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David Marshall - One of the best experts on this subject based on the ideXlab platform.
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natural variation in a homolog of antirrhinum centroradialis contributed to spring growth habit and Environmental Adaptation in cultivated barley
Nature Genetics, 2012Co-Authors: Jordi Comadran, Benjamin Kilian, Joanne Russell, Luke Ramsay, Nils Stein, Martin W Ganal, Paul D Shaw, Micha Bayer, W T B Thomas, David MarshallAbstract:Robbie Waugh and colleagues report that the EARLINESS PER SE (EPS2) locus is associated with spring growth habit and Environmental Adaptation in barley. Resequencing the barley homolog of CENTRORADIALIS, located within the EPS2 locus, in 216 spring and 207 winter barley accessions identified haplotypes at HvCEN that correspond with winter or spring growth habit.
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Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and Environmental Adaptation in cultivated barley
Nature Genetics, 2012Co-Authors: Jordi Comadran, Benjamin Kilian, Joanne Russell, Luke Ramsay, Nils Stein, Martin W Ganal, Paul D Shaw, Micha Bayer, W T B Thomas, David MarshallAbstract:Robbie Waugh and colleagues report that the EARLINESS PER SE (EPS2) locus is associated with spring growth habit and Environmental Adaptation in barley. Resequencing the barley homolog of CENTRORADIALIS, located within the EPS2 locus, in 216 spring and 207 winter barley accessions identified haplotypes at HvCEN that correspond with winter or spring growth habit. As early farming spread from the Fertile Crescent in the Near East around 10,000 years before the present1, domesticated crops encountered considerable ecological and Environmental change. Spring-sown crops that flowered without the need for an extended period of cold to promote flowering and day length–insensitive crops able to exploit the longer, cooler days of higher latitudes emerged and became established. To investigate the genetic consequences of Adaptation to these new environments, we identified signatures of divergent selection in the highly differentiated modern-day spring and winter barleys. In one genetically divergent region, we identify a natural variant of the barley homolog of Antirrhinum CENTRORADIALIS2 (HvCEN) as a contributor to successful Environmental Adaptation. The distribution of HvCEN alleles in a large collection of wild and landrace accessions indicates that this involved selection and enrichment of preexisting genetic variants rather than the acquisition of mutations after domestication.
Joanne Russell - One of the best experts on this subject based on the ideXlab platform.
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Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into Environmental Adaptation
Nature Genetics, 2016Co-Authors: Joanne Russell, Micha Bayer, Martin Mascher, Ian K Dawson, Stylianos Kyriakidis, Cristiane Calixto, Fabian Freund, Iain Milne, Tony Marshall-griffiths, Shane HeinenAbstract:Robbie Waugh, Nils Stein, Gary Muehlbauer and colleagues report the exome sequencing of 267 landraces and wild accessions of barley from diverse regions to study Adaptations to different agricultural environments. They observe correlations of days to heading and height with environment and find that variation in flowering-associated genes has strong geographical structuring. After domestication, during a process of widespread range extension, barley adapted to a broad spectrum of agricultural environments. To explore how the barley genome responded to the Environmental challenges it encountered, we sequenced the exomes of a collection of 267 georeferenced landraces and wild accessions. A combination of genome-wide analyses showed that patterns of variation have been strongly shaped by geography and that variant-by-environment associations for individual genes are prominent in our data set. We observed significant correlations of days to heading (flowering) and height with seasonal temperature and dryness variables in common garden experiments, suggesting that these traits were major drivers of Environmental Adaptation in the sampled germplasm. A detailed analysis of known flowering-associated genes showed that many contain extensive sequence variation and that patterns of single- and multiple-gene haplotypes exhibit strong geographical structuring. This variation appears to have substantially contributed to range-wide ecogeographical Adaptation, but many factors key to regional success remain unidentified.
