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Wang N, Chen P, Xu Y, Guo L, Li X, Yi H, Larkin RM, Zhou Y, Deng X, Xu Q. Phased genomics reveals hidden somatic mutations and provides insight into fruit development in sweet orange. HORTICULTURE RESEARCH 2024; 11:uhad268. [PMID: 38371640 PMCID: PMC10873711 DOI: 10.1093/hr/uhad268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 12/01/2023] [Indexed: 02/20/2024]
Abstract
Although revisiting the discoveries and implications of genetic variations using phased genomics is critical, such efforts are still lacking. Somatic mutations represent a crucial source of genetic diversity for breeding and are especially remarkable in heterozygous perennial and asexual crops. In this study, we focused on a diploid sweet orange (Citrus sinensis) and constructed a haplotype-resolved genome using high fidelity (HiFi) reads, which revealed 10.6% new sequences. Based on the phased genome, we elucidate significant genetic admixtures and haplotype differences. We developed a somatic detection strategy that reveals hidden somatic mutations overlooked in a single reference genome. We generated a phased somatic variation map by combining high-depth whole-genome sequencing (WGS) data from 87 sweet orange somatic varieties. Notably, we found twice as many somatic mutations relative to a single reference genome. Using these hidden somatic mutations, we separated sweet oranges into seven major clades and provide insight into unprecedented genetic mosaicism and strong positive selection. Furthermore, these phased genomics data indicate that genomic heterozygous variations contribute to allele-specific expression during fruit development. By integrating allelic expression differences and somatic mutations, we identified a somatic mutation that induces increases in fruit size. Applications of phased genomics will lead to powerful approaches for discovering genetic variations and uncovering their effects in highly heterozygous plants. Our data provide insight into the hidden somatic mutation landscape in the sweet orange genome, which will facilitate citrus breeding.
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Affiliation(s)
- Nan Wang
- Institute of Horticultural Research, Hunan Academy of Agricultural Sciences, Changsha, China
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peng Chen
- Institute of Horticultural Research, Hunan Academy of Agricultural Sciences, Changsha, China
- Yuelu Mountain Laboratory, Changsha, China
| | - Yuanyuan Xu
- Institute of Horticultural Research, Hunan Academy of Agricultural Sciences, Changsha, China
- Yuelu Mountain Laboratory, Changsha, China
| | - Lingxia Guo
- Institute of Horticultural Research, Hunan Academy of Agricultural Sciences, Changsha, China
- Yuelu Mountain Laboratory, Changsha, China
| | - Xianxin Li
- Institute of Horticultural Research, Hunan Academy of Agricultural Sciences, Changsha, China
- Yuelu Mountain Laboratory, Changsha, China
| | - Hualin Yi
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Robert M Larkin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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de Tomás C, Vicient CM. The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants. EPIGENOMES 2023; 8:2. [PMID: 38247729 PMCID: PMC10801548 DOI: 10.3390/epigenomes8010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/23/2024] Open
Abstract
Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic alterations, including inversions, deletions, and duplications. Host organisms have evolved a set of mechanisms to suppress TE activity and counter the threat that they pose to genome integrity. These includes the epigenetic silencing of TEs mediated by a process of RNA-directed DNA methylation (RdDM). In most cases, the silencing machinery is very efficient for the vast majority of TEs. However, there are specific circumstances in which TEs can evade such silencing mechanisms, for example, a variety of biotic and abiotic stresses or in vitro culture. Hybridization is also proposed as an inductor of TE proliferation. In fact, the discoverer of the transposons, Barbara McClintock, first hypothesized that interspecific hybridization provides a "genomic shock" that inhibits the TE control mechanisms leading to the mobilization of TEs. However, the studies carried out on this topic have yielded diverse results, showing in some cases a total absence of mobilization or being limited to only some TE families. Here, we review the current knowledge about the impact of interspecific hybridization on TEs in plants and the possible implications of changes in the epigenetic mechanisms.
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Affiliation(s)
| | - Carlos M. Vicient
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
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3
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Huanel OR, Quesada-Calderón S, Ríos Molina C, Morales-González S, Saenz-Agudelo P, Nelson WA, Arakaki N, Mauger S, Faugeron S, Guillemin ML. Pre-domestication bottlenecks of the cultivated seaweed Gracilaria chilensis. Mol Ecol 2022; 31:5506-5523. [PMID: 36029170 DOI: 10.1111/mec.16672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 08/02/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022]
Abstract
Gracilaria chilensis is the main cultivated seaweed in Chile. The low genetic diversity observed in the Chilean populations has been associated with the over-exploitation of natural beds and/or the founder effect that occurred during post-glacial colonization from New Zealand. How these processes have affected its evolutionary trajectory before farming and incipient domestication is poorly understood. In this study, we used 2232 single nucleotide polymorphisms (SNPs) to assess how the species' evolutionary history in New Zealand (its region of origin), the founder effect linked to transoceanic dispersion and colonization of South America, and the recent over-exploitation of natural populations have influenced the genetic architecture of G. chilensis in Chile. The contrasting patterns of genetic diversity and structure observed between the two main islands in New Zealand attest to the important effects of Quaternary glacial cycles on G. chilensis. Approximate Bayesian Computation (ABC) analyses indicated that Chatham Island and South America were colonized independently near the end of the Last Glacial Maximum and emphasized the importance of coastal and oceanic currents during that period. Furthermore, ABC analyses inferred the existence of a recent and strong genetic bottleneck in Chile, matching the period of over-exploitation of the natural beds during the 1970s, followed by rapid demographic expansion linked to active clonal propagation used in farming. Recurrent genetic bottlenecks strongly eroded the genetic diversity of G. chilensis prior to its cultivation, raising important challenges for the management of genetic resources in this incipiently domesticated species.
