriptional differentiation of UV-B protectant genes in maize landraces spanning an elevational gradient in Chiapas, Mexico. Evol Appl 2020; 13:1949-1967. [PMID: 32908597 PMCID: PMC7463351 DOI: 10.1111/eva.12954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 01/07/2020] [Accepted: 02/10/2020] [Indexed: 11/29/2022] Open
Abstract
Globally, farmers cultivate and maintain crop landraces (i.e., traditional varieties). Landraces contain unique diversity shaped in part by natural and human-mediated selection and are an indispensable resource for farmers. Since environmental conditions change with elevation, crop landraces grown along elevational gradients have provided ideal locations to explore patterns of local adaptation. To further probe traits underlying this differentiation, transcriptome signatures can help provide a foundation for understanding the ways in which functional genetic diversity may be shaped by environment. In this study, we returned to an elevational gradient in Chiapas, Mexico, to assess transcriptional differentiation of genes underlying UV-B protection in locally adapted maize landraces from multiple elevations. We collected and planted landraces from three elevational zones (lowland, approximately 600 m; midland, approximately 1,550 m; highland approximately 2,100 m) in a common garden at 1,531 m. Using RNA-seq data derived from leaf tissue, we performed differential expression analysis between maize from these distinct elevations. Highland and lowland landraces displayed differential expression in phenylpropanoid and flavonoid biosynthesis genes involved in the production of UV-B protectants and did so at a rate greater than expected based on observed background transcriptional differentiation across the genome. These findings provide evidence for the differentiation of suites of genes involved in complex ecologically relevant pathways. Thus, while neutral evolutionary processes may have played a role in the observed patterns of differentiation, UV-B may have also acted as a selective pressure to differentiate maize landraces in the region. Studies of the distribution of functional crop genetic diversity across variable landscapes can aid us in understanding the response of diversity to abiotic/biotic change and, ultimately, may facilitate its conservation and utilization.
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Affiliation(s)
- Matthew A. Kost
- Department of Horticulture and Crop ScienceThe Ohio State UniversityWoosterOHUSA
| | - Hugo Perales
- Departamento de Agricultura, Sociedad y AmbienteEl Colegio de la Frontera SurSan Cristóbal de Las CasasChiapasMexico
| | - Saranga Wijeratne
- Molecular and Cellular Imaging CenterOhio Agricultural Research and Development CenterThe Ohio State UniversityWoosterOHUSA
| | - Asela J. Wijeratne
- Molecular and Cellular Imaging CenterOhio Agricultural Research and Development CenterThe Ohio State UniversityWoosterOHUSA
- Department of Biological SciencesArkansas State UniversityJonesboroARUSA
| | - Eric J. Stockinger
- Department of Horticulture and Crop ScienceThe Ohio State UniversityWoosterOHUSA
| | - Kristin L. Mercer
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOHUSA
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13
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Orsucci M, Milesi P, Hansen J, Girodolle J, Glémin S, Lascoux M. Shift in ecological strategy helps marginal populations of shepherd's purse ( Capsella bursa-pastoris) to overcome a high genetic load. Proc Biol Sci 2020; 287:20200463. [PMID: 32429810 PMCID: PMC7287375 DOI: 10.1098/rspb.2020.0463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The outcome of species range expansion depends on the interplay of demographic, environmental and genetic factors. Self-fertilizing species usually show a higher invasive ability than outcrossers but selfing and bottlenecks during colonization also lead to an increased genetic load. The relationship between genomic and phenotypic characteristics of expanding populations has, hitherto, rarely been tested experimentally. We analysed how accessions of the shepherd's purse, Capsella bursa-pastoris, from the colonization front or from the core of the natural range performed under increasing density of competitors. First, accessions from the front showed a lower fitness than those from the core. Second, for all accessions, competitor density impacted negatively both vegetative growth and fruit production. However, despite their higher genetic load and lower absolute performances, accessions from the front were less affected by competition than accessions from the core. This seems to be due to phenotypic trade-offs and a shift in phenology that allow accessions from the front to avoid competition.