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natural variation in a homolog of antirrhinum centroradialis contributed to spring growth habit and Environmental Adaptation in cultivated barley
Nature Genetics, 2012Co-Authors: Jordi Comadran, Benjamin Kilian, Joanne Russell, Luke Ramsay, Nils Stein, Martin W Ganal, Paul D Shaw, Micha Bayer, W T B Thomas, David MarshallAbstract:Robbie Waugh and colleagues report that the EARLINESS PER SE (EPS2) locus is associated with spring growth habit and Environmental Adaptation in barley. Resequencing the barley homolog of CENTRORADIALIS, located within the EPS2 locus, in 216 spring and 207 winter barley accessions identified haplotypes at HvCEN that correspond with winter or spring growth habit.
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Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and Environmental Adaptation in cultivated barley
Nature Genetics, 2012Co-Authors: Jordi Comadran, Benjamin Kilian, Joanne Russell, Luke Ramsay, Nils Stein, Martin W Ganal, Paul D Shaw, Micha Bayer, W T B Thomas, David MarshallAbstract:Robbie Waugh and colleagues report that the EARLINESS PER SE (EPS2) locus is associated with spring growth habit and Environmental Adaptation in barley. Resequencing the barley homolog of CENTRORADIALIS, located within the EPS2 locus, in 216 spring and 207 winter barley accessions identified haplotypes at HvCEN that correspond with winter or spring growth habit. As early farming spread from the Fertile Crescent in the Near East around 10,000 years before the present1, domesticated crops encountered considerable ecological and Environmental change. Spring-sown crops that flowered without the need for an extended period of cold to promote flowering and day length–insensitive crops able to exploit the longer, cooler days of higher latitudes emerged and became established. To investigate the genetic consequences of Adaptation to these new environments, we identified signatures of divergent selection in the highly differentiated modern-day spring and winter barleys. In one genetically divergent region, we identify a natural variant of the barley homolog of Antirrhinum CENTRORADIALIS2 (HvCEN) as a contributor to successful Environmental Adaptation. The distribution of HvCEN alleles in a large collection of wild and landrace accessions indicates that this involved selection and enrichment of preexisting genetic variants rather than the acquisition of mutations after domestication.
Paul Williams - One of the best experts on this subject based on the ideXlab platform.
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transcriptomic analysis reveals a global alkyl quinolone independent regulatory role for pqse in facilitating the Environmental Adaptation of pseudomonas aeruginosa to plant and animal hosts
Environmental Microbiology, 2010Co-Authors: Giordano Rampioni, Christian Pustelny, Matthew P Fletcher, Victoria Wright, Mary Bruce, Kendra P Rumbaugh, Stephan Heeb, Miguel Camara, Paul WilliamsAbstract:The quorum sensing (QS) system of Pseudomonas aeruginosa constitutes a sophisticated genome-wide gene regulatory network employing both N-acylhomoserine lactone and 2-alkyl-4-quinolone (AQ) signal molecules. AQ signalling utilizes 2-heptyl-3-hydroxy-4-quinolone (PQS) and its immediate precursor, 2-heptyl-4-quinolone (HHQ). AQ biosynthesis requires the first four genes of the pqsABCDE operon and while the biochemical function of pqsE is not known, it is required for the production of secondary metabolites such as pyocyanin. To gain insights into the relationship between the AQ stimulon, the PqsE stimulon and the regulatory function of PqsE, we constructed a pqsE inducible mutant (pqsEind) and compared the transcriptomes of the induced and uninduced states with a pqsA mutant. Of 158 genes exhibiting altered expression in the pqsA mutant, 51% were also affected in the pqsE mutant. Following induction of pqsE, 237 genes were differentially expressed compared with the wild-type strain. In the pqsEind strain, pqsA was highly expressed but following induction both pqsA expression and AQ biosynthesis were repressed, revealing a negative autoregulatory role for PqsE. Furthermore, pqsE was required for swarming motility and virulence in plant and animal infection models in the absence of AQs, while mature biofilm development required both pqsA and pqsE. Taken together these data reveal that PqsE is a key regulator within the QS circuitry facilitating the Environmental Adaptation of P. aeruginosa.
