The Experts below are selected from a list of 315 Experts worldwide ranked by ideXlab platform
Panagiotis F. Sarris - One of the best experts on this subject based on the ideXlab platform.
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intraspecific diversification of the crop wild relative brassica cretica lam using Demographic Model selection
BMC Genomics, 2020Co-Authors: Antonios Kioukis, Vassiliki A Michalopoulou, Laura Briers, Stergios Pirintsos, Panagiotis F. Sarris, Pavlos Pavlidis, David J StudholmeAbstract:Crop wild relatives (CWRs) contain genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops to adapt to changing conditions that they experience due to climate change. An impressive global effort for the conservation of various CWR will facilitate their use in crop breeding for food security. The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage), a species native to southern and western Europe, has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves. Brassica cretica Lam. (Bc) is a CWR in the brassica group and B. cretica subsp. nivea (Bcn) has been suggested as a separate subspecies. The species Bc has been proposed as a potential gene donor to brassica crops, including broccoli, cabbage, cauliflower, oilseed rape, etc. We sequenced genomes of four Bc individuals, including two Bcn and two Bc. Demographic analysis based on our whole-genome sequence data suggests that populations of Bc are not isolated. Classification of the Bc into distinct subspecies is not supported by the data. Using only the non-coding part of the data (thus, the parts of the genome that has evolved nearly neutrally), we find the gene flow between different Bc population is recent and its genomic diversity is high. Despite predictions on the disruptive effect of gene flow in adaptation, when selection is not strong enough to prevent the loss of locally adapted alleles, studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow. Thus, in the genomic era it is important to link the selected Demographic Models with the underlying processes of genomic variation because, if this variation is largely selectively neutral, we cannot assume that a diverse population of crop wild relatives will necessarily exhibit the wide-ranging adaptive diversity required for further crop improvement.
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draft genome sequence and intraspecific diversification of the wild crop relative brassica cretica lam using Demographic Model selection
bioRxiv, 2019Co-Authors: Antonios Kioukis, Vassiliki A Michalopoulou, Laura Briers, Stergios Pirintsos, Panagiotis F. Sarris, Pavlos Pavlidis, David J StudholmeAbstract:Crop wild relatives contain great levels of genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops become more resistant and resilient, and adapt to the new conditions that they will experience due to climate change. An impressive global effort occurs for the conservation of various wild crop relatives and facilitates their use in crop breeding for food security. The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage) is a species native to coastal southern and western Europe that has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves. Brassica cretica Lam. is a wild relative crop in the brassica group and B. cretica subsp. nivea has been suggested as a separate subspecies. The species B. cretica has been proposed as a potential gene donor to a number of crops in the brassica group, including broccoli, Brussels sprout, cabbage, cauliflower, kale, swede, turnip and oilseed rape. Here, we present the draft de novo genome assemblies of four B. cretica individuals, including two B. cretica subsp. nivea and two B. cretica. De novo assembly of Illumina MiSeq genomic shotgun sequencing data yielded 243,461 contigs totalling 412.5 Mb in length, corresponding to 122 % of the estimated genome size of B. cretica (339 Mb). According to synteny mapping and phylogenetic analysis of conserved genes, B. cretica genome based on our sequence data reveals approximately 30.360 proteins. Furthermore, our Demographic analysis based on whole genome data, suggests that distinct populations of B. cretica are not isolated. Our findings suggest that the classification of the B. cretica in distinct subspecies is not supported from the genome sequence data we analyzed.
A P Gutierrez - One of the best experts on this subject based on the ideXlab platform.
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physiologically based Demographics of bt cotton pest interactions i pink bollworm resistance refuge and risk
Ecological Modelling, 2006Co-Authors: A P Gutierrez, Sergine PonsardAbstract:Abstract Transgenic cotton expressing the genes for the production of protoxin of the bacterium Bacillus thuringiensis (Bt) is used to control lepidopterous pests. Among the most successful applications is for control pink bollworm ( Pectinophora gossypiella Saunders (i.e. PBW)) in irrigated cotton of the southwestern United States. A major threat to this technology is the development of resistance commonly assumed recessive, autosomal and controlled by a single diallelic gene. A physiologically based, distributed maturation time Demographic Model of Bt cotton and 10 of its major pests is developed. Here we used the Model to examine the population dynamics and resistance development in pink bollworm as modified by weather and spatial and temporal refuges. The dynamics of the other pest species are reviewed in the second paper of this series. The economics of Bt cotton for control of PBW in southern California is put in the context of the historical overuse of pesticides and the alternative short season cotton technology. The analysis posits that in the short run, the Bt cotton may be risk reducing and economic, but in the longer term it may be risk increasing.