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Affiliation(s)
- Oscar R Huanel
- Núcleo Milenio MASH, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France
| | - Suany Quesada-Calderón
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,AUSTRAL-omics, Vicerrectoría de Investigación, Desarrollo y Creación Artística, Universidad Austral de Chile, Valdivia, Chile
| | - Cristian Ríos Molina
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Sarai Morales-González
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pablo Saenz-Agudelo
- IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France.,Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,ANID- Millennium Science Initiative Nucleus (NUTME), Las Cruces, Chile
| | - Wendy A Nelson
- National Institute of Water and Atmospheric Research, Wellington, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Natalia Arakaki
- Instituto del Mar del Perú, Banco de Germoplasma de Organismos Acuáticos, Chucuito, Callao, Peru
| | - Stéphane Mauger
- IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France
| | - Sylvain Faugeron
- Núcleo Milenio MASH, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France
| | - Marie-Laure Guillemin
- IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, France.,Núcleo Milenio MASH, Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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Gnutikov AA, Nosov NN, Loskutov IG, Blinova EV, Shneyer VS, Probatova NS, Rodionov AV. New Insights into the Genomic Structure of Avena L.: Comparison of the Divergence of A-Genome and One C-Genome Oat Species. PLANTS (BASEL, SWITZERLAND) 2022; 11:1103. [PMID: 35567104 PMCID: PMC9102028 DOI: 10.3390/plants11091103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
We used next-generation sequencing analysis of the 3′-part of 18S rDNA, ITS1, and a 5′-part of the 5.8S rDNA region to understand genetic variation among seven diploid A-genome Avena species. We used 4−49 accessions per species that represented the As genome (A. atlantica, A. hirtula, and wiestii), Ac genome (A. canariensis), Ad genome (A. damascena), Al genome (A. longiglumis), and Ap genome (A. prostrata). We also took into our analysis one C-genome species, A. clauda, which previously was found to be related to A-genome species. The sequences of 169 accessions revealed 156 haplotypes of which seven haplotypes were shared by two to five species. We found 16 ribotypes that consisted of a unique sequence with a characteristic pattern of single nucleotide polymorphisms and deletions. The number of ribotypes per species varied from one in A. longiglumis to four in A. wiestii. Although most ribotypes were species-specific, we found two ribotypes shared by three species (one for A. damascena, A. hirtula, and A. wiestii, and the second for A. longiglumis, A. atlantica, and A. wiestii), and a third ribotype shared between A. atlantica and A. wiestii. A characteristic feature of the A. clauda ribotype, a diploid C-genome species, is that two different families of ribotypes have been found in this species. Some of these ribotypes are characteristic of Cc-genome species, whereas others are closely related to As-genome ribotypes. This means that A. clauda can be a hybrid between As- and C-genome oats.
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Affiliation(s)
- Alexander A. Gnutikov
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Nikolai N. Nosov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
| | - Igor G. Loskutov
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Elena V. Blinova
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Viktoria S. Shneyer
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
| | - Nina S. Probatova
- Laboratory of Botany, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia;
| | - Alexander V. Rodionov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
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5
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Peringottillam M, Kunhiraman Vasumathy S, Selvakumar HKK, Alagu M. Genetic diversity and population structure of rice (Oryza sativa L.) landraces from Kerala, India analyzed through genotyping-by-sequencing. Mol Genet Genomics 2022; 297:169-182. [PMID: 35039933 DOI: 10.1007/s00438-021-01844-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/28/2021] [Indexed: 11/24/2022]
Abstract
Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for developing dominant strategies for the sustainable management of genetically diverse crops. We attempt to fill the existing research lacuna in the molecular characterization of potent rice landraces in Kerala. Genotyping-by-sequencing (GBS) was performed on 96 Kerala rice accessions to identify single-nucleotide polymorphisms (SNPs), to examine the genetic diversity, population structure, and to delineate linkage disequilibrium (LD) pattern. GBS identified 5856 high-quality SNPs. The structure analysis indicated three subpopulations with the highest probability for population clustering with significant genetic differentiation, confirmed by principal component analysis. The genome-wide LD decay distance was 772 kb, at which the r2 dropped to half its maximum value. The analysis of genetic properties of the identified SNP panel with an average polymorphism information content (PIC) value of 0.22 and a minor allele frequency (MAF) > 0.1 unveiled their efficacy in genome-wide association studies (GWAS). High FST (0.266) and low Nm (0.692) portray a strong genetic differentiation among the rice landraces, complementing the genetic structuring observed in the studied population. Slow LD decay in the rice landraces reflects their self-pollinating behavior and the indirect selection of desired traits by domestication. Moreover, the high LD entails only a minimum number of SNP markers for detecting marker-trait association. The diverse germplasm utilized in this study can be further utilized to disclose genetic variants associated with phenotypic traits and define signatures of selection via GWAS and selective sweep, respectively.
