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Farhat P, Mandáková T, Divíšek J, Kudoh H, German DA, Lysak MA. The evolution of the hypotetraploid Catolobus pendulus genome - the poorly known sister species of Capsella. FRONTIERS IN PLANT SCIENCE 2023; 14:1165140. [PMID: 37223809 PMCID: PMC10200890 DOI: 10.3389/fpls.2023.1165140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/04/2023] [Indexed: 05/25/2023]
Abstract
The establishment of Arabidopsis as the most important plant model has also brought other crucifer species into the spotlight of comparative research. While the genus Capsella has become a prominent crucifer model system, its closest relative has been overlooked. The unispecific genus Catolobus is native to temperate Eurasian woodlands, from eastern Europe to the Russian Far East. Here, we analyzed chromosome number, genome structure, intraspecific genetic variation, and habitat suitability of Catolobus pendulus throughout its range. Unexpectedly, all analyzed populations were hypotetraploid (2n = 30, ~330 Mb). Comparative cytogenomic analysis revealed that the Catolobus genome arose by a whole-genome duplication in a diploid genome resembling Ancestral Crucifer Karyotype (ACK, n = 8). In contrast to the much younger Capsella allotetraploid genomes, the presumably autotetraploid Catolobus genome (2n = 32) arose early after the Catolobus/Capsella divergence. Since its origin, the tetraploid Catolobus genome has undergone chromosomal rediploidization, including a reduction in chromosome number from 2n = 32 to 2n = 30. Diploidization occurred through end-to-end chromosome fusion and other chromosomal rearrangements affecting a total of six of 16 ancestral chromosomes. The hypotetraploid Catolobus cytotype expanded toward its present range, accompanied by some longitudinal genetic differentiation. The sister relationship between Catolobus and Capsella allows comparative studies of tetraploid genomes of contrasting ages and different degrees of genome diploidization.
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Affiliation(s)
- Perla Farhat
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Divíšek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Dmitry A. German
- South-Siberian Botanical Garden, Altai State University, Barnaul, Russia
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czechia
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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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Wu M, Liu H, Li B, Zhu T. Integrated analysis of mRNA-seq and miRNA-seq reveals the advantage of polyploid Solidago canadensis in sexual reproduction. BMC PLANT BIOLOGY 2021; 21:462. [PMID: 34635057 PMCID: PMC8504063 DOI: 10.1186/s12870-021-03240-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The invasion of Solidago canadensis probably related to polyploidy, which may promotes its potential of sexual reproductive. S. canadensis as an invasive species which rapidly widespread through yield huge numbers of seed, but the mechanism remains unknown. To better understand the advantages of sexual reproduction in hexaploid S. canadensis, transcriptome and small RNA sequencing of diploid and hexaploid cytotypes in flower bud and fruit development stages were performed in this study. RESULTS The transcriptome analysis showed that in the flower bud stage, 29 DEGs were MADS-box related genes with 14 up-regulated and 15 down-regulated in hexaploid S. canadensis; 12 SPL genes were detected differentially expressed with 5 up-regulated and 7 down-regulated. In the fruit development stage, 26 MADS-box related genes with 20 up-regulated and 6 down-regulated in hexaploid S. canadensis; 5 SPL genes were all up-regulated; 28 seed storage protein related genes with 18 were up-regulated and 10 down-regulated. The weighted gene co-expression network analysis (WGCNA) identified 19 modules which consisted of co-expressed DEGs with functions such as sexual reproduction, secondary metabolism and transcription factors. Furthermore, we discovered 326 miRNAs with 67 known miRNAs and 259 novel miRNAs. Some of miRNAs, such as miR156, miR156a and miR156f, which target the sexual reproduction related genes. CONCLUSION Our study provides a global view of the advantages of sexual reproduction in hexaploid S. canadensis based on the molecular mechanisms, which may promote hexaploid S. canadensis owing higher yield and fruit quality in the process of sexual reproduction and higher germination rate of seeds, and finally conductive to diffusion, faster propagation process and enhanced invasiveness.
