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A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea

Josh Clevenger, Ye Chu, Brian Scheffler, Peggy Ozias-Akins
Frontiers in plant science 2016 v.7 no.1446 pp. -
Arachis hypogaea, Internet, RNA splicing, accuracy, allopolyploidy, bias, chromosome mapping, flowers, genes, genomics, non-coding RNA, nucleotide sequences, peanuts, plant genetics, researchers, soil, transcriptome
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. Using a set of 8,816 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 9,000 alterative splicing events and over 6,000 non coding RNAs were further identified. 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.