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Affiliation(s)
- Marion Orsucci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Uppsala, Sweden
| | - Johanna Hansen
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Johanna Girodolle
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,ECOBIO UMR 6553 CNRS University of Rennes 1, Rennes, France
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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14
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Price N, Lopez L, Platts AE, Lasky JR. In the presence of population structure: From genomics to candidate genes underlying local adaptation. Ecol Evol 2020; 10:1889-1904. [PMID: 32128123 DOI: 10.1101/642306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 05/26/2023] Open
Abstract
Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis-regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low-frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis-regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic-acid pathway to local adaptation.
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Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences & Pest Management Colorado State University Fort Collins CO USA
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Lua Lopez
- Department of Biology Binghamton University (State University of New York) Binghamton NY USA
| | - Adrian E Platts
- Simons Center for Quantitative Biology Cold Spring Harbor Laboratory Cold Spring Harbor NY USA
- Department of Biology Center for Genomics and Systems Biology New York University New York NY USA
| | - Jesse R Lasky
- Department of Biology Pennsylvania State University University Park PA USA
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15
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Kryvokhyzha D, Milesi P, Duan T, Orsucci M, Wright SI, Glémin S, Lascoux M. Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris). PLoS Genet 2019; 15:e1008131. [PMID: 31083657 PMCID: PMC6532933 DOI: 10.1371/journal.pgen.1008131] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/23/2019] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
Allopolyploidy has played a major role in plant evolution but its impact on genome diversity and expression patterns remains to be understood. Some studies found important genomic and transcriptomic changes in allopolyploids, whereas others detected a strong parental legacy and more subtle changes. The allotetraploid C. bursa-pastoris originated around 100,000 years ago and one could expect the genetic polymorphism of the two subgenomes to follow similar trajectories and their transcriptomes to start functioning together. To test this hypothesis, we sequenced the genomes and the transcriptomes (three tissues) of allotetraploid C. bursa-pastoris and its parental species, the outcrossing C. grandiflora and the self-fertilizing C. orientalis. Comparison of the divergence in expression between subgenomes, on the one hand, and divergence in expression between the parental species, on the other hand, indicated a strong parental legacy with a majority of genes exhibiting a conserved pattern and cis-regulation. However, a large proportion of the genes that were differentially expressed between the two subgenomes, were also under trans-regulation reflecting the establishment of a new regulatory pattern. Parental dominance varied among tissues: expression in flowers was closer to that of C. orientalis and expression in root and leaf to that of C. grandiflora. Since deleterious mutations accumulated preferentially on the C. orientalis subgenome, the bias in expression towards C. orientalis observed in flowers indicates that expression changes could be adaptive and related to the selfing syndrome, while biases in the roots and leaves towards the C. grandiflora subgenome may be reflective of the differential genetic load. Most plant species have a polyploid at some stage of their ancestry. Polyploidy, genome doubling through either multiple copies of a single species or through genomes of different species coming into the same nucleus, is therefore a crucial step in plant evolution. Understanding its impact on basic biological functions is thus a matter of interest. Shepherd’s purse (Capsella bursa-pastoris) is a major weed that appeared about 100,000 years ago through hybridization of two diploid species of the same genus. In the present project, we measured genetic diversity and analyzed gene expression patterns in flowers, roots, and leaves of C. bursa-pastoris individuals as well as in its two parental species, the outcrossing C. grandiflora and the self-fertilizing C. orientalis. Our data shows that, after 100,000 generations of evolution, the origin of the two subgenomes can still be seen: the genome inherited from C. grandiflora still differs from the one inherited from self-fertilizing C. orientalis. However, there are also signs that the two genomes have started to work together and are jointly regulated, and the way expression pattern varied across the three tissues indicates that the evolution of gene expression was adaptive.
