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Andreas Wagner - One of the best experts on this subject based on the ideXlab platform.
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efficient purging of deleterious mutations in plants with haploid Selfing
Genome Biology and Evolution, 2014Co-Authors: Peter Szovenyi, Kentaro K Shimizu, Nicolas Devos, David J Weston, Xiaohan Yang, Zsofia Hock, Jonathan Shaw, Stuart F Mcdaniel, Andreas WagnerAbstract:In diploid organisms, Selfing reduces the efficiency of selection in removing deleterious mutations from a population. This need not be the case for all organisms. Some plants, for example, undergo an extreme form of Selfing known as intragametophytic Selfing, which immediately exposes all recessive deleterious mutations in a parental genome to selective purging. Here, we ask how effectively deleterious mutations are removed from such plants. Specifically, we study the extent to which deleterious mutations accumulate in a predominantly Selfing and a predominantly outcrossing pair of moss species, using genome-wide transcriptome data. We find that the Selfing species purge significantly more nonsynonymous mutations, as well as a greater proportion of radical amino acid changes which alter physicochemical properties of amino acids. Moreover, their purging of deleterious mutation is especially strong in conserved regions of protein-coding genes. Our observations show that Selfing need not impede but can even accelerate the removal of deleterious mutations, and do so on a genome-wide scale.
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The predominantly Selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata
Mobile DNA, 2012Co-Authors: Nicole De La Chaux, Kentaro K Shimizu, Takashi Tsuchimatsu, Andreas WagnerAbstract:Background Transposable elements (TEs) are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through Selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in Selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly Selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences. Results We identified 1,819 TE families representing all known classes of TEs in both species, and found three times more copies in the outcrossing A. lyrata than in the predominantly Selfing A. thaliana , as well as ten times more TE families unique to A. lyrata . On average, elements in A. lyrata are younger than elements in A . thaliana . In particular, A. thaliana shows a marked decrease in element number that occurred during the most recent 10% of the time interval since A. thaliana split from A. lyrata . This most recent period in the evolution of A. thaliana started approximately 500,000 years ago, assuming a splitting time of 5 million years ago, and coincides with the time at which predominant Selfing originated. Conclusions Our results indicate that the mating system may be important for determining TE copy number, and that Selfing species are likely to have fewer TEs.
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the predominantly Selfing plant arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative arabidopsis lyrata
Mobile Dna, 2012Co-Authors: Kentaro K Shimizu, Andreas Wagner, Takashi Tsuchimatsu, Nicole De La ChauxAbstract:Background Transposable elements (TEs) are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through Selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in Selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly Selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences.
Takashi Tsuchimatsu - One of the best experts on this subject based on the ideXlab platform.
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adaptive reduction of male gamete number in the Selfing plant arabidopsis thaliana
Nature Communications, 2020Co-Authors: Takashi Tsuchimatsu, Hiroyuki Kakui, Misako Yamazaki, Cindy Marona, Hiroki Tsutsui, Afif Hedhly, Dazhe MengAbstract:The number of male gametes is critical for reproductive success and varies between and within species. The evolutionary reduction of the number of pollen grains encompassing the male gametes is widespread in Selfing plants. Here, we employ genome-wide association study (GWAS) to identify underlying loci and to assess the molecular signatures of selection on pollen number-associated loci in the predominantly Selfing plant Arabidopsis thaliana. Regions of strong association with pollen number are enriched for signatures of selection, indicating polygenic selection. We isolate the gene REDUCED POLLEN NUMBER1 (RDP1) at the locus with the strongest association. We validate its effect using a quantitative complementation test with CRISPR/Cas9-generated null mutants in nonstandard wild accessions. In contrast to pleiotropic null mutants, only pollen numbers are significantly affected by natural allelic variants. These data support theoretical predictions that reduced investment in male gametes is advantageous in predominantly Selfing species. Reduction of pollen grain number is widespread in Selfing plants, but the determining gene is unknown. Here, the authors show that a ribosome-biogenesis factor encoding gene RDP1 is responsible for adaptive reduction of male gamete number in Arabidopsis thaliana.
