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Quintanilla LG, Aranda I, Clemente-Moreno MJ, Pons-Perpinyà J, Gago J. Ecophysiological Differentiation among Two Resurrection Ferns and Their Allopolyploid Derivative. PLANTS (BASEL, SWITZERLAND) 2023; 12:1529. [PMID: 37050155 PMCID: PMC10096763 DOI: 10.3390/plants12071529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Theoretically, the coexistence of diploids and related polyploids is constrained by reproductive and competitive mechanisms. Although niche differentiation can explain the commonly observed co-occurrence of cytotypes, the underlying ecophysiological differentiation among cytotypes has hardly been studied. We compared the leaf functional traits of the allotetraploid resurrection fern Oeosporangium tinaei (HHPP) and its diploid parents, O. hispanicum (HH) and O. pteridioides (PP), coexisting in the same location. Our experimental results showed that all three species can recover physiological status after severe leaf dehydration, which confirms their 'resurrection' ability. However, compared with PP, HH had much higher investment per unit area of light-capturing surface, lower carbon assimilation rate per unit mass for the same midday water potential, higher non-enzymatic antioxidant capacity, higher carbon content, and lower contents of nitrogen, phosphorus, and other macronutrients. These traits allow HH to live in microhabitats with less availability of water and nutrients (rock crevices) and to have a greater capacity for resurrection. The higher assimilation capacity and lower antioxidant capacity of PP explain its more humid and nutrient-rich microhabitats (shallow soils). HHPP traits were mostly intermediate between those of HH and PP, and they allow the allotetraploid to occupy the free niche space left by the diploids.
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Affiliation(s)
- Luis G. Quintanilla
- School of Environmental Sciences and Technology (ESCET), University Rey Juan Carlos, 28922 Móstoles, Spain
| | - Ismael Aranda
- National Institute for Agricultural and Food Research and Technology (INIA), Spanish National Research Council, 28040 Madrid, Spain
| | - María José Clemente-Moreno
- Agro-Environmental and Water Economics Institute (INAGEA), University of the Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Joan Pons-Perpinyà
- Agro-Environmental and Water Economics Institute (INAGEA), University of the Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Jorge Gago
- Agro-Environmental and Water Economics Institute (INAGEA), University of the Balearic Islands, 07122 Palma de Mallorca, Spain
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2
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Mattingly KZ, Hovick SM. Autopolyploids of Arabidopsis thaliana are more phenotypically plastic than their diploid progenitors. ANNALS OF BOTANY 2023; 131:45-58. [PMID: 34175922 PMCID: PMC9904351 DOI: 10.1093/aob/mcab081] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/25/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Polyploids are often hypothesized to have increased phenotypic plasticity compared with their diploid progenitors, but recent work suggests that the relationship between whole-genome duplication (WGD) and plasticity is not so straightforward. Impacts of WGD on plasticity are moderated by other evolutionary processes in nature, which has impeded generalizations regarding the effects of WGD alone. We assessed shifts in phenotypic plasticity and mean trait values accompanying WGD, as well as the adaptive consequences of these shifts. METHODS To isolate WGD effects, we compared two diploid lineages of Arabidopsis thaliana wiht corresponding autotetraploids grown across different salt and nutrient conditions in a growth chamber. KEY RESULTS For the few cases in which diploids and polyploids differed in plasticity, polyploids were more plastic, consistent with hypotheses that WGD increases plasticity. Under stress, increased plasticity was often adaptive (associated with higher total seed mass), but in other cases plasticity was unrelated to fitness. Mean trait values and plasticity were equally likely to be affected by WGD, but the adaptive consequences of these shifts were often context dependent or lineage specific. For example, polyploids had extended life spans, a shift that was adaptive in one polyploid lineage under amenable conditions but was maladaptive in the other lineage under stress. CONCLUSIONS Our work shows that increased phenotypic plasticity can result from WGD alone, independent of other evolutionary processes. We find that the effects of WGD can differ depending on the genotype of the progenitor and the environmental context. Though our experiment was limited to two genotypes of a single species, these findings support the idea that WGD can indeed increase plasticity.
