Journal Article

A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea

Clevenger, Josh, Scheffler, Brian, Ozias-Akins, Peggy, Chu, Ye

2016

Overview

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.

• Publisher: Frontiers Media SA,Frontiers Media S.A
• Subject: accuracy / allopolyploidy / Alternative Splicing / Arachis hypogaea / Bias / chromosome mapping / developmental co-expression networks / flowers / Gene sequencing / Genes / Genomes / Genomics / homeolog expression bias / Internet / Legumes / Nitrogen / non-coding RNA / nucleotide sequences / Peanuts / plant genetics / Plant Science / researchers / RNA splicing / Seeds / soil / transcriptome / Transcriptomes / Transcriptomics