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evaluating biological control of yellow starthistle centaurea solstitialis in california a gis based supply demand Demographic Model
Biological Control, 2005Co-Authors: A P Gutierrez, Michael J Pitcairn, C K Ellis, Nada Carruthers, Reza GhezelbashAbstract:Abstract The biological control of yellow starthistle (Centaurea solstitialis) by four capitulum-feeding insects (weevils Bangasternus orientalis and Eustenopus villosus, and flies Urophora sirunaseva and Chaetorellia succinea), as affected by plant competition with annual grasses, is analyzed using a weather-driven, physiologically based, age-structured, simulation Model. Seed density in the soil seed bank for yellow starthistle and the number of overwintering insects provide between-season links. Seed germination intensity and pattern is determined by the timing and quantity of autumn rains and temperatures, while season-length is mostly determined by soil–water balance. Output from the yellow starthistle systems Model was integrated into a geographic information system to examine regional differences in abundance for all species across several ecological zones of California. A marginal analysis of the simulation results was performed to examine the efficacy of each capitulum-feeding insect, their within-capitulum competitive interactions, and the effect of competition from annual grasses on yellow starthistle populations. The Model suggests that lack of complete control of yellow starthistle may be due to plant compensation via increased per-plant seed production at lower plant densities and the incomplete destruction of seed in attacked capitula. The Model suggests herbivory that reduces the plant’s ability to compensate and/or kills whole plants before seed maturity would most likely lead to control of yellow starthistle.
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Evaluating biological control of yellow starthistle (Centaurea solstitialis) in California: A GIS based supply–demand Demographic Model
Biological Control, 2005Co-Authors: A P Gutierrez, Michael J Pitcairn, C K Ellis, Nada Carruthers, Reza GhezelbashAbstract:Abstract The biological control of yellow starthistle (Centaurea solstitialis) by four capitulum-feeding insects (weevils Bangasternus orientalis and Eustenopus villosus, and flies Urophora sirunaseva and Chaetorellia succinea), as affected by plant competition with annual grasses, is analyzed using a weather-driven, physiologically based, age-structured, simulation Model. Seed density in the soil seed bank for yellow starthistle and the number of overwintering insects provide between-season links. Seed germination intensity and pattern is determined by the timing and quantity of autumn rains and temperatures, while season-length is mostly determined by soil–water balance. Output from the yellow starthistle systems Model was integrated into a geographic information system to examine regional differences in abundance for all species across several ecological zones of California. A marginal analysis of the simulation results was performed to examine the efficacy of each capitulum-feeding insect, their within-capitulum competitive interactions, and the effect of competition from annual grasses on yellow starthistle populations. The Model suggests that lack of complete control of yellow starthistle may be due to plant compensation via increased per-plant seed production at lower plant densities and the incomplete destruction of seed in attacked capitula. The Model suggests herbivory that reduces the plant’s ability to compensate and/or kills whole plants before seed maturity would most likely lead to control of yellow starthistle.
Reza Ghezelbash - One of the best experts on this subject based on the ideXlab platform.
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evaluating biological control of yellow starthistle centaurea solstitialis in california a gis based supply demand Demographic Model
Biological Control, 2005Co-Authors: A P Gutierrez, Michael J Pitcairn, C K Ellis, Nada Carruthers, Reza GhezelbashAbstract:Abstract The biological control of yellow starthistle (Centaurea solstitialis) by four capitulum-feeding insects (weevils Bangasternus orientalis and Eustenopus villosus, and flies Urophora sirunaseva and Chaetorellia succinea), as affected by plant competition with annual grasses, is analyzed using a weather-driven, physiologically based, age-structured, simulation Model. Seed density in the soil seed bank for yellow starthistle and the number of overwintering insects provide between-season links. Seed germination intensity and pattern is determined by the timing and quantity of autumn rains and temperatures, while season-length is mostly determined by soil–water balance. Output from the yellow starthistle systems Model was integrated into a geographic information system to examine regional differences in abundance for all species across several ecological zones of California. A marginal analysis of the simulation results was performed to examine the efficacy of each capitulum-feeding insect, their within-capitulum competitive interactions, and the effect of competition from annual grasses on yellow starthistle populations. The Model suggests that lack of complete control of yellow starthistle may be due to plant compensation via increased per-plant seed production at lower plant densities and the incomplete destruction of seed in attacked capitula. The Model suggests herbivory that reduces the plant’s ability to compensate and/or kills whole plants before seed maturity would most likely lead to control of yellow starthistle.