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Affiliation(s)
- Maya Peringottillam
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye (PO), Kasaragod, Kerala, 671316, India
| | - Smitha Kunhiraman Vasumathy
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye (PO), Kasaragod, Kerala, 671316, India
| | - Hari Krishna Kumar Selvakumar
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye (PO), Kasaragod, Kerala, 671316, India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye (PO), Kasaragod, Kerala, 671316, India.
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6
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Fijarczyk A, Hénault M, Marsit S, Charron G, Landry CR. Heterogeneous Mutation Rates and Spectra in Yeast Hybrids. Genome Biol Evol 2021; 13:6462191. [PMID: 34908117 PMCID: PMC8715523 DOI: 10.1093/gbe/evab282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2021] [Indexed: 12/11/2022] Open
Abstract
Mutation rates and spectra vary between species and among populations. Hybridization can contribute to this variation, but its role remains poorly understood. Estimating mutation rates requires controlled conditions where the effect of natural selection can be minimized. One way to achieve this is through mutation accumulation experiments coupled with genome sequencing. Here, we investigate 400 mutation accumulation lines initiated from 11 genotypes spanning intralineage, interlineage, and interspecific crosses of the yeasts Saccharomyces paradoxus and S. cerevisiae and propagated for 770 generations. We find significant differences in mutation rates and spectra among crosses, which are not related to the level of divergence of parental strains but are specific to some genotype combinations. Differences in number of generations and departures from neutrality play a minor role, whereas polyploidy and loss of heterozygosity impact mutation rates in some of the hybrid crosses in an opposite way.
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Affiliation(s)
- Anna Fijarczyk
- Département de Biologie, Université Laval, Québec, Québec, Canada.,Institut de Biologie Intégrative et des Systemes (IBIS), Université Laval, Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, La Structure et L'Ingénierie des Protéines, Université Laval, Québec, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Québec, Canada
| | - Mathieu Hénault
- Département de Biologie, Université Laval, Québec, Québec, Canada.,Institut de Biologie Intégrative et des Systemes (IBIS), Université Laval, Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, La Structure et L'Ingénierie des Protéines, Université Laval, Québec, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Québec, Canada
| | - Souhir Marsit
- Département de Biologie, Université Laval, Québec, Québec, Canada.,Institut de Biologie Intégrative et des Systemes (IBIS), Université Laval, Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, La Structure et L'Ingénierie des Protéines, Université Laval, Québec, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Québec, Canada
| | - Guillaume Charron
- Département de Biologie, Université Laval, Québec, Québec, Canada.,Institut de Biologie Intégrative et des Systemes (IBIS), Université Laval, Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, La Structure et L'Ingénierie des Protéines, Université Laval, Québec, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Québec, Canada
| | - Christian R Landry
- Département de Biologie, Université Laval, Québec, Québec, Canada.,Institut de Biologie Intégrative et des Systemes (IBIS), Université Laval, Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, Canada.,PROTEO, Le Réseau Québécois de Recherche sur la Fonction, La Structure et L'Ingénierie des Protéines, Université Laval, Québec, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Québec, Canada
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7
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Krasovec M. The spontaneous mutation rate of Drosophila pseudoobscura. G3 GENES|GENOMES|GENETICS 2021; 11:6265464. [PMID: 33950174 PMCID: PMC8495931 DOI: 10.1093/g3journal/jkab151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
Abstract
The spontaneous mutation rate is a very variable trait that is subject to drift, selection and is sometimes highly plastic. Consequently, its variation between close species, or even between populations from the same species, can be very large. Here, I estimated the spontaneous mutation rate of Drosophila pseudoobscura and Drosophila persimilis crosses to explore the mutation rate variation within the Drosophila genus. All mutation rate estimations in Drosophila varied fourfold, probably explained by the sensitivity of the mutation rate to environmental and experimental conditions. Moreover, I found a very high mutation rate in the hybrid cross between D. pseudoobscura and D. persimilis, in agreement with known elevated mutation rate in hybrids. This mutation rate increase can be explained by heterozygosity and fitness decrease effects in hybrids.
