Journal
FRONTIERS IN PLANT SCIENCE
Volume 7, Issue -, Pages -Publisher
FRONTIERS MEDIA SA
DOI: 10.3389/fpls.2016.01446
Keywords
transcriptomics; Arachis hypogaea; developmental co-expression networks; homeolog expression bias; alternative splicing; non-coding RNA; PRJNA291488
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Funding
- Peanut Foundation
- National Peanut Board
- Georgia Peanut Commission
- Agriculture and Food Research Initiative competitive grant of the USDA National Institute of Food and Agriculture [2012-85117-19435]
- MARs [58-6402-2-723]
- Peanut Genome Initiative
- NIFA [578715, 2012-85117-19435] Funding Source: Federal RePORTER
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The advent of the genome sequences of Arachis duranensis and Arachis ipaensis has ushered in a new era for peanut genomics. With the goal of producing a gene atlas for cultivated peanut (Arachis hypogaea), 22 different tissue types and ontogenies that represent the full development of peanut were sequenced, including a complete reproductive series from flower to peg elongation and peg tip immersion in the soil to fully mature seed. Using a genome-guided assembly pipeline, a homeolog-specific transcriptome assembly for Arachis hypogaea was assembled and its accuracy was validated. The assembly was used to annotate 21 developmental co-expression networks as tools for gene discovery. Using a set of 8816 putative homeologous gene pairs, homeolog expression bias was documented, and although bias was mostly balanced, there were striking differences in expression bias in a tissue-specific context. Over 9000 alterative splicing events and over 6000 non-coding RNAs were further identified and profiled in a developmental context. Together, this work represents a major new resource for cultivated peanut and will be integrated into peanutbase.org as an available resource for all peanut researchers.
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