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Brandon S Gaut - One of the best experts on this subject based on the ideXlab platform.
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Evolutionary Genomics of structural variation in asian rice oryza sativa domestication
Molecular Biology and Evolution, 2020Co-Authors: Brandon S Gaut, Yixuan Kou, Yi Liao, Tuomas Toivainen, Xinmin Tian, J J Emerson, Yongfeng ZhouAbstract:Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered SVs across a population sample of 347 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read data set, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among data sets revealed different features of genome variability. For example, genome alignment identified a large (∼4.3 Mb) inversion in indica rice varieties relative to japonica varieties, and long-read analyses suggest that ∼9% of genes from the outgroup (O. longistaminata) are hemizygous. We focused, however, on the resequencing sample to investigate the population Genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs. However, the site-frequency spectrum of each SV type-which included inversions, duplications, deletions, translocations, and mobile element insertions-was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs may be predominantly deleterious. Among transposable elements, SINE and mariner insertions were found at especially low frequency. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ∼25% more derived SVs and mobile element insertions than O. rufipogon, indicating that SVs contribute to the cost of domestication in rice. Peaks of SV divergence were enriched for known domestication genes, but we also detected hundreds of genes gained and lost during domestication, some of which were enriched for traits of agronomic interest.
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Evolutionary Genomics of structural variation in asian rice oryza sativa and its wild progenitor o rufipogon
bioRxiv, 2019Co-Authors: Yixuan Kou, Brandon S Gaut, Yi Liao, Tuomas Toivainen, Xinmin Tian, J J Emerson, Yongfeng ZhouAbstract:ABSTRACT Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered structural variants (SVs) across a population sample of 358 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read dataset, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among datasets revealed different features of genome variability. For example, genome alignment identified a large (~4.3 Mb) inversion in indica rice varieties relative to an outgroup, and long-read analyses suggest that ~9% of genes from this outgroup are hemizygous. We focused, however, on the resequencing sample to investigate the population Genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs. However, the site-frequency spectrum of each SV type -- which included inversions, duplications, deletions, translocations and mobile element insertions -- was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs are predominantly deleterious. The strength of these deleterious effects varied among SV types, with inversions especially deleterious, and across transposable element (TE) families. Among TEs SINE and mariner insertions were especially deleterious, due to stronger selection against their insertions. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ~25% more derived SVs than O. rufipogon, suggesting these deleterious SVs contribute to the cost of domestication. We also used SVs to study the effects of positive selection on the rice genome. Generally, the search for domestication genes were enriched for known candidates, suggesting some utility for SVs towards this purpose. More importantly, we detected hundreds to thousands of genes gained and lost during domestication, many of which are predicted to contribute to traits of agronomic interest.
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the population genetics of structural variants in grapevine domestication
Nature plants, 2019Co-Authors: Yongfeng Zhou, Melanie Massonnet, Dario Cantu, Andrea Minio, Edwin Solares, T Beridze, Brandon S GautAbstract:Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here, we identify SVs and study their Evolutionary Genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalogue SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using an integrative comparison between Chardonnay and Cabernet Sauvignon genomes by whole-genome, long-read and short-read alignment, we extended SV detection to population samples. We found that strong purifying selection acts against SVs but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex-determination region and the berry colour locus, where independent large, complex inversions have driven convergent phenotypic evolution. This study identified structural variants in grapevine populations, including wild progenitors, using a de novo assembly and comparative Genomics approach, and examined their Evolutionary Genomics and roles in domestication and phenotypic evolution.
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Evolutionary Genomics of grape vitis vinifera ssp vinifera domestication
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Yongfeng Zhou, Melanie Massonnet, Jaleal S Sanjak, Dario Cantu, Brandon S GautAbstract:We gathered genomic data from grapes (Vitis vinifera ssp. vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates that it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ∼22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne ) thereafter. The long decline may reflect low-intensity management by humans before domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development, and stress responses. In contrast, candidate-selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from that of annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.