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Evaluating biological control of yellow starthistle (Centaurea solstitialis) in California: A GIS based supply–demand Demographic Model
Biological Control, 2005Co-Authors: A P Gutierrez, Michael J Pitcairn, C K Ellis, Nada Carruthers, Reza GhezelbashAbstract:Abstract The biological control of yellow starthistle (Centaurea solstitialis) by four capitulum-feeding insects (weevils Bangasternus orientalis and Eustenopus villosus, and flies Urophora sirunaseva and Chaetorellia succinea), as affected by plant competition with annual grasses, is analyzed using a weather-driven, physiologically based, age-structured, simulation Model. Seed density in the soil seed bank for yellow starthistle and the number of overwintering insects provide between-season links. Seed germination intensity and pattern is determined by the timing and quantity of autumn rains and temperatures, while season-length is mostly determined by soil–water balance. Output from the yellow starthistle systems Model was integrated into a geographic information system to examine regional differences in abundance for all species across several ecological zones of California. A marginal analysis of the simulation results was performed to examine the efficacy of each capitulum-feeding insect, their within-capitulum competitive interactions, and the effect of competition from annual grasses on yellow starthistle populations. The Model suggests that lack of complete control of yellow starthistle may be due to plant compensation via increased per-plant seed production at lower plant densities and the incomplete destruction of seed in attacked capitula. The Model suggests herbivory that reduces the plant’s ability to compensate and/or kills whole plants before seed maturity would most likely lead to control of yellow starthistle.
Antonios Kioukis - One of the best experts on this subject based on the ideXlab platform.
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intraspecific diversification of the crop wild relative brassica cretica lam using Demographic Model selection
BMC Genomics, 2020Co-Authors: Antonios Kioukis, Vassiliki A Michalopoulou, Laura Briers, Stergios Pirintsos, Panagiotis F. Sarris, Pavlos Pavlidis, David J StudholmeAbstract:Crop wild relatives (CWRs) contain genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops to adapt to changing conditions that they experience due to climate change. An impressive global effort for the conservation of various CWR will facilitate their use in crop breeding for food security. The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage), a species native to southern and western Europe, has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves. Brassica cretica Lam. (Bc) is a CWR in the brassica group and B. cretica subsp. nivea (Bcn) has been suggested as a separate subspecies. The species Bc has been proposed as a potential gene donor to brassica crops, including broccoli, cabbage, cauliflower, oilseed rape, etc. We sequenced genomes of four Bc individuals, including two Bcn and two Bc. Demographic analysis based on our whole-genome sequence data suggests that populations of Bc are not isolated. Classification of the Bc into distinct subspecies is not supported by the data. Using only the non-coding part of the data (thus, the parts of the genome that has evolved nearly neutrally), we find the gene flow between different Bc population is recent and its genomic diversity is high. Despite predictions on the disruptive effect of gene flow in adaptation, when selection is not strong enough to prevent the loss of locally adapted alleles, studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow. Thus, in the genomic era it is important to link the selected Demographic Models with the underlying processes of genomic variation because, if this variation is largely selectively neutral, we cannot assume that a diverse population of crop wild relatives will necessarily exhibit the wide-ranging adaptive diversity required for further crop improvement.
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draft genome sequence and intraspecific diversification of the wild crop relative brassica cretica lam using Demographic Model selection
bioRxiv, 2019Co-Authors: Antonios Kioukis, Vassiliki A Michalopoulou, Laura Briers, Stergios Pirintsos, Panagiotis F. Sarris, Pavlos Pavlidis, David J StudholmeAbstract:Crop wild relatives contain great levels of genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops become more resistant and resilient, and adapt to the new conditions that they will experience due to climate change. An impressive global effort occurs for the conservation of various wild crop relatives and facilitates their use in crop breeding for food security. The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage) is a species native to coastal southern and western Europe that has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves. Brassica cretica Lam. is a wild relative crop in the brassica group and B. cretica subsp. nivea has been suggested as a separate subspecies. The species B. cretica has been proposed as a potential gene donor to a number of crops in the brassica group, including broccoli, Brussels sprout, cabbage, cauliflower, kale, swede, turnip and oilseed rape. Here, we present the draft de novo genome assemblies of four B. cretica individuals, including two B. cretica subsp. nivea and two B. cretica. De novo assembly of Illumina MiSeq genomic shotgun sequencing data yielded 243,461 contigs totalling 412.5 Mb in length, corresponding to 122 % of the estimated genome size of B. cretica (339 Mb). According to synteny mapping and phylogenetic analysis of conserved genes, B. cretica genome based on our sequence data reveals approximately 30.360 proteins. Furthermore, our Demographic analysis based on whole genome data, suggests that distinct populations of B. cretica are not isolated. Our findings suggest that the classification of the B. cretica in distinct subspecies is not supported from the genome sequence data we analyzed.
Pavlos Pavlidis - One of the best experts on this subject based on the ideXlab platform.