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Affiliation(s)
- Marc Krasovec
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer 66650, France
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8
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Mounger J, Ainouche ML, Bossdorf O, Cavé-Radet A, Li B, Parepa M, Salmon A, Yang J, Richards CL. Epigenetics and the success of invasive plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200117. [PMID: 33866809 PMCID: PMC8059582 DOI: 10.1098/rstb.2020.0117] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
Biological invasions impose ecological and economic problems on a global scale, but also provide extraordinary opportunities for studying contemporary evolution. It is critical to understand the evolutionary processes that underly invasion success in order to successfully manage existing invaders, and to prevent future invasions. As successful invasive species sometimes are suspected to rapidly adjust to their new environments in spite of very low genetic diversity, we are obliged to re-evaluate genomic-level processes that translate into phenotypic diversity. In this paper, we review work that supports the idea that trait variation, within and among invasive populations, can be created through epigenetic or other non-genetic processes, particularly in clonal invaders where somatic changes can persist indefinitely. We consider several processes that have been implicated as adaptive in invasion success, focusing on various forms of 'genomic shock' resulting from exposure to environmental stress, hybridization and whole-genome duplication (polyploidy), and leading to various patterns of gene expression re-programming and epigenetic changes that contribute to phenotypic variation or even novelty. These mechanisms can contribute to transgressive phenotypes, including hybrid vigour and novel traits, and may thus help to understand the huge successes of some plant invaders, especially those that are genetically impoverished. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Jeannie Mounger
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Avenue, Tampa, FL 33617, USA
| | - Malika L. Ainouche
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Armand Cavé-Radet
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Bo Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Madalin Parepa
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Armel Salmon
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Ji Yang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Christina L. Richards
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Avenue, Tampa, FL 33617, USA
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
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9
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Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair. Cells 2021; 10:cells10051224. [PMID: 34067668 PMCID: PMC8156620 DOI: 10.3390/cells10051224] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 01/06/2023] Open
Abstract
We describe the contribution of DNA mismatch repair (MMR) to the stability of the eukaryotic nuclear genome as determined by whole-genome sequencing. To date, wild-type nuclear genome mutation rates are known for over 40 eukaryotic species, while measurements in mismatch repair-defective organisms are fewer in number and are concentrated on Saccharomyces cerevisiae and human tumors. Well-studied organisms include Drosophila melanogaster and Mus musculus, while less genetically tractable species include great apes and long-lived trees. A variety of techniques have been developed to gather mutation rates, either per generation or per cell division. Generational rates are described through whole-organism mutation accumulation experiments and through offspring–parent sequencing, or they have been identified by descent. Rates per somatic cell division have been estimated from cell line mutation accumulation experiments, from systemic variant allele frequencies, and from widely spaced samples with known cell divisions per unit of tissue growth. The latter methods are also used to estimate generational mutation rates for large organisms that lack dedicated germlines, such as trees and hyphal fungi. Mechanistic studies involving genetic manipulation of MMR genes prior to mutation rate determination are thus far confined to yeast, Arabidopsis thaliana, Caenorhabditis elegans, and one chicken cell line. A great deal of work in wild-type organisms has begun to establish a sound baseline, but far more work is needed to uncover the variety of MMR across eukaryotes. Nonetheless, the few MMR studies reported to date indicate that MMR contributes 100-fold or more to genome stability, and they have uncovered insights that would have been impossible to obtain using reporter gene assays.
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10
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Yan Z, Appiano M, van Tuinen A, Meijer-Dekens F, Schipper D, Gao D, Huibers R, Visser RGF, Bai Y, Wolters AMA. Discovery and Characterization of a Novel Tomato mlo Mutant from an EMS Mutagenized Micro-Tom Population. Genes (Basel) 2021; 12:genes12050719. [PMID: 34064921 PMCID: PMC8150974 DOI: 10.3390/genes12050719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/17/2022] Open
Abstract
In tomato (Solanum lycopersicum), there are at least three SlMLO (Mildew resistance Locus O) genes acting as susceptibility genes for the powdery mildew disease caused by Oidium neolycopersici, namely SlMLO1, SlMLO5 and SlMLO8. Of the three homologs, the SlMLO1 gene plays a major role since a natural mutant allele called ol-2 can almost completely prevent fungal penetration by formation of papillae. The ol-2 allele contains a 19-bp deletion in the coding sequence of the SlMLO1 gene, resulting in a premature stop codon within the second cytoplasmic loop of the predicted protein. In this study, we have developed a new genetic resource (M200) in the tomato cv. Micro-Tom genetic background by means of ethyl methane sulfonate (EMS) mutagenesis. The mutant M200 containing a novel allele (the m200 allele) of the tomato SlMLO1 gene showed profound resistance against powdery mildew with no fungal sporulation. Compared to the coding sequence of the SlMLO1 gene, the m200 allele carries a point mutation at T65A. The SNP results in a premature stop codon L22* located in the first transmembrane domain of the complete SlMLO1 protein. The length of the predicted protein is 21 amino acids, while the SlMLO1 full-length protein is 513 amino acids. A high-resolution melting (HRM) marker was developed to distinguish the mutated m200 allele from the SlMLO1 allele in backcross populations. The mutant allele conferred recessive resistance that was associated with papillae formation at fungal penetration sites of plant epidermal cells. A comprehensive list of known mlo mutations found in natural and artificial mutants is presented, which serves as a particularly valuable resource for powdery mildew resistance breeding.