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Affiliation(s)
| | - Stephen M Hovick
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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3
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Dong Y, Hu G, Grover CE, Miller ER, Zhu S, Wendel JF. Parental legacy versus regulatory innovation in salt stress responsiveness of allopolyploid cotton (Gossypium) species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:872-887. [PMID: 35686631 PMCID: PMC9540634 DOI: 10.1111/tpj.15863] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Polyploidy provides an opportunity for evolutionary innovation and species diversification, especially under stressful conditions. In allopolyploids, the conditional dynamics of homoeologous gene expression can be either inherited from ancestral states pre-existing in the parental diploids or novel upon polyploidization, the latter potentially permitting a wider range of phenotypic responses to stresses. To gain insight into regulatory mechanisms underlying the diversity of salt resistance in Gossypium species, we compared global transcriptomic responses to modest salinity stress in two allotetraploid (AD-genome) cotton species, Gossypium hirsutum and G. mustelinum, relative to their model diploid progenitors (A-genome and D-genome). Multivariate and pairwise analyses of salt-responsive changes revealed a profound alteration of gene expression for about one third of the transcriptome. Transcriptional responses and associated functional implications of salt acclimation varied across species, as did species-specific coexpression modules among species and ploidy levels. Salt responsiveness in both allopolyploids was strongly biased toward the D-genome progenitor. A much lower level of transgressive downregulation was observed in the more salt-tolerant G. mustelinum than in the less tolerant G. hirsutum. By disentangling inherited effects from evolved responses, we show that expression biases that are not conditional upon salt stress approximately equally reflect parental legacy and regulatory novelty upon allopolyploidization, whereas stress-responsive biases are predominantly novel, or evolved, in allopolyploids. Overall, our work suggests that allopolyploid cottons acquired a wide range of stress response flexibility relative to their diploid ancestors, most likely mediated by complex suites of duplicated genes and regulatory factors.
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Affiliation(s)
- Yating Dong
- Department of AgronomyZhejiang UniversityHangzhouZhejiang310 053China
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Guanjing Hu
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang455 000China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen518 120China
| | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Emma R. Miller
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
| | - Shuijin Zhu
- Department of AgronomyZhejiang UniversityHangzhouZhejiang310 053China
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology (EEOB), Bessey HallIowa State UniversityAmesIA50011USA
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4
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Bertrand B, Villegas Hincapié AM, Marie L, Breitler JC. Breeding for the Main Agricultural Farming of Arabica Coffee. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.709901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
So far, the main Arabica coffee breeding programmes in Latin America have focused on the selection of varieties adapted to intensive full-sun farming systems. Meanwhile, little attention has been paid to breeding varieties specifically adapted to shade, which is the main characteristic of agroforestry systems (AFS). Yet the specialty coffee sector is currently expanding and seeking specific sensory qualities related to exotic varieties and no breeding programme exists to create new varieties for this type of market. Two trials were set up: one in full sun and the other under shade. F1 hybrids and their parents (pure lines and Ethiopian accessions) were studied in a factorial-crossing design to measure tree volume, yield (3 years), bean size, the bean NIRS signature and the final cupping score. Bean size and the final cupping score seemed to be relatively unaffected by shading. Strong maternal heritability was observed for bean size. In the trials, F1 hybrids produced “75–80%” more than the maternal lines and “40–50%” more than the male parents in the shade trial and in the full-sun trial, respectively. By choosing the F1 hybrid, it is possible to increase productivity under both shade and full sun while simultaneously achieving good sensory qualities. Selecting a F1 hybrid for “specialty coffee” seems exceptional. This raises a fundamental issue concerning the maternal heritability of seed biochemical composition. We conclude that selection under shade is essential for the selection of varieties adapted to AFS.
