A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea

Frontiers in Plant Science

Josh Paul Clevenger¹  Peggy Ozias-Akins¹  Brian Scheffler²  Ye Chu³ 

[1] The University of Georgia;USDA-ARS, , ., Stoneville, MS 38776-0038;University of Georgia;

关键词: Alternative Splicing;    Arachis hypogaea;    non-coding RNA;    Transcriptomics;    homeolog expression bias;    developmental co-expression networks;   

DOI  :  10.3389/fpls.2016.01446

来源: DOAJ

【 摘 要 】

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 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 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.

【 授权许可】

Unknown