Ancient_maize_MS
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ
ORGANISM(S): Zea Mays Subsp. Mays (ncbitaxon:381124)
SUBMITTER: Lisandra Zepeda
PROVIDER: MSV000078888 | MassIVE | Mon Oct 06 11:36:00 BST 2014
SECONDARY ACCESSION(S): PXD001382
REPOSITORIES: MassIVE
Similar Datasets
Project description:We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 maize inbreds that serve as the founders for the maize nested association mapping population. The data indicate that the number of pan-genes in maize exceeds 103,000 and that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres further revealed the locations and internal structures of major cytological landmarks. We show that combining structural variation with SNPs can improve the power of quantitative mapping studies. Finally, we document variation at the level of DNA methylation, and demonstrate that unmethylated regions are enriched for cis-regulatory elements that correlate with known QTLs and changes in gene expression.
2021-02-01 | GSE165787 | GEO
Project description:Ancient maize genomes from ENA
| PRJEB73480 | ENA
Project description:In maize, nitrate regulates root development thanks to the coordinated action of many players. In this study, the involvement of SLs and auxin as putative downstream components of the nitrate regulation of lateral root development was investigated. To this aim, the endogenous SL content of maize root in response to nitrate availability was assessed by means of LC-MS/MS and measurements of lateral root density in the presence of analogues or inhibitors of auxin and strigolactones were performed. Furthermore, un untargeted RNA-seq based approach was used to better characterize the participation of auxin and strigolacotones to the transcriptional signature of maize root response to nitrate. Our results suggested that N deprivation toughly induces zealactone and carlactonoic acid biosynthesis in maize root, to a higher extent if compared to P-deprived roots. Moreover, data on lateral root density led to hypothesise the existence of both auxin-dependent and auxin-independent effects of nitrate on LR development. In addition, the inhibition of SL biosynthesis seems to participate to the auxin-dependent induction of LR, but the involvement of further downstream unknown components cannot be ruled out.
2021-04-11 | GSE162411 | GEO
Project description:Phenotypes of maize male sterile 8 plants are small anthers, meiotic failure, shorter epidermal cells, and non-secreting tapetal cells. Excess callose accumulates around meiotic cells, which later abort. Thousands of transcriptome changes occur including ectopic activation of genes not expressed in fertile siblings, failure to express genes, and differential expression of genes shared with fertile siblings. Sixty-three differentially expressed proteins were identified after 2-D DIGE followed by LC/MS/MS, including those involved in metabolism and cell division. The majority were not identified by differential RNA expression. Keywords: anther development, maize, male-sterile, ms8
2010-08-20 | GSE23615 | GEO
Project description:We performed a retrospective study on CSF from 20 DMT-naïve MS patients to investigate the correlation between intrathecal immune proteins and clinical MS phenotype.
2024-09-25 | GSE256426 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in plant growth and development. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with ~35% of duplicate homeologous miRNA genes retained. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated a bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes. Surveying miRNA genes in 5 maize tissues (root, seedling, tassel, ear, and pollen) by sequencing small RNA libraries using the Illumina Genome Analyzer
2009-11-23 | E-GEOD-17943 | biostudies-arrayexpress
Project description:RNA-sequencing of 5 tissues of maize inbred line Zheng 58: mature silk (MS), mature pollen (MP), mature ovary (MO), and 6-days old seedling (SL), immature silk (IMS)
2013-01-26 | E-MTAB-964 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in plant growth and development. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with ~35% of duplicate homeologous miRNA genes retained. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated a bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.
2009-11-23 | GSE17943 | GEO
Project description:Phenotypes of maize male sterile 8 plants are small anthers, meiotic failure, shorter epidermal cells, and non-secreting tapetal cells. Excess callose accumulates around meiotic cells, which later abort. Thousands of transcriptome changes occur including ectopic activation of genes not expressed in fertile siblings, failure to express genes, and differential expression of genes shared with fertile siblings. Sixty-three differentially expressed proteins were identified after 2-D DIGE followed by LC/MS/MS, including those involved in metabolism and cell division. The majority were not identified by differential RNA expression. Keywords: anther development, maize, male-sterile, ms8 4 replicates of ms8 mutant and 4 replicates of ms8 fertile siblings at 3 anther stages. Spike-in controls were included.
2010-08-20 | E-GEOD-23615 | biostudies-arrayexpress