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Ding Y, Zhang R, Zhu L, Wang M, Ma Y, Yuan D, Liu N, Hu H, Min L, Zhang X. An enhanced photosynthesis and carbohydrate metabolic capability contributes to heterosis of the cotton (Gossypium hirsutum) hybrid 'Huaza Mian H318', as revealed by genome-wide gene expression analysis. BMC Genomics 2021; 22:277. [PMID: 33865322 PMCID: PMC8052695 DOI: 10.1186/s12864-021-07580-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 04/04/2021] [Indexed: 12/15/2022] Open
Abstract
Background Heterosis has been exploited for decades in different crops due to resulting in dramatic increases in yield, but relatively little molecular evidence on this topic was reported in cotton. Results The elite cotton hybrid variety ‘Huaza Mian H318’ (H318) and its parental lines were used to explore the source of its yield heterosis. A four-year investigation of yield-related traits showed that the boll number of H318 showed higher stability than that of its two parents, both in suitable and unsuitable climate years. In addition, the hybrid H318 grew faster and showed higher fresh and dry weights than its parental lines at the seedling stage. Transcriptome analysis of seedlings identified 17,308 differentially expressed genes (DEGs) between H318 and its parental lines, and 3490 extremely changed DEGs were screened out for later analysis. Most DEGs (3472/3490) were gathered between H318 and its paternal line (4–5), and only 64 DEGs were found between H318 and its maternal line (B0011), which implied that H318 displays more similar transcriptional patterns to its maternal parent at the seedling stage. GO and KEGG analyses showed that these DEGs were highly enriched in photosynthesis, lipid metabolic, carbohydrate metabolic and oxidation-reduction processes, and the expression level of these DEGs was significantly higher in H318 relative to its parental lines, which implied that photosynthesis, metabolism and stress resistances were enhanced in H318. Conclusion The enhanced photosynthesis, lipid and carbohydrate metabolic capabilities contribute to the heterosis of H318 at the seedling stage, and establishes a material foundation for subsequent higher boll-setting rates in complex field environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07580-8.
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Affiliation(s)
- Yuanhao Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Rui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nian Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyan Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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6
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Duchoslav M, Jandová M, Kobrlová L, Šafářová L, Brus J, Vojtěchová K. Intricate Distribution Patterns of Six Cytotypes of Allium oleraceum at a Continental Scale: Niche Expansion and Innovation Followed by Niche Contraction With Increasing Ploidy Level. FRONTIERS IN PLANT SCIENCE 2020; 11:591137. [PMID: 33362819 PMCID: PMC7755979 DOI: 10.3389/fpls.2020.591137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/06/2020] [Indexed: 05/23/2023]
Abstract
The establishment and success of polyploids are thought to often be facilitated by ecological niche differentiation from diploids. Unfortunately, most studies compared diploids and polyploids, ignoring variation in ploidy level in polyploids. To fill this gap, we performed a large-scale study of 11,163 samples from 1,283 populations of the polyploid perennial geophyte Allium oleraceum with reported mixed-ploidy populations, revealed distribution ranges of cytotypes, assessed their niches and explored the pattern of niche change with increasing ploidy level. Altogether, six ploidy levels (3x-8x) were identified. The most common were pentaploids (53.6%) followed by hexaploids (22.7%) and tetraploids (21.6%). Higher cytotype diversity was found at lower latitudes than at higher latitudes (>52° N), where only tetraploids and pentaploids occurred. We detected 17.4% of mixed-ploidy populations, usually as a combination of two, rarely of three, cytotypes. The majority of mixed-ploidy populations were found in zones of sympatry of the participating cytotypes, suggesting they have arisen through migration (secondary contact zone). Using coarse-grained variables (climate, soil), we found evidence of both niche expansion and innovation in tetraploids related to triploids, whereas higher ploidy levels showed almost zero niche expansion, but a trend of increased niche unfilling of tetraploids. Niche unfilling in higher ploidy levels was caused by a contraction of niche envelopes toward lower continentality of the climate and resulted in a gradual decrease of niche breadth and a gradual shift in niche optima. Field-recorded data indicated wide habitat breadth of tetraploids and pentaploids, but also a pattern of increasing synanthropy in higher ploidy levels. Wide niche breadth of tetra- and pentaploids might be related to their multiple origins from different environmental conditions, higher "age", and retained sexuality, which likely preserve their adaptive potential. In contrast, other cytotypes with narrower niches are mostly asexual, probably originating from a limited range of contrasting environments. Persistence of local ploidy mixtures could be enabled by the perenniality of A. oleraceum and its prevalence of vegetative reproduction, facilitating the establishment and decreasing exclusion of minority cytotype due to its reproductive costs. Vegetative reproduction might also significantly accelerate colonization of new areas, including recolonization of previously glaciated areas.