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11
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Fujita MK, Singhal S, Brunes TO, Maldonado JA. Evolutionary Dynamics and Consequences of Parthenogenesis in Vertebrates. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-114900] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Parthenogenesis is asexual reproduction without any required participation from males and, as such, is a null model for sexual reproduction. In a comparative context, we can expand our understanding of the evolution and ecology of sex by investigating the consequences of parthenogenesis. In this review, we examine the theoretical predictions of and empirical results on the evolution of asexual reproduction in vertebrates, focusing on recent studies addressing the origins and geographic spread of parthenogenetic lineages and the genomic consequences of an asexual life history. With advances in computational methods and genome technologies, researchers are poised to make rapid and significant progress in studying the origin and evolution of parthenogenesis in vertebrates, thus providing an important perspective on understanding biodiversity patterns of both asexual and sexual populations.
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Affiliation(s)
- Matthew K. Fujita
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, California 90747, USA
| | - Tuliana O. Brunes
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Jose A. Maldonado
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
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12
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Abstract
Interspecific hybridization is the process where closely related species mate and produce offspring with admixed genomes. The genomic revolution has shown that hybridization is common, and that it may represent an important source of novel variation. Although most interspecific hybrids are sterile or less fit than their parents, some may survive and reproduce, enabling the transfer of adaptive variants across the species boundary, and even result in the formation of novel evolutionary lineages. There are two main variants of hybrid species genomes: allopolyploid, which have one full chromosome set from each parent species, and homoploid, which are a mosaic of the parent species genomes with no increase in chromosome number. The establishment of hybrid species requires the development of reproductive isolation against parental species. Allopolyploid species often have strong intrinsic reproductive barriers due to differences in chromosome number, and homoploid hybrids can become reproductively isolated from the parent species through assortment of genetic incompatibilities. However, both types of hybrids can become further reproductively isolated, gaining extrinsic isolation barriers, by exploiting novel ecological niches, relative to their parents. Hybrids represent the merging of divergent genomes and thus face problems arising from incompatible combinations of genes. Thus hybrid genomes are highly dynamic and undergo rapid evolutionary change, including genome stabilization in which selection against incompatible combinations results in fixation of compatible ancestry block combinations within the hybrid species. The potential for rapid adaptation or speciation makes hybrid genomes a particularly exciting subject of in evolutionary biology. Here we summarize how introgressed alleles or hybrid species can establish and how the resulting hybrid genomes evolve.
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Affiliation(s)
- Anna Runemark
- Department of Biology, Lund University, Lund, Sweden
- * E-mail:
| | - Mario Vallejo-Marin
- Biological and Environmental Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Joana I. Meier
- St John's College, Cambridge, Cambridge, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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Effect of Hybridization on Somatic Mutations and Genomic Rearrangements in Plants. Int J Mol Sci 2018; 19:ijms19123758. [PMID: 30486351 PMCID: PMC6320998 DOI: 10.3390/ijms19123758] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 11/16/2022] Open
Abstract
Hybridization has been routinely practiced in agriculture to enhance the crop yield. Principally, it can cause hybrid vigor where hybrid plants display increased size, biomass, fertility, and resistance to diseases, when compared to their parents. During hybridization, hybrid offspring receive a genomic shock due to mixing of distant parental genomes, which triggers a myriad of genomic rearrangements, e.g., transpositions, genome size changes, chromosomal rearrangements, and other effects on the chromatin. Recently, it has been reported that, besides genomic rearrangements, hybridization can also alter the somatic mutation rates in plants. In this review, we provide in-depth insights about hybridization triggered genomic rearrangements and somatic mutations in plants.
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Du MZ, Liu S, Zeng Z, Alemayehu LA, Wei W, Guo FB. Amino acid compositions contribute to the proteins' evolution under the influence of their abundances and genomic GC content. Sci Rep 2018; 8:7382. [PMID: 29743515 PMCID: PMC5943316 DOI: 10.1038/s41598-018-25364-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 04/16/2018] [Indexed: 12/23/2022] Open
Abstract
Inconsistent results on the association between evolutionary rates and amino acid composition of proteins have been reported in eukaryotes. However, there are few studies of how amino acid composition can influence evolutionary rates in bacteria. Thus, we constructed linear regression models between composition frequencies of amino acids and evolutionary rates for bacteria. Compositions of all amino acids can on average explain 21.5% of the variation in evolutionary rates among 273 investigated bacterial organisms. In five model organisms, amino acid composition contributes more to variation in evolutionary rates than protein abundance, and frequency of optimal codons. The contribution of individual amino acid composition to evolutionary rate varies among organisms. The closer the GC-content of genome to its maximum or minimum, the better the correlation between the amino acid content and the evolutionary rate of proteins would appear in that genome. The types of amino acids that significantly contribute to evolutionary rates can be grouped into GC-rich and AT-rich amino acids. Besides, the amino acid with high composition also contributes more to evolutionary rates than amino acid with low composition in proteome. In summary, amino acid composition significantly contributes to the rate of evolution in bacterial organisms and this in turn is impacted by GC-content.