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Affiliation(s)
- Dmytro Kryvokhyzha
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tianlin Duan
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marion Orsucci
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stephen I. Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Sylvain Glémin
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- CNRS, Univ. Rennes, ECOBIO [(Ecosystèmes, biodiversité, évolution)] - UMR 6553, Rennes, France
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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16
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Kryvokhyzha D, Salcedo A, Eriksson MC, Duan T, Tawari N, Chen J, Guerrina M, Kreiner JM, Kent TV, Lagercrantz U, Stinchcombe JR, Glémin S, Wright SI, Lascoux M. Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae). PLoS Genet 2019; 15:e1007949. [PMID: 30768594 PMCID: PMC6395008 DOI: 10.1371/journal.pgen.1007949] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/28/2019] [Accepted: 01/09/2019] [Indexed: 11/18/2022] Open
Abstract
Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (CbpCg) and the other one from the selfing and genetically depauperate Capsella orientalis (CbpCo). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (Ne), signatures of positive and negative selection, and gene expression patterns. In all three regions, Ne of the two subgenomes decreased gradually over time and the CbpCo subgenome accumulated more deleterious changes than CbpCg. There were signs of widespread admixture between C. bursa-pastoris and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of C. bursa-pastoris. Selective sweeps were more common on the CbpCg subgenome in Europe and the Middle East, and on the CbpCo subgenome in Asia. In contrast, differences in expression were limited with the CbpCg subgenome slightly more expressed than CbpCo in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions.
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Affiliation(s)
- Dmytro Kryvokhyzha
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Adriana Salcedo
- Department of Ecology and Evolution, University of Toronto, Toronto, Canada
| | - Mimmi C. Eriksson
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Tianlin Duan
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Nilesh Tawari
- Computational and Systems Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A*Star), Singapore
| | - Jun Chen
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maria Guerrina
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Julia M. Kreiner
- Department of Ecology and Evolution, University of Toronto, Toronto, Canada
| | - Tyler V. Kent
- Department of Ecology and Evolution, University of Toronto, Toronto, Canada
| | - Ulf Lagercrantz
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Sylvain Glémin
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- CNRS, Université de Rennes 1, ECOBIO (Ecosystémes, biodiversité, évolution) - UMR 6553, F-35000 Rennes, France
| | - Stephen I. Wright
- Department of Ecology and Evolution, University of Toronto, Toronto, Canada
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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17
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Blischak PD, Mabry ME, Conant GC, Pires JC. Integrating Networks, Phylogenomics, and Population Genomics for the Study of Polyploidy. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-121415-032302] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Duplication events are regarded as sources of evolutionary novelty, but our understanding of general trends for the long-term trajectory of additional genomic material is still lacking. Organisms with a history of whole genome duplication (WGD) offer a unique opportunity to study potential trends in the context of gene retention and/or loss, gene and network dosage, and changes in gene expression. In this review, we discuss the prevalence of polyploidy across the tree of life, followed by an overview of studies investigating genome evolution and gene expression. We then provide an overview of methods in network biology, phylogenomics, and population genomics that are critical for advancing our understanding of evolution post-WGD, highlighting the need for models that can accommodate polyploids. Finally, we close with a brief note on the importance of random processes in the evolution of polyploids with respect to neutral versus selective forces, ancestral polymorphisms, and the formation of autopolyploids versus allopolyploids.
