Gossypium
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA274882 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2015840_1.fastq.gz | Fastqsanger.gz | |||
| SRR2015840_2.fastq.gz | Fastqsanger.gz | |||
| SRR2015850_1.fastq.gz | Fastqsanger.gz | |||
| SRR2015850_2.fastq.gz | Fastqsanger.gz | |||
| SRR2015860_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae) Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaption of newly formed allopolyploid species. In spite of significant progress made the last years, a few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions. We used Agilent Rice oligo-microarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classical example of recent allopolyploid speciation, S. anglica formed during the 19th century following genome duplication of the hybrid S. x townsendii. Our data indicate important, thought different effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered. Maternal dominance is attenuated following genome duplication in S. anglica while this species exhibits an increased number of transgressively over expressed genes. These results reflect the decoupled effects of the “genomic shock” following hybridization and genome redundancy, on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploids.
2010-11-10 | GSE18961 | GEO
Project description:Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae) Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaption of newly formed allopolyploid species. In spite of significant progress made the last years, a few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions. We used Agilent Rice oligo-microarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classical example of recent allopolyploid speciation, S. anglica formed during the 19th century following genome duplication of the hybrid S. x townsendii. Our data indicate important, thought different effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered. Maternal dominance is attenuated following genome duplication in S. anglica while this species exhibits an increased number of transgressively over expressed genes. These results reflect the decoupled effects of the “genomic shock” following hybridization and genome redundancy, on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploids. We used Agilent Rice oligo-microarrays to explore gene expression changes among Spartina species, following interspesific hybridization and genome duplication (allopolyploidy). The analysed species included the parents S. maritima & S.alterniflora, the hybrid F1 S x. towensendii and the allopolyploid S.anglica. A total of 20 slides (five replicates per species) were hybridized on a 44 K Rice Agilent array using a one color desgin.
2010-11-10 | E-GEOD-18961 | biostudies-arrayexpress
Project description:Genome resequencing provides insights into genetic variations during modern cotton breeding
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Project description:Cotton is the most important economic crop that provides natural fibre and by-products such as oil and protein. The global gene expression could provide insight into the biological processes underlying growth and development, which involving suites of genes expressed with temporal and spatial controls by regulatory networks. Improvement of cotton fiber in yield and quality is the main goal for molecular breeding, but many previous research have been largely focused on identifying genes only in fibres, so that we ignore seed which may play an important role in the development of fibers. In this study, we constructed and systematically analyzed twenty-one strand-specific RNA-Seq libraries on Gossypium hirsutum L. covering different tissues, organs and development stages, of which approximately 970 million reads were generated. In total, 5,6754 transcripts derived from 2,9541 unigenes were obtained to provide a global view of gene expression for cotton development. Hierarchical clustering of transcriptional profiles suggests that transcriptomes among tissues or organs corresponded well to their developmental relatedness. The organ (tissue)-specific gene expressions were investigated efficiently and provided further insight into the dynamic programming of the transcriptome, in particularly for coordinating development between fiber cell and seed (ovule). We identified series of transcription factors and seed-specific genes, which as the candidate genes should help elucidate key mechanisms and regulatory networks that underlie fiber and seed development. This report identified comprehensive transcriptome changes in different stage of cotton development and will serves as a valuable genome-wide transcriptome resource for cotton breeding. Examination of transcriptome of cotton
2016-02-29 | E-GEOD-70369 | biostudies-arrayexpress
Project description:Cotton is the most important economic crop that provides natural fibre and by-products such as oil and protein. The global gene expression could provide insight into the biological processes underlying growth and development, which involving suites of genes expressed with temporal and spatial controls by regulatory networks. Improvement of cotton fiber in yield and quality is the main goal for molecular breeding, but many previous research have been largely focused on identifying genes only in fibres, so that we ignore seed which may play an important role in the development of fibers. In this study, we constructed and systematically analyzed twenty-one strand-specific RNA-Seq libraries on Gossypium hirsutum L. covering different tissues, organs and development stages, of which approximately 970 million reads were generated. In total, 5,6754 transcripts derived from 2,9541 unigenes were obtained to provide a global view of gene expression for cotton development. Hierarchical clustering of transcriptional profiles suggests that transcriptomes among tissues or organs corresponded well to their developmental relatedness. The organ (tissue)-specific gene expressions were investigated efficiently and provided further insight into the dynamic programming of the transcriptome, in particularly for coordinating development between fiber cell and seed (ovule). We identified series of transcription factors and seed-specific genes, which as the candidate genes should help elucidate key mechanisms and regulatory networks that underlie fiber and seed development. This report identified comprehensive transcriptome changes in different stage of cotton development and will serves as a valuable genome-wide transcriptome resource for cotton breeding.
2016-02-29 | GSE70369 | GEO
Project description:Genome resequencing provides insights into genetic variations during modern cotton breeding RNAseq data
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Project description:Evolution and adaptation of living organisms are results of permanent fights against diverse threats, which imply specific responses from the genome itself. Allopolyploidy, combining interspecific hybridization with whole genome duplication, is recognised as an important evolutionary force in plants. Its evolutionary success can be related to the rapid and profound genome reorganizations generated in response to the “Genome Shock” that allow the neo-allopolyploid to adapt efficiently to new environments. While work has focused on the structural and functional consequences of allopolyploidy, studies dedicated to the response of the neo-allopolyploid genome at the level of the functional regulation of genome expression have been rarely conducted. Recently, the hypothesis of a major role for small non coding RNAs (sRNAs) in mediating the immediate functional response of neo-allopolyploid genomes has progressively emerged. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independent resynthesized B. napus allotetraploids surveyed at two different generations in comparison with their diploid progenitors, by high-throughput sequencing of sRNAs. Our evidence suggests an immediate but transient response of specific sRNA populations, targeting non-coding components of the genome. We identify the early accumulation of both 21- and 24-nt sRNAs involved in the regulation of the same targets, supporting a PTGS-to-TGS shift at the first stages of the neo-allopolyploid formation. We propose that sRNAs are early mobilized in response to allopolyploidy to control the unexpected transcriptional reactivation of various non-coding elements thus, playing the role of guardians of genome integrity during the first steps of neo-allopolyploid formation.
2017-09-15 | GSE94076 | GEO
Project description:This study was initiated with the objective of identifying the anther/tapetum specific promoters from cotton floral buds. Cotton is an important commercial crop. Hybrid cotton varieties are developed to obtain improved yield and fiber quality. Most of the hybrid seed production in cotton is carried out by hand emasculation, which requires large amount of manpower, resulting in high cost of hybrid seed. We are developing barnase-barstar based male sterility system, which would be a better alternative for hybrid development. The tapetum specific promoters are main requirement for such a system. The study was thus carried out to identify genes expressed in the anthers.
2013-10-31 | GSE51779 | GEO
Project description:Histone modifications define expression bias of homoeologous genomes in allotetraploid cotton
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