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Affiliation(s)
- Meng-Ze Du
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Shuo Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhi Zeng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Labena Abraham Alemayehu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Wen Wei
- School of Life Sciences, Chongqing University, Chongqing, China.
| | - Feng-Biao Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China. .,Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China. .,Key Laboratory for Neuroinformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China.
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15
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Xie Z, Wang L, Wang L, Wang Z, Lu Z, Tian D, Yang S, Hurst LD. Mutation rate analysis via parent-progeny sequencing of the perennial peach. I. A low rate in woody perennials and a higher mutagenicity in hybrids. Proc Biol Sci 2017; 283:rspb.2016.1016. [PMID: 27798292 PMCID: PMC5095371 DOI: 10.1098/rspb.2016.1016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/01/2016] [Indexed: 12/30/2022] Open
Abstract
Mutation rates vary between species, between strains within species and between regions within a genome. What are the determinants of these forms of variation? Here, via parent–offspring sequencing of the peach we ask whether (i) woody perennials tend to have lower per unit time mutation rates compared to annuals, and (ii) hybrid strains have high mutation rates. Between a leaf from a low heterozygosity individual, derived from an intraspecific cross, to a leaf of its selfed progeny, the mutation rate is 7.77 × 10−9 point mutations per bp per generation, similar to Arabidopsis thaliana (7.0–7.4 × 10−9 point mutations per bp per generation). This suggests a low per unit time mutation rate as the generation time is much longer in peach. This is supported by our estimate of 9.48 × 10−9 point mutations per bp per generation from a 200-year-old low heterozygosity peach to its progeny. From a more highly heterozygous individual derived from an interspecific cross to its selfed progeny, the mutation rate is 1.38 × 10−8 mutations per site per generation, consistent with raised rates in hybrids. Our data thus suggest that (i) peach has an approximately order of magnitude lower mutation rate per unit time than Arabidopsis, consistent with reports of low evolutionary rates in woody perennials, and (ii) hybridization may, indeed, be associated with increased mutation rates as considered over a century ago.
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Affiliation(s)
- Zhengqing Xie
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Lirong Wang
- Chinese Academy of Agriculture Sciences, Zhengzhou Fruit Research Institute, Zhengzhou 450009, People's Republic of China
| | - Zhiqiang Wang
- Chinese Academy of Agriculture Sciences, Zhengzhou Fruit Research Institute, Zhengzhou 450009, People's Republic of China
| | - Zhenhua Lu
- Chinese Academy of Agriculture Sciences, Zhengzhou Fruit Research Institute, Zhengzhou 450009, People's Republic of China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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Saini R, Singh AK, Dhanapal S, Saeed TH, Hyde GJ, Baskar R. Brief temperature stress during reproductive stages alters meiotic recombination and somatic mutation rates in the progeny of Arabidopsis. BMC PLANT BIOLOGY 2017; 17:103. [PMID: 28615006 PMCID: PMC5471674 DOI: 10.1186/s12870-017-1051-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 06/01/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Plants exposed to environmental stresses draw upon many genetic and epigenetic strategies, with the former sometimes modulated by the latter. This can help the plant, and its immediate progeny, at least, to better endure the stress. Some evidence has led to proposals that (epi) genetic changes can be both selective and sustainably heritable, while other evidence suggests that changes are effectively stochastic, and important only because they induce genetic variation. One type of stress with an arguably high level of stochasticity in its effects is temperature stress. Studies of how heat and cold affect the rates of meiotic recombination (MR) and somatic mutations (SMs, which are potentially heritable in plants) report increases, decreases, or no effect. Collectively, they do not point to any consistent patterns. Some of this variability, however, might arise from the stress being applied for such an extended time, typically days or weeks. Here, we adopted a targeted approach by (1) limiting exposure to one hour; and (2) timing it to coincide with (a) gamete, and early gametophyte, development, a period of high stress sensitivity; and (b) a late stage of vegetative development. RESULTS For plants (Arabidopsis thaliana) otherwise grown at 22 °C, we measured the effects of a 1 h exposure to cold (12 °C) or heat (32 °C) on the rates of MR, and four types of SMs (frameshift mutations; intrachromosomal recombination; base substitutions; transpositions) in the F1 progeny. One parent (wild type) was stressed, the other (unstressed) carried a genetic event detector. When rates were compared to those in progeny of control (both parents unstressed) two patterns emerged. In the progeny of younger plants (stressed at 36 days; pollinated at 40 days) heat and cold either had no effect (on MR) or (for SMs) had effects that were rare and stochastic. In the progeny of older plants (stressed at 41 days; pollinated at 45 days), while effects were also infrequent, those that were seen followed a consistent pattern: rates of all five genetic events were lowest at 12 °C and highest at 32 °C, i.e. they varied in a "dose-response" manner. This pattern was strongest (or, in the case of MR, only apparent) in progeny whose stressed parent was female. CONCLUSION While the infrequency of effects suggests the need for cautious inference, the consistency of responses in the progeny of older plants, indicate that in some circumstances the level of stochasticity in inherited genetic responses to heat or cold stress can be context-dependent, possibly reflecting life-cycle stages in the parental generation that are variably stress sensitive.
