A developmental transcriptome map for allotetraploid arachis hypogaea

Authors: CLEVENGER, JOSH - University Of Georgia; CHU, YE - University Of Georgia; Scheffler, Brian; OZIAS-AKINS, PEGGY - University Of Georgia

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/12/2016
Publication Date: 9/30/2016
Publication URL: https://handle.nal.usda.gov/10113/5695449
Citation: Clevenger, J., Chu, Y., Scheffler, B.E., Ozias-Akins, P. 2016. A developmental transcriptome map for allotetraploid arachis hypogaea. Frontiers in Plant Science. 7:1446. doi: 10.3389/fpls.2016.01446.

Interpretive Summary: Cultivated peanut is a tetraploid species and the polyploid event that made it a tetraploid is calculated to be a rather recent evolutionary event. This means the genes of cultivated peanut are very similar to their diploid parents. To better understand the various peanut genes and associate them with their parental diploid genomes, an extensive analysis of gene expression was conducted. Twenty-two different tissue types or developmental stages of cultivated peanut were sampled with replication to allow for statistical analysis. Gene expression studies were then conducted using a method called RNASeq which is a DNA sequencing based technology. Of the RNA fragments sequenced, a 100bp from each fragment end was sequenced. Depth of coverage was estimated at 50,000,000 to 120,000,000 reads per sample. This is by far the most extensive gene expression study ever taken in cultivated peanut or most plant species. The progenitor diploid reference genomes were used to associate the RNASeq data to the genes and the sequences were assembled into complete gene transcripts using a technique called genome guided assembly. With this extensive dataset it was possible to demonstrate a bias of gene expression for homeologous genes (corresponding genes from each diploid parent). Striking differences were noticed for some genes when looking at tissue specific content. However, no one parental genome dominated in this bias. Due to the depth of sequence coverage, it was possible to identify 9000 alternative splicing events. Alternative splicing is when the RNA products from the same gene are different due to processing differences in the formation of mRNA. In peanut, a biological function has not been uncovered for these alternative splice products. This extensive gene expression dataset will be a valuable tool for breeders and other legume researchers as they associate genes with known phenotypes.

Technical 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. 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. 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.