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Affiliation(s)
- Martin Duchoslav
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Michaela Jandová
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
- Institute of Botany, Czech Academy of Sciences, Pruhonice, Czechia
| | - Lucie Kobrlová
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Lenka Šafářová
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jan Brus
- Department of Geoinformatics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Kateřina Vojtěchová
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
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7
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Li H, Jiang S, Li C, Liu L, Lin Z, He H, Deng XW, Zhang Z, Wang X. The hybrid protein interactome contributes to rice heterosis as epistatic effects. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:116-128. [PMID: 31736145 DOI: 10.1111/tpj.14616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 05/15/2023]
Abstract
Heterosis is the phenomenon in which hybrid progeny exhibits superior traits in comparison with those of their parents. Genomic variations between the two parental genomes may generate epistasis interactions, which is one of the genetic hypotheses explaining heterosis. We postulate that protein-protein interactions specific to F1 hybrids (F1 -specific PPIs) may occur when two parental genomes combine, as the proteome of each parent may supply novel interacting partners. To test our assumption, an inter-subspecies hybrid interactome was simulated by in silico PPI prediction between rice japonica (cultivar Nipponbare) and indica (cultivar 9311). Four-thousand, six-hundred and twelve F1 -specific PPIs accounting for 20.5% of total PPIs in the hybrid interactome were found. Genes participating in F1 -specific PPIs tend to encode metabolic enzymes and are generally localized in genomic regions harboring metabolic gene clusters. To test the genetic effect of F1 -specific PPIs in heterosis, genomic selection analysis was performed for trait prediction with additive, dominant and epistatic effects separately considered in the model. We found that the removal of single nucleotide polymorphisms associated with F1 -specific PPIs reduced prediction accuracy when epistatic effects were considered in the model, but no significant changes were observed when additive or dominant effects were considered. In summary, genomic divergence widely dispersed between japonica and indica rice may generate F1 -specific PPIs, part of which may accumulatively contribute to heterosis according to our computational analysis. These candidate F1 -specific PPIs, especially for those involved in metabolic biosynthesis pathways, are worthy of experimental validation when large-scale protein interactome datasets are generated in hybrid rice in the future.
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Affiliation(s)
- Hong Li
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Shuqin Jiang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Lei Liu
- Beijing Key Laboratory of Plant Resources Research and Development, School of Sciences, Beijing Technology and Business University, Beijing, 100048, China
| | - Zechuan Lin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Xing-Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiangfeng Wang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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8
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Martinez Palacios P, Jacquemot MP, Tapie M, Rousselet A, Diop M, Remoué C, Falque M, Lloyd A, Jenczewski E, Lassalle G, Chévre AM, Lelandais C, Crespi M, Brabant P, Joets J, Alix K. Assessing the Response of Small RNA Populations to Allopolyploidy Using Resynthesized Brassica napus Allotetraploids. Mol Biol Evol 2019; 36:709-726. [PMID: 30657939 PMCID: PMC6445299 DOI: 10.1093/molbev/msz007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Allopolyploidy, combining interspecific hybridization with whole genome duplication, has had significant impact on plant evolution. Its evolutionary success is related to the rapid and profound genome reorganizations that allow neoallopolyploids to form and adapt. Nevertheless, how neoallopolyploid genomes adapt to regulate their expression remains poorly understood. The hypothesis of a major role for small noncoding RNAs (sRNAs) in mediating the transcriptional response of neoallopolyploid genomes has progressively emerged. Generally, 21-nt sRNAs mediate posttranscriptional gene silencing by mRNA cleavage, whereas 24-nt sRNAs repress transcription (transcriptional gene silencing) through epigenetic modifications. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independently resynthesized Brassica napus allotetraploids originating from crosses between diploid Brassica oleracea and Brassica rapa accessions, surveyed at two different generations in comparison with their diploid progenitors. Our results suggest an immediate but transient response of specific sRNA populations to allopolyploidy. These sRNA populations mainly target noncoding components of the genome but also target the transcriptional regulation of genes involved in response to stresses and in metabolism; this suggests a broad role in adapting to allopolyploidy. We finally identify the early accumulation of both 21- and 24-nt sRNAs involved in regulating the same targets, supporting a posttranscriptional gene silencing to transcriptional gene silencing shift at the first stages of the neoallopolyploid formation. We propose that reorganization of sRNA production is an early response to allopolyploidy in order to control the transcriptional reactivation of various noncoding elements and stress-related genes, thus ensuring genome stability during the first steps of neoallopolyploid formation.