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Affiliation(s)
- Paul D. Blischak
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Makenzie E. Mabry
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Gavin C. Conant
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
- Current affiliation: Bioinformatics Research Center, Program in Genetics and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - J. Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211-7310, USA
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18
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Huang HR, Liu JJ, Xu Y, Lascoux M, Ge XJ, Wright SI. Homeologue-specific expression divergence in the recently formed tetraploid Capsella bursa-pastoris (Brassicaceae). THE NEW PHYTOLOGIST 2018; 220:624-635. [PMID: 30028022 DOI: 10.1111/nph.15299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
Following allopolyploid formation, extensive genome evolution occurs, with the eventual loss of many homeologous gene copies. Although this process of diploidization has occurred many times independently, the evolutionary forces determining the probability and rate of gene loss remain poorly understood. Here, we conduct genome and transcriptome sequencing in a broad sample of Chinese accessions of Capsella bursa-pastoris, a recently formed allotetraploid. Our whole genome data reveal three groups of these accessions: an Eastern group from low-altitude regions, a Western group from high-altitude regions, and a much more differentiated Northwestern group. Population differentiation in total expression was limited among closely related populations; by contrast, the relative expression of the two homeologous copies closely mirrors the genome-wide SNP divergence. Consistent with this, we observe a negative correlation between expression changes in the two homeologues. However, genes showing population genomic evidence for adaptive evolution do not show an enrichment for expression divergence between homeologues, providing no clear evidence for adaptive shifts in relative gene expression. Overall, these patterns suggest that neutral drift may contribute to the population differentiation in the expression of the homeologues, and drive eventual gene loss over longer periods of time.
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Affiliation(s)
- Hui-Run Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jia-Jia Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yong Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, 75236, Sweden
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, ON, Canada
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19
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Neuffer B, Wesse C, Voss I, Scheibe R. The role of ecotypic variation in driving worldwide colonization by a cosmopolitan plant. AOB PLANTS 2018; 10:ply005. [PMID: 29479407 PMCID: PMC5815058 DOI: 10.1093/aobpla/ply005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 01/18/2018] [Indexed: 05/13/2023]
Abstract
For almost 100 years now, ecotypic differentiation of plant species has been a major topic of research. In changing environments, the question needs to be answered as to how long it takes to adapt, and which parameters are subject to this fast adaptation. Short-living colonizing plant species are excellent examples, especially when they are selfing. Shepherd's Purse Capsella bursa-pastoris (Brassicaceae) is one of the most wide-spread flowering species on earth and avoids only the hot and humid tropics. Many studies demonstrated the ecotypic differentiation of C. bursa-pastoris in various regions of the world but ecotypic differentiation regarding adaptability of anatomy and physiology of rosette leaves so far remained less recognized. However, the leaves are relevant for subsequent seed set; in particular, winter-annual accessions require a robust rosette to survive adverse conditions. Leaf-related traits such as the thickness of the mesophyll and epidermis, stomatal density, photosynthetic capacity and the ability to withstand and even use high light conditions were therefore analysed in provenances from various climatic zones. Photosynthetic capacity depends on leaf anatomy and cellular physiological parameters. In particular, the ability to dynamically adjust the photosynthetic capacity to changing environmental conditions results in higher fitness. Here, we attempt to relate these results to the four Mendelian leaf types according to Shull.
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Affiliation(s)
- Barbara Neuffer
- Department of Botany, University of Osnabrück, Barbarastr., Osnabrück, Germany
| | - Christina Wesse
- Department of Botany, University of Osnabrück, Barbarastr., Osnabrück, Germany
| | - Ingo Voss
- Department of Plant Physiology, University of Osnabrück, Barbarastr., Osnabrück, Germany
| | - Renate Scheibe
- Department of Plant Physiology, University of Osnabrück, Barbarastr., Osnabrück, Germany
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Guo Q, Wang JX, Su LZ, Lv W, Sun YH, Li Y. Development and Evaluation of a Novel Set of EST-SSR Markers Based on Transcriptome Sequences of Black Locust (Robinia pseudoacacia L.). Genes (Basel) 2017; 8:genes8070177. [PMID: 28686183 PMCID: PMC5541310 DOI: 10.3390/genes8070177] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 12/20/2022] Open
Abstract
Black locust (Robinia pseudoacacia L. of the family Fabaceae) is an ecologically and economically important deciduous tree. However, few genomic resources are available for this forest species, and few effective expressed sequence tag-derived simple sequence repeat (EST-SSR) markers have been developed to date. In this study, paired-end sequencing was used to sequence transcriptomes of R. pseudoacacia by the Illumina HiSeq TM2000 platform, and EST-SSR loci were identified by de novo assembly. Furthermore, a total of 1697 primer pairs were successfully designed, from which 286 primers met the selection screening criteria; 94 pairs were randomly selected and tested for validation using polymerase chain reaction amplification. Forty-five primers were verified as polymorphic, with clear bands. The polymorphism information content values were 0.033–0.765, the number of alleles per locus ranged from 2 to 10, and the observed and expected heterozygosities were 0.000–0.931 and 0.035–0.810, respectively, indicating a high level of informativeness. Subsequently, 45 polymorphic EST-SSR loci were tested for amplification efficiency, using the verified primers, in an additional nine species of Leguminosae, 23 loci were amplified in more than three species, of which two loci were amplified successfully in all species. These EST-SSR markers provide a valuable tool for investigating the genetic diversity and population structure of R. pseudoacacia, constructing a DNA fingerprint database, performing quantitative trait locus mapping, and preserving genetic information.