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intraspecific diversification of the crop wild relative brassica cretica lam using Demographic Model selection
BMC Genomics, 2020Co-Authors: Antonios Kioukis, Vassiliki A Michalopoulou, Laura Briers, Stergios Pirintsos, Panagiotis F. Sarris, Pavlos Pavlidis, David J StudholmeAbstract:Crop wild relatives (CWRs) contain genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops to adapt to changing conditions that they experience due to climate change. An impressive global effort for the conservation of various CWR will facilitate their use in crop breeding for food security. The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage), a species native to southern and western Europe, has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves. Brassica cretica Lam. (Bc) is a CWR in the brassica group and B. cretica subsp. nivea (Bcn) has been suggested as a separate subspecies. The species Bc has been proposed as a potential gene donor to brassica crops, including broccoli, cabbage, cauliflower, oilseed rape, etc. We sequenced genomes of four Bc individuals, including two Bcn and two Bc. Demographic analysis based on our whole-genome sequence data suggests that populations of Bc are not isolated. Classification of the Bc into distinct subspecies is not supported by the data. Using only the non-coding part of the data (thus, the parts of the genome that has evolved nearly neutrally), we find the gene flow between different Bc population is recent and its genomic diversity is high. Despite predictions on the disruptive effect of gene flow in adaptation, when selection is not strong enough to prevent the loss of locally adapted alleles, studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow. Thus, in the genomic era it is important to link the selected Demographic Models with the underlying processes of genomic variation because, if this variation is largely selectively neutral, we cannot assume that a diverse population of crop wild relatives will necessarily exhibit the wide-ranging adaptive diversity required for further crop improvement.
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draft genome sequence and intraspecific diversification of the wild crop relative brassica cretica lam using Demographic Model selection
bioRxiv, 2019Co-Authors: Antonios Kioukis, Vassiliki A Michalopoulou, Laura Briers, Stergios Pirintsos, Panagiotis F. Sarris, Pavlos Pavlidis, David J StudholmeAbstract:Crop wild relatives contain great levels of genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops become more resistant and resilient, and adapt to the new conditions that they will experience due to climate change. An impressive global effort occurs for the conservation of various wild crop relatives and facilitates their use in crop breeding for food security. The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage) is a species native to coastal southern and western Europe that has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves. Brassica cretica Lam. is a wild relative crop in the brassica group and B. cretica subsp. nivea has been suggested as a separate subspecies. The species B. cretica has been proposed as a potential gene donor to a number of crops in the brassica group, including broccoli, Brussels sprout, cabbage, cauliflower, kale, swede, turnip and oilseed rape. Here, we present the draft de novo genome assemblies of four B. cretica individuals, including two B. cretica subsp. nivea and two B. cretica. De novo assembly of Illumina MiSeq genomic shotgun sequencing data yielded 243,461 contigs totalling 412.5 Mb in length, corresponding to 122 % of the estimated genome size of B. cretica (339 Mb). According to synteny mapping and phylogenetic analysis of conserved genes, B. cretica genome based on our sequence data reveals approximately 30.360 proteins. Furthermore, our Demographic analysis based on whole genome data, suggests that distinct populations of B. cretica are not isolated. Our findings suggest that the classification of the B. cretica in distinct subspecies is not supported from the genome sequence data we analyzed.
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A survey of methods and tools to detect recent and strong positive selection
Journal of Biological Research-Thessaloniki, 2017Co-Authors: Pavlos Pavlidis, Nikolaos AlachiotisAbstract:Positive selection occurs when an allele is favored by natural selection. The frequency of the favored allele increases in the population and due to genetic hitchhiking the neighboring linked variation diminishes, creating so-called selective sweeps. Detecting traces of positive selection in genomes is achieved by searching for signatures introduced by selective sweeps, such as regions of reduced variation, a specific shift of the site frequency spectrum, and particular LD patterns in the region. A variety of methods and tools can be used for detecting sweeps, ranging from simple implementations that compute summary statistics such as Tajima’s D, to more advanced statistical approaches that use combinations of statistics, maximum likelihood, machine learning etc. In this survey, we present and discuss summary statistics and software tools, and classify them based on the selective sweep signature they detect, i.e., SFS-based vs. LD-based, as well as their capacity to analyze whole genomes or just subgenomic regions. Additionally, we summarize the results of comparisons among four open-source software releases (SweeD, SweepFinder, SweepFinder2, and OmegaPlus) regarding sensitivity, specificity, and execution times. In equilibrium neutral Models or mild bottlenecks, both SFS- and LD-based methods are able to detect selective sweeps accurately. Methods and tools that rely on LD exhibit higher true positive rates than SFS-based ones under the Model of a single sweep or recurrent hitchhiking. However, their false positive rate is elevated when a misspecified Demographic Model is used to represent the null hypothesis. When the correct (or similar to the correct) Demographic Model is used instead, the false positive rates are considerably reduced. The accuracy of detecting the true target of selection is decreased in bottleneck scenarios. In terms of execution time, LD-based methods are typically faster than SFS-based methods, due to the nature of required arithmetic.