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evolution of Selfing recurrent patterns in molecular adaptation
Annual Review of Ecology Evolution and Systematics, 2015Co-Authors: Kentaro K Shimizu, Takashi TsuchimatsuAbstract:Selfing has evolved in animals, fungi, and plants, and since Darwin's pioneering study, it is considered one of the most frequent evolutionary trends in flowering plants. Generally, the evolution of Selfing is characterized by a loss of self-incompatibility, the Selfing syndrome, and changes in genome-wide polymorphism patterns. Recent interdisciplinary studies involving molecular functional experiments, genome-wide data, experimental evolution, and evolutionary ecology using Arabidopsis thaliana, Caenorhabditis elegans, and other species show that the evolution of Selfing is not merely a degradation of outcrossing traits but a model for studying the recurrent patterns underlying adaptive molecular evolution. For example, in wild Arabidopsis relatives, self-compatibility evolved from mutations in the male specificity gene, S-LOCUS CYSTEINE-RICH PROTEIN/S-LOCUS PROTEIN 11 (SCR/SP11), rather than the female specificity gene, S-LOCUS RECEPTOR KINASE (SRK), supporting the theoretical prediction of sexual asym...
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The predominantly Selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata
Mobile DNA, 2012Co-Authors: Nicole De La Chaux, Kentaro K Shimizu, Takashi Tsuchimatsu, Andreas WagnerAbstract:Background Transposable elements (TEs) are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through Selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in Selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly Selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences. Results We identified 1,819 TE families representing all known classes of TEs in both species, and found three times more copies in the outcrossing A. lyrata than in the predominantly Selfing A. thaliana , as well as ten times more TE families unique to A. lyrata . On average, elements in A. lyrata are younger than elements in A . thaliana . In particular, A. thaliana shows a marked decrease in element number that occurred during the most recent 10% of the time interval since A. thaliana split from A. lyrata . This most recent period in the evolution of A. thaliana started approximately 500,000 years ago, assuming a splitting time of 5 million years ago, and coincides with the time at which predominant Selfing originated. Conclusions Our results indicate that the mating system may be important for determining TE copy number, and that Selfing species are likely to have fewer TEs.
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the predominantly Selfing plant arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative arabidopsis lyrata
Mobile Dna, 2012Co-Authors: Kentaro K Shimizu, Andreas Wagner, Takashi Tsuchimatsu, Nicole De La ChauxAbstract:Background Transposable elements (TEs) are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through Selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in Selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly Selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences.
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evolution of self compatibility in arabidopsis by a mutation in the male specificity gene
Nature, 2010Co-Authors: Takashi Tsuchimatsu, Keita Suwabe, Rie Shimizuinatsugi, Sachiyo Isokawa, Pavlos Pavlidis, Thomas Stadler, Go Suzuki, Seiji TakayamaAbstract:Ever since Darwin's pioneering research, the evolution of self-fertilisation (Selfing) has been regarded as one of the most prevalent evolutionary transitions in flowering plants. A major mechanism to prevent Selfing is the self-incompatibility (SI) recognition system, which consists of male and female specificity genes at the S-locus and SI modifier genes. Under conditions that favour Selfing, mutations disabling the male recognition component are predicted to enjoy a relative advantage over those disabling the female component, because male mutations would increase through both pollen and seeds whereas female mutations would increase only through seeds. Despite many studies on the genetic basis of loss of SI in the predominantly Selfing plant Arabidopsis thaliana, it remains unknown whether Selfing arose through mutations in the female specificity gene (S-receptor kinase, SRK), male specificity gene (S-locus cysteine-rich protein, SCR; also known as S-locus protein 11, SP11) or modifier genes, and whether any of them rose to high frequency across large geographic regions. Here we report that a disruptive 213-base-pair (bp) inversion in the SCR gene (or its derivative haplotypes with deletions encompassing the entire SCR-A and a large portion of SRK-A) is found in 95% of European accessions, which contrasts with the genome-wide pattern of polymorphism in European A. thaliana. Importantly, interspecific crossings using Arabidopsis halleri as a pollen donor reveal that some A. thaliana accessions, including Wei-1, retain the female SI reaction, suggesting that all female components including SRK are still functional. Moreover, when the 213-bp inversion in SCR was inverted and expressed in transgenic Wei-1 plants, the functional SCR restored the SI reaction. The inversion within SCR is the first mutation disrupting SI shown to be nearly fixed in geographically wide samples, and its prevalence is consistent with theoretical predictions regarding the evolutionary advantage of mutations in male components.
Kentaro K Shimizu - One of the best experts on this subject based on the ideXlab platform.