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Affiliation(s)
- Ramswaroop Saini
- Department of Biotechnology, Indian Institute of Technology–Madras, Bhupat and Jyoti Mehta School of Biosciences, Chennai, 600 036 India
| | - Amit Kumar Singh
- Department of Biotechnology, Indian Institute of Technology–Madras, Bhupat and Jyoti Mehta School of Biosciences, Chennai, 600 036 India
| | - Shanmuhapreya Dhanapal
- Department of Biotechnology, Indian Institute of Technology–Madras, Bhupat and Jyoti Mehta School of Biosciences, Chennai, 600 036 India
| | - Thoufeequl Hakeem Saeed
- Department of Biotechnology, Indian Institute of Technology–Madras, Bhupat and Jyoti Mehta School of Biosciences, Chennai, 600 036 India
| | - Geoffrey J. Hyde
- Write about Research, 14 Randwick Street, Randwick, Sydney, 2031 Australia
| | - Ramamurthy Baskar
- Department of Biotechnology, Indian Institute of Technology–Madras, Bhupat and Jyoti Mehta School of Biosciences, Chennai, 600 036 India
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Liu H, Jia Y, Sun X, Tian D, Hurst LD, Yang S. Direct Determination of the Mutation Rate in the Bumblebee Reveals Evidence for Weak Recombination-Associated Mutation and an Approximate Rate Constancy in Insects. Mol Biol Evol 2017; 34:119-130. [PMID: 28007973 PMCID: PMC5854123 DOI: 10.1093/molbev/msw226] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Accurate knowledge of the mutation rate provides a base line for inferring expected rates of evolution, for testing evolutionary hypotheses and for estimation of key parameters. Advances in sequencing technology now permit direct estimates of the mutation rate from sequencing of close relatives. Within insects there have been three prior such estimates, two in nonsocial insects (Drosophila: 2.8 × 10-9 per bp per haploid genome per generation; Heliconius: 2.9 × 10-9) and one in a social species, the honeybee (3.4 × 10-9). Might the honeybee's rate be ∼20% higher because it has an exceptionally high recombination rate and recombination may be directly or indirectly mutagenic? To address this possibility, we provide a direct estimate of the mutation rate in the bumblebee (Bombus terrestris), this being a close relative of the honeybee but with a much lower recombination rate. We confirm that the crossover rate of the bumblebee is indeed much lower than honeybees (8.7 cM/Mb vs. 37 cM/Mb). Importantly, we find no significant difference in the mutation rates: we estimate for bumblebees a rate of 3.6 × 10-9 per haploid genome per generation (95% confidence intervals 2.38 × 10-9 and 5.37 × 10-9) which is just 5% higher than the estimate that of honeybees. Both genomes have approximately one new mutation per haploid genome per generation. While we find evidence for a direct coupling between recombination and mutation (also seen in honeybees), the effect is so weak as to leave almost no footprint on any between-species differences. The similarity in mutation rates suggests an approximate constancy of the mutation rate in insects.
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Affiliation(s)
- Haoxuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yanxiao Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiaoguang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Laurence D Hurst
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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Shah JM, Ramakrishnan AM, Singh AK, Ramachandran S, Unniyampurath U, Jayshankar A, Balasundaram N, Dhanapal S, Hyde G, Baskar R. Suppression of different classes of somatic mutations in Arabidopsis by vir gene-expressing Agrobacterium strains. BMC PLANT BIOLOGY 2015; 15:210. [PMID: 26307100 PMCID: PMC4549908 DOI: 10.1186/s12870-015-0595-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 08/14/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Agrobacterium infection, which is widely used to generate transgenic plants, is often accompanied by T-DNA-linked mutations and transpositions in flowering plants. It is not known if Agrobacterium infection also affects the rates of point mutations, somatic homologous recombinations (SHR) and frame-shift mutations (FSM). We examined the effects of Agrobacterium infection on five types of somatic mutations using a set of mutation detector lines of Arabidopsis thaliana. To verify the effect of secreted factors, we exposed the plants to different Agrobacterium strains, including wild type (Ach5), its derivatives lacking vir genes, oncogenes or T-DNA, and the heat-killed form for 48 h post-infection; also, for a smaller set of strains, we examined the rates of three types of mutations at multiple time-points. The mutation detector lines carried a non-functional β-glucuronidase gene (GUS) and a reversion of mutated GUS to its functional form resulted in blue spots. Based on the number of blue spots visible in plants grown for a further two weeks, we estimated the mutation frequencies. RESULTS For plants co-cultivated for 48 h with Agrobacterium, if the strain contained vir genes, then the rates of transversions, SHRs and FSMs (measured 2 weeks later) were lower than those of uninfected controls. In contrast, co-cultivation for 48 h with any of the Agrobacterium strains raised the transposition rates above control levels. The multiple time-point study showed that in seedlings co-cultivated with wild type Ach5, the reduced rates of transversions and SHRs after 48 h co-cultivation represent an apparent suppression of an earlier short-lived increase in mutation rates (peaking for plants co-cultivated for 3 h). An increase after 3 h co-cultivation was also seen for rates of transversions (but not SHR) in seedlings exposed to the strain lacking vir genes, oncogenes and T-DNA. However, the mutation rates in plants co-cultivated for longer times with this strain subsequently dropped below levels seen in uninfected controls, consistent with the results of the single time-point study. CONCLUSIONS The rates of various classes of mutations that result from Agrobacterium infection depend upon the duration of infection and the type of pathogen derived factors (such as Vir proteins, oncoproteins or T-DNA) possessed by the strain. Strains with vir genes, including the type used for plant transformation, suppressed selected classes of somatic mutations. Our study also provides evidence of a pathogen that can at least partly counter the induction of mutations in an infected plant.