Xiao-hua Zhang - One of the best experts on this subject based on the ideXlab platform.
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Comparative genomic analysis reveals the evolution and Environmental Adaptation strategies of vibrios
BMC Genomics, 2018Co-Authors: Heyu Lin, Min Yu, Xiaolei Wang, Xiao-hua ZhangAbstract:BackgroundVibrios are among the most diverse and ecologically important marine bacteria, which have evolved many characteristics and lifestyles to occupy various niches. The relationship between genome features and Environmental Adaptation strategies is an essential part for understanding the ecological functions of vibrios in the marine system. The advent of complete genome sequencing technology has provided an important method of examining the genetic characteristics of vibrios on the genomic level.ResultsTwo Vibrio genomes were sequenced and found to occupy many unique orthologues families which absent from the previously genes pool of the complete genomes of vibrios. Comparative genomics analysis found vibrios encompass a steady core-genome and tremendous pan-genome with substantial gene gain and horizontal gene transfer events in the evolutionary history. Evolutionary analysis based on the core-genome tree suggested that V. fischeri emerged ~ 385 million years ago, along with the occurrence of cephalopods and the flourish of fish. The relatively large genomes, the high number of 16S rRNA gene copies, and the presence of R-M systems and CRISPR system help vibrios live in various marine environments. Chitin-degrading related genes are carried in nearly all the Vibrio genomes. The number of chitinase genes in vibrios has been extremely expanded compared to which in the most recent ancestor of the genus. The chitinase A genes were estimated to have evolved along with the genus, and have undergone significant purifying selective force to conserve the ancestral state.ConclusionsVibrios have experienced extremely genome expansion events during their evolutionary history, allowing them to develop various functions to spread globally. Despite their close phylogenetic relationships, vibrios were found to have a tremendous pan-genome with a steady core-genome, which indicates the highly plastic genome of the genus. Additionally, the existence of various chitin-degrading related genes and the expansion of chitinase A in the genus demonstrate the importance of the chitin utilization for vibrios. Defensive systems in the Vibrio genomes may protect them from the invasion of external DNA. These genomic features investigated here provide a better knowledge of how the evolutionary process has forged Vibrio genomes to occupy various niches.
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Comparative genomic analysis reveals the evolution and Environmental Adaptation strategies of vibrios.
BMC Genomics, 2018Co-Authors: Heyu Lin, Xiaolei Wang, Xiao-hua ZhangAbstract:Vibrios are among the most diverse and ecologically important marine bacteria, which have evolved many characteristics and lifestyles to occupy various niches. The relationship between genome features and Environmental Adaptation strategies is an essential part for understanding the ecological functions of vibrios in the marine system. The advent of complete genome sequencing technology has provided an important method of examining the genetic characteristics of vibrios on the genomic level. Two Vibrio genomes were sequenced and found to occupy many unique orthologues families which absent from the previously genes pool of the complete genomes of vibrios. Comparative genomics analysis found vibrios encompass a steady core-genome and tremendous pan-genome with substantial gene gain and horizontal gene transfer events in the evolutionary history. Evolutionary analysis based on the core-genome tree suggested that V. fischeri emerged ~ 385 million years ago, along with the occurrence of cephalopods and the flourish of fish. The relatively large genomes, the high number of 16S rRNA gene copies, and the presence of R-M systems and CRISPR system help vibrios live in various marine environments. Chitin-degrading related genes are carried in nearly all the Vibrio genomes. The number of chitinase genes in vibrios has been extremely expanded compared to which in the most recent ancestor of the genus. The chitinase A genes were estimated to have evolved along with the genus, and have undergone significant purifying selective force to conserve the ancestral state. Vibrios have experienced extremely genome expansion events during their evolutionary history, allowing them to develop various functions to spread globally. Despite their close phylogenetic relationships, vibrios were found to have a tremendous pan-genome with a steady core-genome, which indicates the highly plastic genome of the genus. Additionally, the existence of various chitin-degrading related genes and the expansion of chitinase A in the genus demonstrate the importance of the chitin utilization for vibrios. Defensive systems in the Vibrio genomes may protect them from the invasion of external DNA. These genomic features investigated here provide a better knowledge of how the evolutionary process has forged Vibrio genomes to occupy various niches.