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Affiliation(s)
- Paulina Martinez Palacios
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Marie-Pierre Jacquemot
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France.,Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Marion Tapie
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Agnès Rousselet
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mamoudou Diop
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Carine Remoué
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Matthieu Falque
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Andrew Lloyd
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Eric Jenczewski
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Gilles Lassalle
- IGEPP, INRA, Agrocampus Ouest, Univ. Rennes I, Le Rheu, France.,ESE, INRA, Agrocampus Ouest, Rennes, France
| | | | - Christine Lelandais
- IPS2, Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris Sud and Evry, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Martin Crespi
- IPS2, Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris Sud and Evry, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Brabant
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Johann Joets
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Karine Alix
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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9
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Takahagi K, Inoue K, Shimizu M, Uehara-Yamaguchi Y, Onda Y, Mochida K. Homoeolog-specific activation of genes for heat acclimation in the allopolyploid grass Brachypodium hybridum. Gigascience 2018; 7:4924998. [PMID: 29697823 PMCID: PMC5915950 DOI: 10.1093/gigascience/giy020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 03/01/2018] [Indexed: 11/21/2022] Open
Abstract
Background Allopolyploid plants often show wider environmental tolerances than their ancestors; this is expected to be due to the merger of multiple distinct genomes with a fixed heterozygosity. The complex homoeologous gene expression could have been evolutionarily advantageous for the adaptation of allopolyploid plants. Despite multiple previous studies reporting homoeolog-specific gene expression in allopolyploid species, there are no clear examples of homoeolog-specific function in acclimation to a long-term stress condition. Results We found that the allopolyploid grass Brachypodium hybridum and its ancestor Brachypodium stacei show long-term heat stress tolerance, unlike its other ancestor, Brachypodium distachyon. To understand the physiological traits of B. hybridum, we compared the transcriptome of the 3 Brachypodium species grown under normal and heat stress conditions. We found that the expression patterns of approximately 26% and approximately 38% of the homoeolog groups in B. hybridum changed toward nonadditive expression and nonancestral expression, respectively, under normal condition. Moreover, we found that B. distachyon showed similar expression patterns between normal and heat stress conditions, whereas B. hybridum and B. stacei significantly altered their transcriptome in response to heat after 3 days of stress exposure, and homoeologs that were inherited from B. stacei may have contributed to the transcriptional stress response to heat in B. hybridum. After 15 days of heat exposure, B. hybridum and B. stacei maintained transcriptional states similar to those under normal conditions. These results suggest that an earlier response to heat that was specific to homoeologs originating from B. stacei contributed to cellular homeostasis under long-term heat stress in B. hybridum. Conclusions Our results provide insights into different regulatory events of the homoeo-transcriptome that are associated with stress acclimation in allopolyploid plants.
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Affiliation(s)
- Kotaro Takahagi
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan.,Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Minami Shimizu
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yukiko Uehara-Yamaguchi
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshihiko Onda
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiichi Mochida
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan.,Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
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10
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Baduel P, Bray S, Vallejo-Marin M, Kolář F, Yant L. The “Polyploid Hop”: Shifting Challenges and Opportunities Over the Evolutionary Lifespan of Genome Duplications. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00117] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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11
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Schou MF, Bechsgaard J, Muñoz J, Kristensen TN. Genome-wide regulatory deterioration impedes adaptive responses to stress in inbred populations of Drosophila melanogaster. Evolution 2018; 72:1614-1628. [PMID: 29738620 DOI: 10.1111/evo.13497] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 04/21/2018] [Accepted: 05/01/2018] [Indexed: 02/28/2024]
Abstract
Inbreeding depression is often intensified under environmental stress (i.e., inbreeding-stress interaction). Although the fitness consequences of this phenomenon are well-described, underlying mechanisms such as an increased expression of deleterious alleles under stress, or a lower capacity for adaptive responses to stress with inbreeding, have rarely been investigated. We investigated a fitness component (egg-to-adult viability) and gene-expression patterns using RNA-seq analyses in noninbred control lines and in inbred lines of Drosophila melanogaster exposed to benign temperature or heat stress. We find little support for an increase in the cumulative expression of deleterious alleles under stress. Instead, inbred individuals had a reduced ability to induce an adaptive gene regulatory stress response compared to controls. The decrease in egg-to-adult viability due to stress was most pronounced in the lines with the largest deviation in the adaptive stress response (R2 = 0.48). Thus, we find strong evidence for a lower capacity of inbred individuals to respond by gene regulation to stress and that this is the main driver of inbreeding-stress interactions. In comparison, the altered gene expression due to inbreeding at benign temperature showed no correlation with fitness and was pronounced in genomic regions experiencing the highest increase in homozygosity.
