Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Zea mays Transcriptome or Gene expression

ABSTRACT: We perform a quantitative RNA-seq analysis of embryo sacs, comparator ovules with the embryo sacs removed, mature pollen, and seedlings to assist the identification of gametophyte functions in maize. Expression levels were determined for annotated genes in both gametophytes, and novel transcripts were identified from de novo assembly of RNA-seq reads. RNA-seq was performed on four tissue types: nine-day old, above-ground seedling (S); mature pollen (MP); embryo-sac-enriched samples with some remaining nucellar cells (ES); and ovules with embryo sacs removed (Ov).

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Zea mays

SUBMITTER: Antony Chettoor

PROVIDER: E-MTAB-4128 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes.

Chettoor Antony M AM Givan Scott A SA Cole Rex A RA Coker Clayton T CT Unger-Wallace Erica E Vejlupkova Zuzana Z Vollbrecht Erik E Fowler John E JE Evans Matthew Ms MM

Genome biology 20140731 7

<h4>Background</h4>Plant gametophytes play central roles in sexual reproduction. A hallmark of the plant life cycle is that gene expression is required in the haploid gametophytes. Consequently, many mutant phenotypes are expressed in this phase.<h4>Results</h4>We perform a quantitative RNA-seq analysis of embryo sacs, comparator ovules with the embryo sacs removed, mature pollen, and seedlings to assist the identification of gametophyte functions in maize. Expression levels were determined for ...[more]

PMID: 25084966

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Project description:Purpose: Alternative splicing is fundamental for post-transcriptional regulation and proteome diversity. The goals of this study are to compare transcriptome and splicing profiling (RNA-seq) between wild type and prp8a prp8b mutant ovules of the spliceosome subunit and define the molecular signature of prp8a prp8b pollen tube attraction phenotype. Methods: mRNA profiles from mature ovules of 6-weeks-old wild-type (WT) and pre-mRNA processing factor 8 (PRP8Aa prp8bb) Arabidopsis plants were generated by deep sequencing, in triplicates, using Illumina HiSeq4000 100bp paired-end reads. The sequence reads that passed quality filters were were mapped to TAIR10 whole genome and analyzed for differential expression, differential exone usage and intron retention as indicated in DATA PROCESSING PIPELINE section. Results: Using an optimized data analysis workflow, about 15 million sequence read pairs per sample were mapped to the Arabidopsis genome (TAIR10). Approximately 2.9% of the transcripts showed differential expression between the WT and PRP8Aa prp8bb ovules, with a fold change ≥1.5 and p value <0.05. Analysis for differential gene expression, exon usage and intron retention with DESeq2 v1.22.1 and DEXseq v1.28.0 or IRFinder v1.2.3 respectively, uncovered several as yet uncharacterized genes that may contribute to pollen tube attraction and female gametophyte cell fate specification. Conclusions: Our work has uncovered a molecular signature through which PRP8A/PRP8B subunits act redundantly to define male-female signaling competence for successful pollen tube attraction in Arabidopsis. Application of DESeq2 algorithms to our ovule RNA-seq data identified downregulation of over 50 different CRP genes with yet unknown function from the synergid and the central cells including all LURE pollen tube attractants. Whereas use of DEXseq workflow, revealed mis-splicing of key genes involved embryo sac specificiation and genes of the secretory pathway. We concluded that 100bp paired-end RNAseq was a sufficient compromise for detection of differential gene expression and splice isoforms, however, our experiment would have benefited with more number of replicates.

Dataset Information

Zea mays Transcriptome or Gene expression

Publications

Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes.

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