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the Evolutionary Genomics of grape vitis vinifera ssp vinifera domestication
bioRxiv, 2017Co-Authors: Yongfeng Zhou, Melanie Massonnet, Jaleal S Sanjak, Dario Cantu, Brandon S GautAbstract:The domestication history of grapes (Vitis vinifera ssp. vinifera) has not yet been investigated with genome sequencing data. We gathered data for a sample of 18 cultivars and nine putatively wild accessions to address three features of domestication history. The first was demography. We estimated that the wild and cultivated samples diverged ~22,000 years ago. Thereafter the cultivated lineage experienced a steady decline in population size (Ne), reaching its nadir near the time of domestication ~8,000 years ago. The long decline may reflect low intensity cultivation by humans prior to domestication. Ne of the wild sample fluctuated over the same timeframe, commensurate with glacial expansion and retraction. Second, we characterized regions of putative selective sweeps, identifying 309 candidate-selected genes in the cultivated sample. The set included genes that function in sugar metabolism, flower development and stress responses. Selected genes in the wild sample were enriched exclusively for functions related to biotic and abiotic stresses. A genomic region of high differentiation between wild and domesticated samples corresponded to the sex determination region, which included a candidate gene for a male sterility factor and additional genes that vary in gene expression among sexes. Finally, we investigated the cost of domestication. Despite the lack of a strong domestication bottleneck, grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. We confirm that clonal propagation leads to the accumulation of recessive deleterious mutations, which is a likely cause of severe inbreeding depression in grapes.
Yongfeng Zhou - One of the best experts on this subject based on the ideXlab platform.
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Evolutionary Genomics of structural variation in asian rice oryza sativa domestication
Molecular Biology and Evolution, 2020Co-Authors: Brandon S Gaut, Yixuan Kou, Yi Liao, Tuomas Toivainen, Xinmin Tian, J J Emerson, Yongfeng ZhouAbstract:Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered SVs across a population sample of 347 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read data set, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among data sets revealed different features of genome variability. For example, genome alignment identified a large (∼4.3 Mb) inversion in indica rice varieties relative to japonica varieties, and long-read analyses suggest that ∼9% of genes from the outgroup (O. longistaminata) are hemizygous. We focused, however, on the resequencing sample to investigate the population Genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs. However, the site-frequency spectrum of each SV type-which included inversions, duplications, deletions, translocations, and mobile element insertions-was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs may be predominantly deleterious. Among transposable elements, SINE and mariner insertions were found at especially low frequency. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ∼25% more derived SVs and mobile element insertions than O. rufipogon, indicating that SVs contribute to the cost of domestication in rice. Peaks of SV divergence were enriched for known domestication genes, but we also detected hundreds of genes gained and lost during domestication, some of which were enriched for traits of agronomic interest.
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Evolutionary Genomics of structural variation in asian rice oryza sativa and its wild progenitor o rufipogon
bioRxiv, 2019Co-Authors: Yixuan Kou, Brandon S Gaut, Yi Liao, Tuomas Toivainen, Xinmin Tian, J J Emerson, Yongfeng ZhouAbstract:ABSTRACT Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered structural variants (SVs) across a population sample of 358 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read dataset, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among datasets revealed different features of genome variability. For example, genome alignment identified a large (~4.3 Mb) inversion in indica rice varieties relative to an outgroup, and long-read analyses suggest that ~9% of genes from this outgroup are hemizygous. We focused, however, on the resequencing sample to investigate the population Genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs. However, the site-frequency spectrum of each SV type -- which included inversions, duplications, deletions, translocations and mobile element insertions -- was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs are predominantly deleterious. The strength of these deleterious effects varied among SV types, with inversions especially deleterious, and across transposable element (TE) families. Among TEs SINE and mariner insertions were especially deleterious, due to stronger selection against their insertions. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ~25% more derived SVs than O. rufipogon, suggesting these deleterious SVs contribute to the cost of domestication. We also used SVs to study the effects of positive selection on the rice genome. Generally, the search for domestication genes were enriched for known candidates, suggesting some utility for SVs towards this purpose. More importantly, we detected hundreds to thousands of genes gained and lost during domestication, many of which are predicted to contribute to traits of agronomic interest.
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the population genetics of structural variants in grapevine domestication
Nature plants, 2019Co-Authors: Yongfeng Zhou, Melanie Massonnet, Dario Cantu, Andrea Minio, Edwin Solares, T Beridze, Brandon S GautAbstract:Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here, we identify SVs and study their Evolutionary Genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalogue SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using an integrative comparison between Chardonnay and Cabernet Sauvignon genomes by whole-genome, long-read and short-read alignment, we extended SV detection to population samples. We found that strong purifying selection acts against SVs but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex-determination region and the berry colour locus, where independent large, complex inversions have driven convergent phenotypic evolution. This study identified structural variants in grapevine populations, including wild progenitors, using a de novo assembly and comparative Genomics approach, and examined their Evolutionary Genomics and roles in domestication and phenotypic evolution.
