title: A Developmental Transcriptome Map for AllotetraploidArachis hypogaea.
abstract: The advent of the genome sequences ofArachis duranensisandArachis ipaensishas 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 forArachis hypogaeawas 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.
authors.affiliation: Institute of Plant Breeding, Genetics, and Genomics, University of Georgia Tifton, GA, USA.
authors.forename: Josh
authors.initials: J
authors.lastname: Clevenger
authors.affiliation: Institute of Plant Breeding, Genetics, and Genomics, University of Georgia Tifton, GA, USA.
authors.forename: Ye
authors.initials: Y
authors.lastname: Chu
authors.affiliation: United States Department of Agriculture - Agricultural Research Service, Genomics and Bioinformatics Research Unit Stoneville, MS, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Scheffler
authors.affiliation: Institute of Plant Breeding, Genetics, and Genomics, University of Georgia Tifton, GA, USA.
authors.forename: Peggy
authors.initials: P
authors.lastname: Ozias-Akins
keywords: Arachis hypogaea; PRJNA291488; alternative splicing; developmental co-expression networks; homeolog expression bias; non-coding RNA; transcriptomics