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evolution of Selfing recurrent patterns in molecular adaptation
Annual Review of Ecology Evolution and Systematics, 2015Co-Authors: Kentaro K Shimizu, Takashi TsuchimatsuAbstract:Selfing has evolved in animals, fungi, and plants, and since Darwin's pioneering study, it is considered one of the most frequent evolutionary trends in flowering plants. Generally, the evolution of Selfing is characterized by a loss of self-incompatibility, the Selfing syndrome, and changes in genome-wide polymorphism patterns. Recent interdisciplinary studies involving molecular functional experiments, genome-wide data, experimental evolution, and evolutionary ecology using Arabidopsis thaliana, Caenorhabditis elegans, and other species show that the evolution of Selfing is not merely a degradation of outcrossing traits but a model for studying the recurrent patterns underlying adaptive molecular evolution. For example, in wild Arabidopsis relatives, self-compatibility evolved from mutations in the male specificity gene, S-LOCUS CYSTEINE-RICH PROTEIN/S-LOCUS PROTEIN 11 (SCR/SP11), rather than the female specificity gene, S-LOCUS RECEPTOR KINASE (SRK), supporting the theoretical prediction of sexual asym...
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evolution of the Selfing syndrome in arabis alpina brassicaceae
PLOS ONE, 2015Co-Authors: Andrew Tedder, Samuel Carleial, Martyna Golebiewska, Christian Kappel, Kentaro K Shimizu, Marc StiftAbstract:Introduction The transition from cross-fertilisation (outcrossing) to self-fertilisation (Selfing) frequently coincides with changes towards a floral morphology that optimises self-pollination, the Selfing syndrome. Population genetic studies have reported the existence of both outcrossing and Selfing populations in Arabis alpina (Brassicaceae), which is an emerging model species for studying the molecular basis of perenniality and local adaptation. It is unknown whether its Selfing populations have evolved a Selfing syndrome. Methods Using macro-photography, microscopy and automated cell counting, we compared floral syndromes (size, herkogamy, pollen and ovule numbers) between three outcrossing populations from the Apuan Alps and three Selfing populations from the Western and Central Alps (Maritime Alps and Dolomites). In addition, we genotyped the plants for 12 microsatellite loci to confirm previous measures of diversity and inbreeding coefficients based on allozymes, and performed Bayesian clustering. Results and Discussion Plants from the three Selfing populations had markedly smaller flowers, less herkogamy and lower pollen production than plants from the three outcrossing populations, whereas pistil length and ovule number have remained constant. Compared to allozymes, microsatellite variation was higher, but revealed similar patterns of low diversity and high Fis in Selfing populations. Bayesian clustering revealed two clusters. The first cluster contained the three outcrossing populations from the Apuan Alps, the second contained the three Selfing populations from the Maritime Alps and Dolomites. Conclusion We conclude that in comparison to three outcrossing populations, three populations with high Selfing rates are characterised by a flower morphology that is closer to the Selfing syndrome. The presence of outcrossing and Selfing floral syndromes within a single species will facilitate unravelling the genetic basis of the Selfing syndrome, and addressing which selective forces drive its evolution.
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efficient purging of deleterious mutations in plants with haploid Selfing
Genome Biology and Evolution, 2014Co-Authors: Peter Szovenyi, Kentaro K Shimizu, Nicolas Devos, David J Weston, Xiaohan Yang, Zsofia Hock, Jonathan Shaw, Stuart F Mcdaniel, Andreas WagnerAbstract:In diploid organisms, Selfing reduces the efficiency of selection in removing deleterious mutations from a population. This need not be the case for all organisms. Some plants, for example, undergo an extreme form of Selfing known as intragametophytic Selfing, which immediately exposes all recessive deleterious mutations in a parental genome to selective purging. Here, we ask how effectively deleterious mutations are removed from such plants. Specifically, we study the extent to which deleterious mutations accumulate in a predominantly Selfing and a predominantly outcrossing pair of moss species, using genome-wide transcriptome data. We find that the Selfing species purge significantly more nonsynonymous mutations, as well as a greater proportion of radical amino acid changes which alter physicochemical properties of amino acids. Moreover, their purging of deleterious mutation is especially strong in conserved regions of protein-coding genes. Our observations show that Selfing need not impede but can even accelerate the removal of deleterious mutations, and do so on a genome-wide scale.
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The predominantly Selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata
Mobile DNA, 2012Co-Authors: Nicole De La Chaux, Kentaro K Shimizu, Takashi Tsuchimatsu, Andreas WagnerAbstract:Background Transposable elements (TEs) are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through Selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in Selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly Selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences. Results We identified 1,819 TE families representing all known classes of TEs in both species, and found three times more copies in the outcrossing A. lyrata than in the predominantly Selfing A. thaliana , as well as ten times more TE families unique to A. lyrata . On average, elements in A. lyrata are younger than elements in A . thaliana . In particular, A. thaliana shows a marked decrease in element number that occurred during the most recent 10% of the time interval since A. thaliana split from A. lyrata . This most recent period in the evolution of A. thaliana started approximately 500,000 years ago, assuming a splitting time of 5 million years ago, and coincides with the time at which predominant Selfing originated. Conclusions Our results indicate that the mating system may be important for determining TE copy number, and that Selfing species are likely to have fewer TEs.