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Evolutionary Genomics of grape vitis vinifera ssp vinifera domestication
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Yongfeng Zhou, Melanie Massonnet, Jaleal S Sanjak, Dario Cantu, Brandon S GautAbstract:We gathered genomic data from grapes (Vitis vinifera ssp. vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates that it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ∼22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne ) thereafter. The long decline may reflect low-intensity management by humans before domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development, and stress responses. In contrast, candidate-selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from that of annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.
-
the Evolutionary Genomics of grape vitis vinifera ssp vinifera domestication
bioRxiv, 2017Co-Authors: Yongfeng Zhou, Melanie Massonnet, Jaleal S Sanjak, Dario Cantu, Brandon S GautAbstract:The domestication history of grapes (Vitis vinifera ssp. vinifera) has not yet been investigated with genome sequencing data. We gathered data for a sample of 18 cultivars and nine putatively wild accessions to address three features of domestication history. The first was demography. We estimated that the wild and cultivated samples diverged ~22,000 years ago. Thereafter the cultivated lineage experienced a steady decline in population size (Ne), reaching its nadir near the time of domestication ~8,000 years ago. The long decline may reflect low intensity cultivation by humans prior to domestication. Ne of the wild sample fluctuated over the same timeframe, commensurate with glacial expansion and retraction. Second, we characterized regions of putative selective sweeps, identifying 309 candidate-selected genes in the cultivated sample. The set included genes that function in sugar metabolism, flower development and stress responses. Selected genes in the wild sample were enriched exclusively for functions related to biotic and abiotic stresses. A genomic region of high differentiation between wild and domesticated samples corresponded to the sex determination region, which included a candidate gene for a male sterility factor and additional genes that vary in gene expression among sexes. Finally, we investigated the cost of domestication. Despite the lack of a strong domestication bottleneck, grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. We confirm that clonal propagation leads to the accumulation of recessive deleterious mutations, which is a likely cause of severe inbreeding depression in grapes.
Melanie Massonnet - One of the best experts on this subject based on the ideXlab platform.
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the population genetics of structural variants in grapevine domestication
Nature plants, 2019Co-Authors: Yongfeng Zhou, Melanie Massonnet, Dario Cantu, Andrea Minio, Edwin Solares, T Beridze, Brandon S GautAbstract:Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here, we identify SVs and study their Evolutionary Genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalogue SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using an integrative comparison between Chardonnay and Cabernet Sauvignon genomes by whole-genome, long-read and short-read alignment, we extended SV detection to population samples. We found that strong purifying selection acts against SVs but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex-determination region and the berry colour locus, where independent large, complex inversions have driven convergent phenotypic evolution. This study identified structural variants in grapevine populations, including wild progenitors, using a de novo assembly and comparative Genomics approach, and examined their Evolutionary Genomics and roles in domestication and phenotypic evolution.
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Evolutionary Genomics of grape vitis vinifera ssp vinifera domestication
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Yongfeng Zhou, Melanie Massonnet, Jaleal S Sanjak, Dario Cantu, Brandon S GautAbstract:We gathered genomic data from grapes (Vitis vinifera ssp. vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates that it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ∼22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne ) thereafter. The long decline may reflect low-intensity management by humans before domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development, and stress responses. In contrast, candidate-selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from that of annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.
-
the Evolutionary Genomics of grape vitis vinifera ssp vinifera domestication
bioRxiv, 2017Co-Authors: Yongfeng Zhou, Melanie Massonnet, Jaleal S Sanjak, Dario Cantu, Brandon S GautAbstract:The domestication history of grapes (Vitis vinifera ssp. vinifera) has not yet been investigated with genome sequencing data. We gathered data for a sample of 18 cultivars and nine putatively wild accessions to address three features of domestication history. The first was demography. We estimated that the wild and cultivated samples diverged ~22,000 years ago. Thereafter the cultivated lineage experienced a steady decline in population size (Ne), reaching its nadir near the time of domestication ~8,000 years ago. The long decline may reflect low intensity cultivation by humans prior to domestication. Ne of the wild sample fluctuated over the same timeframe, commensurate with glacial expansion and retraction. Second, we characterized regions of putative selective sweeps, identifying 309 candidate-selected genes in the cultivated sample. The set included genes that function in sugar metabolism, flower development and stress responses. Selected genes in the wild sample were enriched exclusively for functions related to biotic and abiotic stresses. A genomic region of high differentiation between wild and domesticated samples corresponded to the sex determination region, which included a candidate gene for a male sterility factor and additional genes that vary in gene expression among sexes. Finally, we investigated the cost of domestication. Despite the lack of a strong domestication bottleneck, grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. We confirm that clonal propagation leads to the accumulation of recessive deleterious mutations, which is a likely cause of severe inbreeding depression in grapes.