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Affiliation(s)
- Qi Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Jin-Xing Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Li-Zhuo Su
- State-owned Linghai Hongqi Forest, Jinzhou 121228, China.
| | - Wei Lv
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Yu-Han Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Yun Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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Kasianov AS, Klepikova AV, Kulakovskiy IV, Gerasimov ES, Fedotova AV, Besedina EG, Kondrashov AS, Logacheva MD, Penin AA. High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:278-291. [PMID: 28387959 DOI: 10.1111/tpj.13563] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/01/2017] [Accepted: 03/31/2017] [Indexed: 05/22/2023]
Abstract
Polyploidization and subsequent sub- and neofunctionalization of duplicated genes represent a major mechanism of plant genome evolution. Capsella bursa-pastoris, a widespread ruderal plant, is a recent allotetraploid and, thus, is an ideal model organism for studying early changes following polyploidization. We constructed a high-quality assembly of C. bursa-pastoris genome and a transcriptome atlas covering a broad sample of organs and developmental stages (available online at http://travadb.org/browse/Species=Cbp). We demonstrate that expression of homeologs is mostly symmetric between subgenomes, and identify a set of homeolog pairs with discordant expression. Comparison of promoters within such pairs revealed emerging asymmetry of regulatory elements. Among them there are multiple binding sites for transcription factors controlling the regulation of photosynthesis and plant development by light (PIF3, HY5) and cold stress response (CBF). These results suggest that polyploidization in C. bursa-pastoris enhanced its plasticity of response to light and temperature, and allowed substantial expansion of its distribution range.
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Affiliation(s)
- Artem S Kasianov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina str, Moscow, 119333, Russia
| | - Anna V Klepikova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
| | - Ivan V Kulakovskiy
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina str, Moscow, 119333, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Building 3, Moscow, 143026, Russia
| | - Evgeny S Gerasimov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anna V Fedotova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Elizaveta G Besedina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexey S Kondrashov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Ecology and Evolution, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, MI, USA
| | - Maria D Logacheva
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlevskaya str, Kazan, 420008, Russia
| | - Aleksey A Penin
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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Construction of co-expression network based on natural expression variation of xylogenesis-related transcripts in Eucalyptus tereticornis. Mol Biol Rep 2016; 43:1129-46. [DOI: 10.1007/s11033-016-4046-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 07/20/2016] [Indexed: 12/23/2022]
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23
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Cornille A, Salcedo A, Kryvokhyzha D, Glémin S, Holm K, Wright SI, Lascoux M. Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris). Mol Ecol 2016; 25:616-29. [PMID: 26607306 DOI: 10.1111/mec.13491] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 12/29/2022]
Abstract
Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C. bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C. bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C. bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C. bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.
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Affiliation(s)
- A Cornille
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - A Salcedo
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON M6R 1M3, Canada
| | - D Kryvokhyzha
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - S Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - K Holm
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - S I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON M6R 1M3, Canada
| | - M Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
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