Maize B chromosome transcriptomic atlas
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ABSTRACT:
PROVIDER: PRJEB86173 | ENA |
REPOSITORIES: ENA
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Project description:Using high-throughput RNA sequencing, we developed a spatiotemporal transcriptome atlas for seed development of eight maize inbred lines based on 144 samples from the middle to late stages of grain development. A total of 26,747 genes with FPKM value more than 1 at least one sample were found to be involved in programming grain development. Global comparisons of genes expression highlighted the fundamental transcriptomic reprogramming and the phases of development. Coexpression analysis provided further insight into the dynamic reprogramming of the transcriptome by revealing functional transitions during maturation. Combined with grain moisture content and grain dehydration rate of different developmental time points of eight maize inbred lines, we captured a large number of genes related to grain moisture content and grain dehydration rate, which should help elucidate key mechanisms and regulatory networks that underlie grain dehydration during maize grain development. These results provide a comprehensive understanding of which biological processes are involved in the regulation of moisture variety of maize grain, the general principles of which provide a new perspective on improving maize grain dehydration characteristics. Meanwhile, this study provides a valuable resource for understanding the genetic regulation of maize grain development.
2022-10-01 | GSE158816 | GEO
Project description:To determine the centromere of the maize B chromosome, we used previously published anti-CENH3-ChIP-seq data from TB-9Sb, which contain a complete functional B centromere. Distribution of centromere-specific DNA repeats, including CentC, CRM element and B-repeat, were observed in the proximal end of the assembled maize B chromosome, and this region was shown to be associated with CENH3 nucleosomes. Furthermore, six small scaffolds with sizes ranging from 10 to 174 kilobase display CENH3 enrichment, also with the distribution of these repeat sequences. These results were consistent with previously cytogenetic observation. Therefore, approximately 520 kb centromeric regions were determined in the assembled maize B chromosome.
2021-05-22 | GSE152074 | GEO
Project description:Transcriptomic and Epigenetic Adaptation of the Maize Chromosome in Oat–Maize Addition Lines
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Project description:A cis-regulatory atlas of maize single cells
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Project description:Transcriptomic atlas of thalamic nuclei
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Project description:New reference sequence of the maize B chromosome
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Project description:A small fragment from maize chromosome 3 was created by irradiation by Stadler and Roman and named Duplication 3a (or Dp3a). This small chromosome does not contain any detectable CentC and CRM sequences, but when molecular features of functional centromeres such as CENH3 and CENP-C were examined, they were present. Immunolocalization analysis of phosphorylation of Ser-10 of histone H3 levels on Dp3a shows a pattern typical of a functional centromere. Meiotic analysis revealed that sister chromatids divided equationally at meiosis I as do all small chromosomes examined to date in maize. To examine the sequences associated with CENH3, chromatin immunoprecipitation (ChIP) was carried out with anti-CENH3 antibodies using material from young seedlings with and without Dp3 chromosome as the tissue source. The ChIPed DNA sample was then labeled for FISH detection and prepared for Illumina sequencing.The ChIP-Seq reads were mapped to the B73 reference genome and a significant peak was detected in the Dp3a sample that span 350 kb of the long arm of chromosome 3, which is the candidate region for association with CENH3. ChIP-bisulfite-seq results indicated that there is a slightly increased DNA methylation level after the centromere formation, approaching the level similar to normal centromere regions. Collectively, the results suggest the formation of a de novo centromere on this fragment that initially must have started at the time of X-irradiation release from the progenitor chromosome. These observations add further evidence for the epigenetic nature of centromere function in maize.
2013-06-25 | GSE43138 | GEO
Project description:A small fragment from maize chromosome 3 was created by irradiation by Stadler and Roman and named Duplication 3a (or Dp3a). This small chromosome does not contain any detectable CentC and CRM sequences, but when molecular features of functional centromeres such as CENH3 and CENP-C were examined, they were present. Immunolocalization analysis of phosphorylation of Ser-10 of histone H3 levels on Dp3a shows a pattern typical of a functional centromere. Meiotic analysis revealed that sister chromatids divided equationally at meiosis I as do all small chromosomes examined to date in maize. To examine the sequences associated with CENH3, chromatin immunoprecipitation (ChIP) was carried out with anti-CENH3 antibodies using material from young seedlings with and without Dp3 chromosome as the tissue source. The ChIPed DNA sample was then labeled for FISH detection and prepared for Illumina sequencing.The ChIP-Seq reads were mapped to the B73 reference genome and a significant peak was detected in the Dp3a sample that span 350 kb of the long arm of chromosome 3, which is the candidate region for association with CENH3. ChIP-bisulfite-seq results indicated that there is a slightly increased DNA methylation level after the centromere formation, approaching the level similar to normal centromere regions. Collectively, the results suggest the formation of a de novo centromere on this fragment that initially must have started at the time of X-irradiation release from the progenitor chromosome. These observations add further evidence for the epigenetic nature of centromere function in maize. ChIP-seq was carried out with anti-CENH3 antibodies using material from young seedlings with and without Dp3a chromosome. For Dp3a, some ChIPed DNA was treated with sodium bisulfite and prepared for Illumina sequencing to test its methylation level.
2013-06-25 | E-GEOD-43138 | biostudies-arrayexpress
Project description:A time-resolved transcriptome atlas of maize grain development
| PRJNA666644 | ENA
Project description:Maize earshoot is a metabolic sink espcially related to nitrogen metabolism. Studies on the transcriptomic and metabolic changes occuring in earshoot can provide interesting answers about the nitrogen metabolic potential of the maize variety under study. B73 X Mo17 is a model maize hybrid. Developing earshoots from this genotype grown at nitrogen-deficient and nitrogen-sufficient conditions were sampled, processed and analyzed through microarray technology.
2010-01-14 | GSE17932 | GEO