Analysis of five species of Gossypium allotetraploids and a synthetic F1 hybrid compared to model diploid projenitors
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ABSTRACT:
PROVIDER: PRJNA119863 | ENA |
REPOSITORIES: ENA
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Project description:We compare gene expression among petals tissues in 5 species of natural allotetraploid and F1 hybrid cottons to the antecedent conditions existing prior to genome merger and duplication, thus revealing the effects of genome merger and polyploidy on gene expression evolution 27 total samples, including 3 reps. each of five natural tetraploid species, a F1 hybrid, two parental species, and a 1:1 RNA mix of the parental species
2009-09-01 | E-GEOD-17927 | biostudies-arrayexpress
Project description:We compare gene expression among petals tissues in 5 species of natural allotetraploid and F1 hybrid cottons to the antecedent conditions existing prior to genome merger and duplication, thus revealing the effects of genome merger and polyploidy on gene expression evolution
2009-09-02 | GSE17927 | GEO
Project description:Purpose: The goal of this experiment was to use RNA-seq to compare the two commercial cotton species Gossypium hirsutum and Gossypium barbadense and determine what transcripts may account for the better fiber quality in the latter. Methods: RNA was extracted from Gossypium barbadense or Gossypium hirsutum fibers at 10, 15, 18, 21, and 28 days post anthesis. Paired-end, 100-bp RNA-seq was performed on an Illumina HiSeq2000 and the reads were mapped to the Gossypium raimondii genome at www.phytozome.net and non-homologous contig assemblies from Gossypium arboreum. Results from RNA-seq were combined with non-targeted metabolomics. Results: Approximately 38,000 transcripts were expressed (RPKM>2) in each fiber type and approximately 2,000 of these transcripts were differentially expressed in a cross-species comparison at each timepoint. Enriched Gene Ontology biological processes in differentially expressed transcripts suggested that Gh fibers were more stressed. Conclusions: Both metabolomic and transcriptomic data suggest that better mechanisms for managing reactive oxygen species contribute to the increased fiber length in Gossypium barbadense. This appears to result from enhanced ascorbate biosynthesis via gulono-1,4-lactone oxidase and ascorbate recycling via dehydroascorbate reductase.
2015-06-26 | GSE64958 | GEO
Project description:Purpose: The goal of this experiment was to use RNA-seq to compare the two commercial cotton species Gossypium hirsutum and Gossypium barbadense and determine what transcripts may account for the better fiber quality in the latter. Methods: RNA was extracted from Gossypium barbadense or Gossypium hirsutum fibers at 10, 15, 18, 21, and 28 days post anthesis. Paired-end, 100-bp RNA-seq was performed on an Illumina HiSeq2000 and the reads were mapped to the Gossypium raimondii genome at www.phytozome.net and non-homologous contig assemblies from Gossypium arboreum. Results from RNA-seq were combined with non-targeted metabolomics. Results: Approximately 38,000 transcripts were expressed (RPKM>2) in each fiber type and approximately 2,000 of these transcripts were differentially expressed in a cross-species comparison at each timepoint. Enriched Gene Ontology biological processes in differentially expressed transcripts suggested that Gh fibers were more stressed. Conclusions: Both metabolomic and transcriptomic data suggest that better mechanisms for managing reactive oxygen species contribute to the increased fiber length in Gossypium barbadense. This appears to result from enhanced ascorbate biosynthesis via gulono-1,4-lactone oxidase and ascorbate recycling via dehydroascorbate reductase. See Bioproject PRJNA263926 and SRA accession SRP049330 for study design and raw sequencing data and Bioproject PRJNA269608 and TSA accession GBYK00000000 for Gossypium arboreum assembled contig sequences used for transcriptome mapping - Cotton fiber mRNA from 10,15,18,21 and 28 day post anthesis fiber from either Gossypium hirusutm or Gossypium barbadense was sequenced and differential gene expression analysis was conducted between species for each timepoint and between adjacent timepoints. Each timepoint was representative of fiber from 9 individual plants processed as 3 biological replicate pools (material from 3 individual plants per pool).