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Affiliation(s)
- Mads F Schou
- Department of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Jesper Bechsgaard
- Department of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Joaquin Muñoz
- Department of Chemistry and Bioscience, Aalborg University, DK-9220 Aalborg East, Denmark
| | - Torsten N Kristensen
- Department of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark
- Department of Chemistry and Bioscience, Aalborg University, DK-9220 Aalborg East, Denmark
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12
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Novikova PY, Hohmann N, Van de Peer Y. Polyploid Arabidopsis species originated around recent glaciation maxima. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:8-15. [PMID: 29448159 DOI: 10.1016/j.pbi.2018.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/17/2018] [Indexed: 05/20/2023]
Abstract
Polyploidy may provide adaptive advantages and is considered to be important for evolution and speciation. Polyploidy events are found throughout the evolutionary history of plants, however they do not seem to be uniformly distributed along the time axis. For example, many of the detected ancient whole-genome duplications (WGDs) seem to cluster around the K/Pg boundary (∼66Mya), which corresponds to a drastic climate change event and a mass extinction. Here, we discuss more recent polyploidy events using Arabidopsis as the most developed plant model at the level of the entire genus. We review the history of the origin of allotetraploid species A. suecica and A. kamchatica, and tetraploid lineages of A. lyrata, A. arenosa and A. thaliana, and discuss potential adaptive advantages. Also, we highlight an association between recent glacial maxima and estimated times of origins of polyploidy in Arabidopsis. Such association might further support a link between polyploidy and environmental challenge, which has been observed now for different time-scales and for both ancient and recent polyploids.
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Affiliation(s)
- Polina Yu Novikova
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Nora Hohmann
- University of Basel, Department of Environmental Sciences, Basel, Switzerland
| | - Yves Van de Peer
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium; Department of Genetics, University of Pretoria, Pretoria, South Africa.
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13
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Pinzon-Rodriguez A, Bensch S, Muheim R. Expression patterns of cryptochrome genes in avian retina suggest involvement of Cry4 in light-dependent magnetoreception. J R Soc Interface 2018; 15:20180058. [PMID: 29593090 PMCID: PMC5908540 DOI: 10.1098/rsif.2018.0058] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/05/2018] [Indexed: 12/23/2022] Open
Abstract
The light-dependent magnetic compass of birds provides orientation information about the spatial alignment of the geomagnetic field. It is proposed to be located in the avian retina, and be mediated by a light-induced, biochemical radical-pair mechanism involving cryptochromes as putative receptor molecules. At the same time, cryptochromes are known for their role in the negative feedback loop in the circadian clock. We measured gene expression of Cry1, Cry2 and Cry4 in the retina, muscle and brain of zebra finches over the circadian day to assess whether they showed any circadian rhythmicity. We hypothesized that retinal cryptochromes involved in magnetoreception should be expressed at a constant level over the circadian day, because birds use a light-dependent magnetic compass for orientation not only during migration, but also for spatial orientation tasks in their daily life. Cryptochromes serving in circadian tasks, on the other hand, are expected to be expressed in a rhythmic (circadian) pattern. Cry1 and Cry2 displayed a daily variation in the retina as expected for circadian clock genes, while Cry4 expressed at constant levels over time. We conclude that Cry4 is the most likely candidate magnetoreceptor of the light-dependent magnetic compass in birds.
