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

http://ir.library.oregonstate.edu/concern/articles/td96k443z

This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by BioMed Central Ltd. The published article can be found at:  http://genomebiology.com/.

Descriptions

Attribute NameValues
Creator
Abstract or Summary
  • BACKGROUND: 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. RESULTS: 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. Transposon-related transcripts are present in high levels in both gametophytes, suggesting a connection between gamete production and transposon expression in maize not previously identified in any female gametophytes. Two classes of small signaling proteins and several transcription factor gene families are enriched in gametophyte transcriptomes. Expression patterns of maize genes with duplicates in subgenome 1 and subgenome 2 indicate that pollen-expressed genes in subgenome 2 are retained at a higher rate than subgenome 2 genes with other expression patterns. Analysis of available insertion mutant collections shows a statistically significant deficit in insertions in gametophyte-expressed genes. CONCLUSIONS: This analysis, the first RNA-seq study to compare both gametophytes in a monocot, identifies maize gametophyte functions, gametophyte expression of transposon-related sequences, and unannotated, novel transcripts. Reduced recovery of mutations in gametophyte-expressed genes is supporting evidence for their function in the gametophytes. Expression patterns of extant, duplicated maize genes reveals that selective pressures based on male gametophytic function have likely had a disproportionate effect on plant genomes.
Resource Type
DOI
Date Available
Date Issued
Citation
  • Chettoor, A. M., Givan, S. A., Cole, R. A., Coker, C. T., Unger-Wallace, E., Vejlupkova, Z., ... & Evans, M. (2014). Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes. Genome Biology, 15(7), 414. doi:10.1186/s13059-014-0414-2
Series
Rights Statement
Funding Statement (additional comments about funding)
Publisher
Peer Reviewed
Language
Replaces
Additional Information
  • description.provenance : Approved for entry into archive by Erin Clark(erin.clark@oregonstate.edu) on 2015-01-29T20:01:28Z (GMT) No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) ColeRexBotanyPlantPathologyDiscoveryNovelTranscripts.pdf: 2340076 bytes, checksum: c39822bb20c34ab229ee6f4393dda3ed (MD5) ColeRexBotanyPlantPathologyDiscoveryNovelTranscripts_AdditionalFiles.zip: 34407495 bytes, checksum: d63b28be2ca5b623d6d0ab7be1a018e0 (MD5)
  • description.provenance : Made available in DSpace on 2015-01-29T20:01:28Z (GMT). No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) ColeRexBotanyPlantPathologyDiscoveryNovelTranscripts.pdf: 2340076 bytes, checksum: c39822bb20c34ab229ee6f4393dda3ed (MD5) ColeRexBotanyPlantPathologyDiscoveryNovelTranscripts_AdditionalFiles.zip: 34407495 bytes, checksum: d63b28be2ca5b623d6d0ab7be1a018e0 (MD5) Previous issue date: 2014-07-31
  • description.provenance : Submitted by Erin Clark (erin.clark@oregonstate.edu) on 2015-01-29T20:01:13Z No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) ColeRexBotanyPlantPathologyDiscoveryNovelTranscripts.pdf: 2340076 bytes, checksum: c39822bb20c34ab229ee6f4393dda3ed (MD5) ColeRexBotanyPlantPathologyDiscoveryNovelTranscripts_AdditionalFiles.zip: 34407495 bytes, checksum: d63b28be2ca5b623d6d0ab7be1a018e0 (MD5)

Relationships

In Administrative Set:
Last modified: 07/26/2017 Default
Citations:

EndNote | Zotero | Mendeley

Items