Micha Bayer - One of the best experts on this subject based on the ideXlab platform.
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Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into Environmental Adaptation
Nature Genetics, 2016Co-Authors: Joanne Russell, Micha Bayer, Martin Mascher, Ian K Dawson, Stylianos Kyriakidis, Cristiane Calixto, Fabian Freund, Iain Milne, Tony Marshall-griffiths, Shane HeinenAbstract:Robbie Waugh, Nils Stein, Gary Muehlbauer and colleagues report the exome sequencing of 267 landraces and wild accessions of barley from diverse regions to study Adaptations to different agricultural environments. They observe correlations of days to heading and height with environment and find that variation in flowering-associated genes has strong geographical structuring. After domestication, during a process of widespread range extension, barley adapted to a broad spectrum of agricultural environments. To explore how the barley genome responded to the Environmental challenges it encountered, we sequenced the exomes of a collection of 267 georeferenced landraces and wild accessions. A combination of genome-wide analyses showed that patterns of variation have been strongly shaped by geography and that variant-by-environment associations for individual genes are prominent in our data set. We observed significant correlations of days to heading (flowering) and height with seasonal temperature and dryness variables in common garden experiments, suggesting that these traits were major drivers of Environmental Adaptation in the sampled germplasm. A detailed analysis of known flowering-associated genes showed that many contain extensive sequence variation and that patterns of single- and multiple-gene haplotypes exhibit strong geographical structuring. This variation appears to have substantially contributed to range-wide ecogeographical Adaptation, but many factors key to regional success remain unidentified.
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natural variation in a homolog of antirrhinum centroradialis contributed to spring growth habit and Environmental Adaptation in cultivated barley
Nature Genetics, 2012Co-Authors: Jordi Comadran, Benjamin Kilian, Joanne Russell, Luke Ramsay, Nils Stein, Martin W Ganal, Paul D Shaw, Micha Bayer, W T B Thomas, David MarshallAbstract:Robbie Waugh and colleagues report that the EARLINESS PER SE (EPS2) locus is associated with spring growth habit and Environmental Adaptation in barley. Resequencing the barley homolog of CENTRORADIALIS, located within the EPS2 locus, in 216 spring and 207 winter barley accessions identified haplotypes at HvCEN that correspond with winter or spring growth habit.
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Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and Environmental Adaptation in cultivated barley
Nature Genetics, 2012Co-Authors: Jordi Comadran, Benjamin Kilian, Joanne Russell, Luke Ramsay, Nils Stein, Martin W Ganal, Paul D Shaw, Micha Bayer, W T B Thomas, David MarshallAbstract:Robbie Waugh and colleagues report that the EARLINESS PER SE (EPS2) locus is associated with spring growth habit and Environmental Adaptation in barley. Resequencing the barley homolog of CENTRORADIALIS, located within the EPS2 locus, in 216 spring and 207 winter barley accessions identified haplotypes at HvCEN that correspond with winter or spring growth habit. As early farming spread from the Fertile Crescent in the Near East around 10,000 years before the present1, domesticated crops encountered considerable ecological and Environmental change. Spring-sown crops that flowered without the need for an extended period of cold to promote flowering and day length–insensitive crops able to exploit the longer, cooler days of higher latitudes emerged and became established. To investigate the genetic consequences of Adaptation to these new environments, we identified signatures of divergent selection in the highly differentiated modern-day spring and winter barleys. In one genetically divergent region, we identify a natural variant of the barley homolog of Antirrhinum CENTRORADIALIS2 (HvCEN) as a contributor to successful Environmental Adaptation. The distribution of HvCEN alleles in a large collection of wild and landrace accessions indicates that this involved selection and enrichment of preexisting genetic variants rather than the acquisition of mutations after domestication.