Poaceae
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB15949 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR477951_1.fastq.gz | Fastqsanger.gz | |||
| DRR477951_2.fastq.gz | Fastqsanger.gz | |||
| DRR477952_1.fastq.gz | Fastqsanger.gz | |||
| DRR477952_2.fastq.gz | Fastqsanger.gz | |||
| DRR477953_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptome of rice zygotes produced by in vitro fertilization
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Project description:The Poaceae family, also known as the grasses, includes agronomically important cereal crops such as rice, maize, sorghum, and wheat. Previous comparative studies have shown that much of the gene content is shared among the grasses; however, functional conservation of orthologous genes has yet to be explored. To gain an understanding of the genome-wide patterns of evolution of gene expression across reproductive tissues, we employed a sequence-based approach to compare analogous transcriptomes in species representing three Poaceae subgroups including the Pooideae (Brachypodium distachyon), the Panicoideae (sorghum), and the Ehrhartoideae (rice). Our transcriptome analyses reveal that only a fraction of orthologous genes exhibit conserved expression patterns. A high proportion of conserved orthologs include genes that are upregulated in physiologically similar tissues such as leaves, anther, pistil, and embryo, while orthologs that are highly expressed in seeds show the most diverged expression patterns. This experiment is related to E-MTAB-4401 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4401/) and E-MTAB-4402 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4402/)
2012-04-04 | E-MTAB-4400 | biostudies-arrayexpress
Project description:The Poaceae family, also known as the grasses, includes agronomically important cereal crops such as rice, maize, sorghum, and wheat. Previous comparative studies have shown that much of the gene content is shared among the grasses; however, functional conservation of orthologous genes has yet to be explored. To gain an understanding of the genome-wide patterns of evolution of gene expression across reproductive tissues, we employed a sequence-based approach to compare analogous transcriptomes in species representing three Poaceae subgroups including the Pooideae (Brachypodium distachyon), the Panicoideae (sorghum), and the Ehrhartoideae (rice). Our transcriptome analyses reveal that only a fraction of orthologous genes exhibit conserved expression patterns. A high proportion of conserved orthologs include genes that are upregulated in physiologically similar tissues such as leaves, anther, pistil, and embryo, while orthologs that are highly expressed in seeds show the most diverged expression patterns. This experiment is related to E-MTAB-4400 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4400/) and E-MTAB-4402 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4402/)
2012-04-04 | E-MTAB-4401 | biostudies-arrayexpress
Project description:Transcriptome of rice gametes and early zygotes produced by vitro fertilization
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Project description:Common wheat is an allohexaploid species, derived through endoreduplication of an inter-specific triploid hybrid produced from a cross between cultivated tetraploid wheat and the wild diploid relative Aegilops tauschii Coss. Hybrid incompatibilities, including hybrid necrosis, have been observed in triploid wheat hybrids. A limited number of Ae. tauschii accessions show hybrid lethality in triploid hybrids crossed with tetraploid wheat due to developmental arrest at the early seedling stage, which is termed severe growth abortion (SGA). Despite the potential severity of this condition, the genetic mechanisms underlying SGA are not well understood. We conducted comparative analyses of gene expression profiles in crown tissues to characterize developmental arrest in triploid hybrids displaying SGA. A number of defense-related genes were highly up-regulated, whereas many transcription factor genes, such as the KNOTTED1-type homeobox gene, which function in shoot apical meristem (SAM) and leaf primordia, were down-regulated in the crown tissues of SGA plants. Transcript accumulation levels of cell cycle-related genes were also markedly reduced in SGA plants, and no histone H4-expressing cells were observed in the SAM of SGA hybrid plants. Our findings demonstrate that SGA shows unique features among other types of abnormal growth phenotypes, such as type II and III necrosis.
2011-11-01 | GSE33357 | GEO
Project description:Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. CRWs were completely lost in the ditelosomic line 4DS, but a 994 kb ectopic genomic DNA sequence was involved in de novo centromere formation on the 4DS chromosome. In addition, two ectopic sequences were incorporated in a de novo centromere in a wheat-Th. intermedium addition line. Centromeric sequences were also expanded to the chromosome arm in wide hybridizations. Stable alien chromosomes with two and three regions containing centromeric sequences were found in wheat-Th. elongatum hybrid derivatives, but only one is functional. In wheat-rye (Secale cereale) hybrids, rye centromere specific sequences spread to the chromosome arm and may cause centromere expansion. Thus, distant wheat hybridizations cause frequent and significant changes to the centromere via centromere misdivision, which may affect retention or loss of alien chromosomes in hybrids.
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Project description:Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. CRWs were completely lost in the ditelosomic line 4DS, but a 994 kb ectopic genomic DNA sequence was involved in de novo centromere formation on the 4DS chromosome. In addition, two ectopic sequences were incorporated in a de novo centromere in a wheat-Th. intermedium addition line. Centromeric sequences were also expanded to the chromosome arm in wide hybridizations. Stable alien chromosomes with two and three regions containing centromeric sequences were found in wheat-Th. elongatum hybrid derivatives, but only one is functional. In wheat-rye (Secale cereale) hybrids, rye centromere specific sequences spread to the chromosome arm and may cause centromere expansion. Thus, distant wheat hybridizations cause frequent and significant changes to the centromere via centromere misdivision, which may affect retention or loss of alien chromosomes in hybrids. ChIP-seq was carried out with anti-CENH3 antibody using material 4DS and control (Chinese Spring, CS as short).
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Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in grass-clump dwarf lines, which are synthetic hexaploid lines from triploid hybrids crossed between tetraploid wheat (Triticum turgidum ssp. durum cv. Langdon or T. turgidum ssp. carthlicum) and diploid wheat progenitor Aegilops tauschii (KU2025). No up-regulation of defense-related genes was observed under the normal temperature, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf lines. Together with small RNA sequencing analysis of the grass-clump dwarf line, unusual expression of the miR156/SPLs module could explain the grass-clump dwarf phenotype.
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