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Affiliation(s)
- Jasmine M Shah
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
- Department of Plant Science, Central University of Kerala, Kasaragod, 671328, India.
| | - Anantha Maharasi Ramakrishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
| | - Amit Kumar Singh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
| | - Subalakshmi Ramachandran
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
| | | | - Ajitha Jayshankar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
| | - Nithya Balasundaram
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
| | - Shanmuhapreya Dhanapal
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
| | - Geoff Hyde
- , 14 Randwick St, Sydney, 2031, Australia.
| | - Ramamurthy Baskar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600036, India.
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Singh AK, Bashir T, Sailer C, Gurumoorthy V, Ramakrishnan AM, Dhanapal S, Grossniklaus U, Baskar R. Parental age affects somatic mutation rates in the progeny of flowering plants. PLANT PHYSIOLOGY 2015; 168:247-57. [PMID: 25810093 PMCID: PMC4424033 DOI: 10.1104/pp.15.00291] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 03/21/2015] [Indexed: 05/18/2023]
Abstract
In humans, it is well known that the parental reproductive age has a strong influence on mutations transmitted to their progeny. Meiotic nondisjunction is known to increase in older mothers, and base substitutions tend to go up with paternal reproductive age. Hence, it is clear that the germinal mutation rates are a function of both maternal and paternal ages in humans. In contrast, it is unknown whether the parental reproductive age has an effect on somatic mutation rates in the progeny, because these are rare and difficult to detect. To address this question, we took advantage of the plant model system Arabidopsis (Arabidopsis thaliana), where mutation detector lines allow for an easy quantitation of somatic mutations, to test the effect of parental age on somatic mutation rates in the progeny. Although we found no significant effect of parental age on base substitutions, we found that frameshift mutations and transposition events increased in the progeny of older parents, an effect that is stronger through the maternal line. In contrast, intrachromosomal recombination events in the progeny decrease with the age of the parents in a parent-of-origin-dependent manner. Our results clearly show that parental reproductive age affects somatic mutation rates in the progeny and, thus, that some form of age-dependent information, which affects the frequency of double-strand breaks and possibly other processes involved in maintaining genome integrity, is transmitted through the gametes.
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Affiliation(s)
- Amit Kumar Singh
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600 036, India (A.K.S., T.B., V.G., A.M.R., S.D., R.B.); andInstitute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland (C.S., U.G.)
| | - Tufail Bashir
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600 036, India (A.K.S., T.B., V.G., A.M.R., S.D., R.B.); andInstitute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland (C.S., U.G.)
| | - Christian Sailer
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600 036, India (A.K.S., T.B., V.G., A.M.R., S.D., R.B.); andInstitute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland (C.S., U.G.)
| | - Viswanathan Gurumoorthy
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600 036, India (A.K.S., T.B., V.G., A.M.R., S.D., R.B.); andInstitute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland (C.S., U.G.)
| | - Anantha Maharasi Ramakrishnan
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600 036, India (A.K.S., T.B., V.G., A.M.R., S.D., R.B.); andInstitute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland (C.S., U.G.)
| | - Shanmuhapreya Dhanapal
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600 036, India (A.K.S., T.B., V.G., A.M.R., S.D., R.B.); andInstitute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland (C.S., U.G.)
| | - Ueli Grossniklaus
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600 036, India (A.K.S., T.B., V.G., A.M.R., S.D., R.B.); andInstitute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland (C.S., U.G.)
| | - Ramamurthy Baskar
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600 036, India (A.K.S., T.B., V.G., A.M.R., S.D., R.B.); andInstitute of Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zurich, Switzerland (C.S., U.G.)
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