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Affiliation(s)
| | - Staffan Bensch
- Department of Biology, Lund University, Ecology Building, Lund 223 62, Sweden
| | - Rachel Muheim
- Department of Biology, Lund University, Biology Building B, Lund 223 62, Sweden
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14
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Takahagi K, Inoue K, Mochida K. Gene Co-expression Network Analysis Suggests the Existence of Transcriptional Modules Containing a High Proportion of Transcriptionally Differentiated Homoeologs in Hexaploid Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1163. [PMID: 30135697 PMCID: PMC6092485 DOI: 10.3389/fpls.2018.01163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/23/2018] [Indexed: 05/20/2023]
Abstract
Genome duplications aid in the formation of novel molecular networks through regulatory differentiation of the duplicated genes and facilitate adaptation to environmental change. Hexaploid wheat, Triticum aestivum, contains three homoeologous chromosome sets, the A-, B-, and D-subgenomes, which evolved through interspecific hybridization and subsequent whole-genome duplication. The divergent expression patterns of the homoeologs in hexaploid wheat suggest that they have undergone transcriptional and/or functional differentiation during wheat evolution. However, the distribution of transcriptionally differentiated homoeologs in gene regulatory networks and their related biological functions in hexaploid wheat are still largely unexplored. Therefore, we retrieved 727 publicly available wheat RNA-sequencing (RNA-seq) datasets from various tissues, developmental stages, and conditions, and identified 10,415 expressed homoeologous triplets. Examining the co-expression modules in the wheat transcriptome, we found that 66% of the expressed homoeologous triplets possess all three homoeologs grouped in the same co-expression modules. Among these, 15 triplets contain co-expressed homoeologs with differential expression levels between homoeoalleles across ≥ 95% of the 727 RNA-seq datasets, suggesting a consistent trend of homoeolog expression bias. In addition, we identified 2,831 differentiated homoeologs that showed gene expression patterns that deviated from those of the other two homoeologs. We found that seven co-expression modules contained a high proportion of such differentiated homoeologs, which accounted for ≥ 20% of the genes in each module. We also found that five of the co-expression modules are abundantly composed of genes involved in biological processes such as chloroplast biogenesis, RNA metabolism, putative defense response, putative posttranscriptional modification, and lipid metabolism, thereby suggesting that, the differentiated homoeologs might highly contribute to these biological functions in the gene network of hexaploid wheat.
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Affiliation(s)
- Kotaro Takahagi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- *Correspondence: Keiichi Mochida,
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15
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Carlson KD, Fernandez-Pozo N, Bombarely A, Pisupati R, Mueller LA, Madlung A. Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica. BMC Genomics 2017; 18:653. [PMID: 28830347 PMCID: PMC5567635 DOI: 10.1186/s12864-017-4067-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 08/16/2017] [Indexed: 12/26/2022] Open
Abstract
Background Allopolyploids contain genomes composed of more than two complete sets of chromosomes that originate from at least two species. Allopolyploidy has been suggested as an important evolutionary mechanism that can lead to instant speciation. Arabidopsis suecica is a relatively recent allopolyploid species, suggesting that its natural accessions might be genetically very similar to each other. Nonetheless, subtle phenotypic differences have been described between different geographic accessions of A. suecica grown in a common garden. Results To determine the degree of genomic similarity between different populations of A. suecica, we obtained transcriptomic sequence, quantified SNP variation within the gene space, and analyzed gene expression levels genome-wide from leaf material grown in controlled lab conditions. Despite their origin from the same progenitor species, the two accessions of A. suecica used in our study show genomic and transcriptomic variation. We report significant gene expression differences between the accessions, mostly in genes with stress-related functions. Among the differentially expressed genes, there are a surprising number of homoeologs coordinately regulated between sister accessions. Conclusions Many of these homoeologous genes and other differentially expressed genes affect transpiration and stomatal regulation, suggesting that they might be involved in the establishment of the phenotypic differences between the two accessions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4067-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keisha D Carlson
- Department of Biology, University of Puget Sound, 1500 N Warner St, CMB 1088, Tacoma, WA, 98416, USA
| | | | - Aureliano Bombarely
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA.,Present Address: Virginia Tech, Department of Horticulture, 216 Latham Hall, Blacksburg, VA, 24061, USA
| | - Rahul Pisupati
- Gregor Mendel Institute of Molecular Plant Biology, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Lukas A Mueller
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA
| | - Andreas Madlung
- Department of Biology, University of Puget Sound, 1500 N Warner St, CMB 1088, Tacoma, WA, 98416, USA.
