Project description:Seeds of the legume Castanospermum australe are shed at relatively high moisture contents, and to do not acquire desiccation tolerance during their seed development, they are referred to as 'recalcitrant'. To characterize the regulatory pathways and molecular mechnanisms are occur during seed development and to allow for a comparative analysis with seed development of desiccation-tolerant species, cotyledon and embryonic axes were harvested at different stages of development, arbitrarily defined in terms of seed weight (grams) and color. Transcriptomes of 6 stages were analysed using Nimblegen slides: 2.5g - 4.5g - 7.5g - yellow-green (YG) - green (G) - brown (B) for cotyledons (C) and YG, G and B for emrbyonic axes (A)
Project description:Purpose: The goal of this experiment was to use RNA-seq to compare the two commercial cotton species Gossypium hirsutum and Gossypium barbadense and determine what transcripts may account for the better fiber quality in the latter. Methods: RNA was extracted from Gossypium barbadense or Gossypium hirsutum fibers at 10, 15, 18, 21, and 28 days post anthesis. Paired-end, 100-bp RNA-seq was performed on an Illumina HiSeq2000 and the reads were mapped to the Gossypium raimondii genome at www.phytozome.net and non-homologous contig assemblies from Gossypium arboreum. Results from RNA-seq were combined with non-targeted metabolomics. Results: Approximately 38,000 transcripts were expressed (RPKM>2) in each fiber type and approximately 2,000 of these transcripts were differentially expressed in a cross-species comparison at each timepoint. Enriched Gene Ontology biological processes in differentially expressed transcripts suggested that Gh fibers were more stressed. Conclusions: Both metabolomic and transcriptomic data suggest that better mechanisms for managing reactive oxygen species contribute to the increased fiber length in Gossypium barbadense. This appears to result from enhanced ascorbate biosynthesis via gulono-1,4-lactone oxidase and ascorbate recycling via dehydroascorbate reductase.
