@ARTICLE{10.3389/fpls.2016.01446, AUTHOR={Clevenger, Josh and Chu, Ye and Scheffler, Brian and Ozias-Akins, Peggy}, TITLE={A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea}, JOURNAL={Frontiers in Plant Science}, VOLUME={7}, YEAR={2016}, URL={https://www.frontiersin.org/articles/10.3389/fpls.2016.01446}, DOI={10.3389/fpls.2016.01446}, ISSN={1664-462X}, ABSTRACT={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.} }