Dario Cantu - One of the best experts on this subject based on the ideXlab platform.
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the population genetics of structural variants in grapevine domestication
Nature plants, 2019Co-Authors: Yongfeng Zhou, Melanie Massonnet, Dario Cantu, Andrea Minio, Edwin Solares, T Beridze, Brandon S GautAbstract:Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here, we identify SVs and study their Evolutionary Genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalogue SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using an integrative comparison between Chardonnay and Cabernet Sauvignon genomes by whole-genome, long-read and short-read alignment, we extended SV detection to population samples. We found that strong purifying selection acts against SVs but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex-determination region and the berry colour locus, where independent large, complex inversions have driven convergent phenotypic evolution. This study identified structural variants in grapevine populations, including wild progenitors, using a de novo assembly and comparative Genomics approach, and examined their Evolutionary Genomics and roles in domestication and phenotypic evolution.
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Evolutionary Genomics of grape vitis vinifera ssp vinifera domestication
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Yongfeng Zhou, Melanie Massonnet, Jaleal S Sanjak, Dario Cantu, Brandon S GautAbstract:We gathered genomic data from grapes (Vitis vinifera ssp. vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates that it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ∼22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne ) thereafter. The long decline may reflect low-intensity management by humans before domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development, and stress responses. In contrast, candidate-selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from that of annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.
-
the Evolutionary Genomics of grape vitis vinifera ssp vinifera domestication
bioRxiv, 2017Co-Authors: Yongfeng Zhou, Melanie Massonnet, Jaleal S Sanjak, Dario Cantu, Brandon S GautAbstract:The domestication history of grapes (Vitis vinifera ssp. vinifera) has not yet been investigated with genome sequencing data. We gathered data for a sample of 18 cultivars and nine putatively wild accessions to address three features of domestication history. The first was demography. We estimated that the wild and cultivated samples diverged ~22,000 years ago. Thereafter the cultivated lineage experienced a steady decline in population size (Ne), reaching its nadir near the time of domestication ~8,000 years ago. The long decline may reflect low intensity cultivation by humans prior to domestication. Ne of the wild sample fluctuated over the same timeframe, commensurate with glacial expansion and retraction. Second, we characterized regions of putative selective sweeps, identifying 309 candidate-selected genes in the cultivated sample. The set included genes that function in sugar metabolism, flower development and stress responses. Selected genes in the wild sample were enriched exclusively for functions related to biotic and abiotic stresses. A genomic region of high differentiation between wild and domesticated samples corresponded to the sex determination region, which included a candidate gene for a male sterility factor and additional genes that vary in gene expression among sexes. Finally, we investigated the cost of domestication. Despite the lack of a strong domestication bottleneck, grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. We confirm that clonal propagation leads to the accumulation of recessive deleterious mutations, which is a likely cause of severe inbreeding depression in grapes.
Remo Sanges - One of the best experts on this subject based on the ideXlab platform.
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Evolutionary Genomics of the cold-adapted diatom Fragilariopsis cylindrus.
Nature, 2017Co-Authors: Thomas Mock, Pirita Paajanen, Jan Strauss, Mark Mcmullan, Robert Otillar, Jeremy Schmutz, Asaf Salamov, Remo Sanges, Andrew Toseland, Ben J WardAbstract:The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.
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Evolutionary Genomics of the cold adapted diatom fragilariopsis cylindrus
Nature, 2017Co-Authors: Thomas Mock, Pirita Paajanen, Jan Strauss, Mark Mcmullan, Robert Otillar, Jeremy Schmutz, Asaf Salamov, Remo SangesAbstract:The genome of the Southern Ocean phytoplankton Fragilariopsis cylindrus differs markedly from the genomes of its more temperate relatives, with divergent alleles being differentially expressed in environmentally specific conditions such as freezing and darkness. Diatoms are the main primary producers in the Southern Ocean, but how they have adapted to an environment with such extremes of light and temperature has remained unknown. Here Thomas Mock et al. report the genome sequence of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, and compare this 'psychrophile' with diatoms that evolved in temperate oceans. They find that its genome contains highly diverged alleles that are differentially expressed across environmental conditions. The Southern Ocean houses a diverse and productive community of organisms1,2. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice3,4,5,6,7. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus8,9, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.