2015-06-26 | E-GEOD-64958 | biostudies-arrayexpress
Project description:Comparative RNA-Seq study of expression in Gossypium hirsutum nectaries
2018-04-19 | GSE113373 | GEO
Project description:affy_cotton_2011_12 - affy_cotton_2011_12 - In this study we characterized the fiber transcriptomes of the two species, Gossypium hirsutum and Gossypium barbadense that were parental genotypes of a RIL mapping population used previously for phenotypic QTL and expression QTL mapping., We used 454 deep pyrosequencing to characterize cDNAs from developing fibers at two key developmental time-points; 10 and 22 days post anthesis. A unigene set was assembled and annotated, and differential digital gene expression was assessed from the different time-point and genotype representations of the reads within assembled contigs. As a complementary approach, we conducted microarray-based hybridization profiling using the cotton Affymetrix gene chip and labeled cDNAs from fibers at 11 dpa and for the same two genotypes and compared differentially expressed genes identified by the two platforms. The 454 unigenes were also mined for the presence of microsatellite repeats and SNPs that will be useful markers for mapping and marker-assisted selection in cotton improvement.-Total RNA was extracted from 11 dpa-old fibers from the two genotypes, Guazuncho 2 (Gossypium hirsutum) and VH8-4602 (G. barbadense), and included two replicates of each. RNA was checked for quality and quantity using an Agilent Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA, http://www.home.agilent.com) following the manufacturer’s recommendations. The RNA was sent to the Australian Genome Research Facility Ltd. (http://www.agrf.org.au, Melbourne, Victoria, Australia) for labeling and hybridization to the Affymetrix Genechip® Cotton Genome Array (21,854 genes) (Affymetrix, http://www.affymetrix.com/). -
2013-07-01 | GSE43528 | GEO
Project description:affy_cotton_2011_12 - affy_cotton_2011_12 - In this study we characterized the fiber transcriptomes of the two species, Gossypium hirsutum and Gossypium barbadense that were parental genotypes of a RIL mapping population used previously for phenotypic QTL and expression QTL mapping., We used 454 deep pyrosequencing to characterize cDNAs from developing fibers at two key developmental time-points; 10 and 22 days post anthesis. A unigene set was assembled and annotated, and differential digital gene expression was assessed from the different time-point and genotype representations of the reads within assembled contigs. As a complementary approach, we conducted microarray-based hybridization profiling using the cotton Affymetrix gene chip and labeled cDNAs from fibers at 11 dpa and for the same two genotypes and compared differentially expressed genes identified by the two platforms. The 454 unigenes were also mined for the presence of microsatellite repeats and SNPs that will be useful markers for mapping and marker-assisted selection in cotton improvement.-Total RNA was extracted from 11 dpa-old fibers from the two genotypes, Guazuncho 2 (Gossypium hirsutum) and VH8-4602 (G. barbadense), and included two replicates of each. RNA was checked for quality and quantity using an Agilent Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA, http://www.home.agilent.com) following the manufacturer’s recommendations. The RNA was sent to the Australian Genome Research Facility Ltd. (http://www.agrf.org.au, Melbourne, Victoria, Australia) for labeling and hybridization to the Affymetrix Genechip® Cotton Genome Array (21,854 genes) (Affymetrix, http://www.affymetrix.com/). -
2012-10-03 | GSE36876 | GEO
Project description:affy_cotton_2011_12 - affy_cotton_2011_12 - In this study we characterized the fiber transcriptomes of the two species, Gossypium hirsutum and Gossypium barbadense that were parental genotypes of a RIL mapping population used previously for phenotypic QTL and expression QTL mapping., We used 454 deep pyrosequencing to characterize cDNAs from developing fibers at two key developmental time-points; 10 and 22 days post anthesis. A unigene set was assembled and annotated, and differential digital gene expression was assessed from the different time-point and genotype representations of the reads within assembled contigs. As a complementary approach, we conducted microarray-based hybridization profiling using the cotton Affymetrix gene chip and labeled cDNAs from fibers at 11 dpa and for the same two genotypes and compared differentially expressed genes identified by the two platforms. The 454 unigenes were also mined for the presence of microsatellite repeats and SNPs that will be useful markers for mapping and marker-assisted selection in cotton improvement.-Total RNA was extracted from 11 dpa-old fibers from the two genotypes, Guazuncho 2 (Gossypium hirsutum) and VH8-4602 (G. barbadense), and included two replicates of each. RNA was checked for quality and quantity using an Agilent Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA, http://www.home.agilent.com) following the manufacturer’s recommendations. The RNA was sent to the Australian Genome Research Facility Ltd. (http://www.agrf.org.au, Melbourne, Victoria, Australia) for labeling and hybridization to the Affymetrix Genechip® Cotton Genome Array (21,854 genes) (Affymetrix, http://www.affymetrix.com/). - 4 arrays - Cotton; x comparison between two genotypes in cell type This represents the gene expression component of the study only
2012-10-03 | E-GEOD-36876 | biostudies-arrayexpress
Project description:affy_cotton_2011_12 - affy_cotton_2011_12 - In this study we characterized the fiber transcriptomes of the two species, Gossypium hirsutum and Gossypium barbadense that were parental genotypes of a RIL mapping population used previously for phenotypic QTL and expression QTL mapping., We used 454 deep pyrosequencing to characterize cDNAs from developing fibers at two key developmental time-points; 10 and 22 days post anthesis. A unigene set was assembled and annotated, and differential digital gene expression was assessed from the different time-point and genotype representations of the reads within assembled contigs. As a complementary approach, we conducted microarray-based hybridization profiling using the cotton Affymetrix gene chip and labeled cDNAs from fibers at 11 dpa and for the same two genotypes and compared differentially expressed genes identified by the two platforms. The 454 unigenes were also mined for the presence of microsatellite repeats and SNPs that will be useful markers for mapping and marker-assisted selection in cotton improvement.-Total RNA was extracted from 11 dpa-old fibers from the two genotypes, Guazuncho 2 (Gossypium hirsutum) and VH8-4602 (G. barbadense), and included two replicates of each. RNA was checked for quality and quantity using an Agilent Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA, http://www.home.agilent.com) following the manufacturer’s recommendations. The RNA was sent to the Australian Genome Research Facility Ltd. (http://www.agrf.org.au, Melbourne, Victoria, Australia) for labeling and hybridization to the Affymetrix Genechip® Cotton Genome Array (21,854 genes) (Affymetrix, http://www.affymetrix.com/). - 4 arrays - Cotton; x comparison between two genotypes in cell type
2013-07-01 | E-GEOD-43528 | biostudies-arrayexpress