A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea

• Published in: Frontiers in plant science 2016-09, Vol.7, p.1446-1446
• Main Authors: Clevenger, Josh, Chu, Ye, Scheffler, Brian, Ozias-Akins, Peggy
• Format: Article
• Language: English
• Subjects: Alternative Splicing; Arachis hypogaea; developmental co-expression networks; homeolog expression bias; non-coding RNA; Plant Science; Transcriptomics
• ISSN: 1664-462X; 1664-462X
• DOI: 10.3389/fpls.2016.01446

The advent of the genome sequences of and has ushered in a new era for peanut genomics. With the goal of producing a gene atlas for cultivated peanut ( ), 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 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.