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Affiliation(s)
- Miao Wu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467041, Henan, China.
| | - Huiyuan Liu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467041, Henan, China
| | - Bingbing Li
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467041, Henan, China
| | - Tao Zhu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, 467041, Henan, China
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Glémin S. Balancing selection in self-fertilizing populations. Evolution 2021; 75:1011-1029. [PMID: 33675041 DOI: 10.1111/evo.14194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/17/2021] [Indexed: 11/30/2022]
Abstract
Self-fertilization commonly occurs in hermaphroditic species, either occasionally or as the main reproductive mode. It strongly affects the genetic functioning of a population by increasing homozygosity and genetic drift and reducing the effectiveness of recombination. Balancing selection is a form of selection that maintains polymorphism, which has been extensively studied in outcrossing species. Yet, despite recent developments, the analysis of balancing selection in partially selfing species is limited to specific cases and a general treatment is still lacking. In particular, it is unclear whether selfing globally reduced the efficacy of balancing selection as in the well-known case of overdominance. I provide a unifying framework, quantify how selfing affects the maintenance of polymorphism and the efficacy of the different form of balancing selection, and show that they can be classified into two main categories: overdominance-like selection (including true overdominance, selection variable in space and time, and antagonistic selection), which is strongly affected by selfing, and negative frequency dependent selection, which is barely affected by selfing, even at multiple loci. I also provide simple analytical results for all cases under the assumption of weak selection. This framework provides theoretical background to analyze the genomic signature of balancing selection in partially selfing species. It also sheds new light on the evolution of selfing species, including the evolution of selfing syndrome, the interaction with pathogens, and the evolutionary fate of selfing lineages.
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Affiliation(s)
- Sylvain Glémin
- CNRS, ECOBIO (Ecosystèmes, biodiversité, évolution), University of Rennes 1, UMR 6553, Rennes, France.,Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, 752 36, Sweden
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Kaj I, Glémin S, Tahir D, Lascoux M. Analysis of diversity-dependent species evolution using concepts in population genetics. J Math Biol 2021; 82:22. [PMID: 33634353 PMCID: PMC7907050 DOI: 10.1007/s00285-021-01559-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 10/28/2020] [Accepted: 11/24/2020] [Indexed: 11/26/2022]
Abstract
In this work, we consider a two-type species model with trait-dependent speciation, extinction and transition rates under an evolutionary time scale. The scaling approach and the diffusion approximation techniques which are widely used in mathematical population genetics provide modeling tools and conceptual background to assist in the study of species dynamics, and help exploring the analogy between trait-dependent species diversification and the evolution of allele frequencies in the population genetics setting. The analytical framework specified is then applied to models incorporating diversity-dependence, in order to infer effective results from processes in which the net diversification of species depends on the total number of species. In particular, the long term fate of a rare trait may be analyzed under a partly symmetric scenario, using a time-change transform technique.
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Affiliation(s)
- Ingemar Kaj
- Department of Mathematics, Uppsala University, Box 480, Uppsala, 751 06 Sweden
| | - Sylvain Glémin
- CNRS, Université Rennes 1, ECOBIO (écosystèmes, biodiversité, évolution) – UMR 6553, Avenue du général Leclerc, 35042 Rennes, France
| | - Daniah Tahir
- Department of Mathematics, Uppsala University, Box 480, Uppsala, 751 06 Sweden
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC, Uppsala University, Norbyvägen 18D, Uppsala, 752 36 Sweden
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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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Cheng J, Yang X, Xue L, Yao B, Lu H, Tian Z, Li J, Zhou X, Zhang Y, Zia Ul Haq M, Wu S, Song X, Hu S, Qiang S. Polyploidization contributes to evolution of competitive ability: a long term common garden study on the invasive
Solidago canadensis
in China. OIKOS 2020. [DOI: 10.1111/oik.07095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jiliang Cheng
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Xianghong Yang
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Lifang Xue
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Beibei Yao
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Huan Lu
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Zhongsai Tian
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Jun Li
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Xin Zhou
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Yu Zhang
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Muhammad Zia Ul Haq
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Shuqi Wu
- College of Resources and Environmental Sciences, Nanjing Agricultural Univ. Nanjing PR China
| | - Xiaoling Song
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
| | - Shuijin Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural Univ. Nanjing PR China
| | - Sheng Qiang
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural Univ. Nanjing CN‐210095 Jiangsu PR China
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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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