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16
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Novikova PY, Tsuchimatsu T, Simon S, Nizhynska V, Voronin V, Burns R, Fedorenko OM, Holm S, Säll T, Prat E, Marande W, Castric V, Nordborg M. Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica. Mol Biol Evol 2017; 34:957-968. [PMID: 28087777 PMCID: PMC5400380 DOI: 10.1093/molbev/msw299] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual-a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-of-function allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.
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Affiliation(s)
- Polina Yu Novikova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.,Vienna Graduate School of Population Genetics, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria
| | - Takashi Tsuchimatsu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Samson Simon
- Université de Lille CNRS, UMR 8198 - Evo-Eco-Paleo, Villeneuve d'Ascq, France
| | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Viktor Voronin
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Robin Burns
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Olga M Fedorenko
- Institute of Biology, Karelian Research Center of the Russian Academy of Sciences, Republic of Karelia, Petrozavodsk, Russia
| | - Svante Holm
- Faculty of Science, Technology and Media, Department of Natural Sciences, Mid Sweden University, Sundsvall, Sweden
| | - Torbjörn Säll
- Department of Biology, Lund University, Lund, Sweden
| | - Elisa Prat
- Centre National de Ressources Génomiques Végétales, INRA-CNRGV, Castanet-Tolosan, France
| | - William Marande
- Centre National de Ressources Génomiques Végétales, INRA-CNRGV, Castanet-Tolosan, France
| | - Vincent Castric
- Université de Lille CNRS, UMR 8198 - Evo-Eco-Paleo, Villeneuve d'Ascq, France
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
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17
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Winkler M, Escobar García P, Gattringer A, Sonnleitner M, Hülber K, Schönswetter P, Schneeweiss GM. A novel method to infer the origin of polyploids from Amplified Fragment Length Polymorphism data reveals that the alpine polyploid complex of Senecio carniolicus (Asteraceae) evolved mainly via autopolyploidy. Mol Ecol Resour 2017; 17:877-892. [PMID: 27978605 DOI: 10.1111/1755-0998.12641] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/24/2016] [Accepted: 12/06/2016] [Indexed: 11/30/2022]
Abstract
Despite its evolutionary and ecological relevance, the mode of polyploid origin has been notoriously difficult to be reconstructed from molecular data. Here, we present a method to identify the putative parents of polyploids and thus to infer the mode of their origin (auto- vs. allopolyploidy) from Amplified Fragment Length Polymorphism (AFLP) data. To this end, we use Cohen's d of distances between in silico polyploids, generated within a priori defined scenarios of origin from a priori delimited putative parental entities (e.g. taxa, genetic lineages), and natural polyploids. Simulations show that the discriminatory power of the proposed method increases mainly with increasing divergence between the lower-ploid putative ancestors and less so with increasing delay of polyploidization relative to the time of divergence. We apply the new method to the Senecio carniolicus aggregate, distributed in the European Alps and comprising two diploid, one tetraploid and one hexaploid species. In the eastern part of its distribution, the S. carniolicus aggregate was inferred to comprise an autopolyploid series, whereas for western populations of the tetraploid species, an allopolyploid origin involving the two diploid species was the most likely scenario. Although this suggests that the tetraploid species has two independent origins, other evidence (ribotype distribution, morphology) is consistent with the hypothesis of an autopolyploid origin with subsequent introgression by the second diploid species. Altogether, identifying the best among alternative scenarios using Cohen's d can be straightforward, but particular scenarios, such as allopolyploid origin vs. autopolyploid origin with subsequent introgression, remain difficult to be distinguished.
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Affiliation(s)
- Manuela Winkler
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.,GLORIA Co-ordination, Center for Global Change and Sustainability, University of Natural Resources and Life Sciences Vienna (BOKU) & Institute for Interdisciplinary Mountain Research, Austrian Academy of Sciences, Silbergasse 30/3, Vienna, A-1190, Austria
| | - Pedro Escobar García
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Andreas Gattringer
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Michaela Sonnleitner
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Karl Hülber
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.,Vienna Institute for Nature Conservation & Analyses, Giessergasse 6/7, Vienna, A-1090, Austria
| | - Peter Schönswetter
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, Innsbruck, A-6020, Austria
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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