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the predominantly Selfing plant arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative arabidopsis lyrata
Mobile Dna, 2012Co-Authors: Kentaro K Shimizu, Andreas Wagner, Takashi Tsuchimatsu, Nicole De La ChauxAbstract:Background Transposable elements (TEs) are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through Selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in Selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly Selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences.
Nicole De La Chaux - One of the best experts on this subject based on the ideXlab platform.
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The predominantly Selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata
Mobile DNA, 2012Co-Authors: Nicole De La Chaux, Kentaro K Shimizu, Takashi Tsuchimatsu, Andreas WagnerAbstract:Background Transposable elements (TEs) are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through Selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in Selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly Selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences. Results We identified 1,819 TE families representing all known classes of TEs in both species, and found three times more copies in the outcrossing A. lyrata than in the predominantly Selfing A. thaliana , as well as ten times more TE families unique to A. lyrata . On average, elements in A. lyrata are younger than elements in A . thaliana . In particular, A. thaliana shows a marked decrease in element number that occurred during the most recent 10% of the time interval since A. thaliana split from A. lyrata . This most recent period in the evolution of A. thaliana started approximately 500,000 years ago, assuming a splitting time of 5 million years ago, and coincides with the time at which predominant Selfing originated. Conclusions Our results indicate that the mating system may be important for determining TE copy number, and that Selfing species are likely to have fewer TEs.
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the predominantly Selfing plant arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative arabidopsis lyrata
Mobile Dna, 2012Co-Authors: Kentaro K Shimizu, Andreas Wagner, Takashi Tsuchimatsu, Nicole De La ChauxAbstract:Background Transposable elements (TEs) are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through Selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in Selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly Selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences.
Qing Jun Li - One of the best experts on this subject based on the ideXlab platform.
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autonomous Selfing provides reproductive assurance in an alpine ginger roscoea schneideriana zingiberaceae
Annals of Botany, 2008Co-Authors: Zhi-qiang Zhang, Qing Jun LiAbstract:† Background and Aims Reproductive assurance, the ability to produce seeds when pollinators or mates are scarce, is thought to be the major advantage of Selfing in flowering plants. However, few studies have performed a direct cost‐ benefit analysis of the selective advantage of Selfing, particularly given a long-term perspective among populations or across several flowering seasons within population. This study examined the fertility consequences of autonomous Selfing in Roscoea schneideriana (Zingiberaceae), a small perennial Himalayan ginger typically found in habitats at around 3000 m a.s.l. † Methods The floral biology of R. schneideriana was studied in natural populations; the capacity for autonomous Selfing was estimated using pollinator exclusion experiments; the timing of Selfing was quantified by anther removal at different times during flowering; whether autonomous Selfing increases seed production was tested by emasculating flowers; and the magnitude of inbreeding depression was estimated by comparing relative performance of progeny from self- and cross-pollinations. Pollinator observations were also conducted in the natural populations. † Key Results The hooked stigmas of most flowers curl towards the anther and can contact pollen grains at an early stage of anthesis. Flowers with potential pollinators excluded set of as many seeds per fruit as hand-selfed and opened flowers. Autonomous Selfing mostly occurs within 2 d of anthesis and can increase seed production by an average of 84 % in four populations during the flowering seasons of 2005‐2007. Visits by effective pollinators were extremely rare. The cumulative inbreeding depression of R. schneideriana was 0.226. † Conclusions Autonomous Selfing in R. schneideriana is achieved by stigmas curling towards the anthers early in flowering. It is suggested that under the poor pollination conditions, autonomous Selfing has been selected for in this alpine ginger because it provides substantial reproductive assurance with very low costs.
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Autonomous Selfing provides reproductive assurance in an alpine ginger Roscoea schneideriana (Zingiberaceae)
Annals of Botany, 2008Co-Authors: Zhi-qiang Zhang, Qing Jun LiAbstract:Reproductive assurance, the ability to produce seeds when pollinators or mates are scarce, is thought to be the major advantage of Selfing in flowering plants. However, few studies have performed a direct cost-benefit analysis of the selective advantage of Selfing, particularly given a long-term perspective among populations or across several flowering seasons within population. This study examined the fertility consequences of autonomous Selfing in Roscoea schneideriana (Zingiberaceae), a small perennial Himalayan ginger typically found in habitats at around 3000 m a.s.l.
