Abstract Detail

Genomics / Proteomics

Coate, Jeremy [1], Powell, Adrian [2], Koenig, Max [3], Doyle, Jeff [4].

Patterns of homoeologue usage within and among three Glycine allopolyploid species.

Two fundamental questions about polyploidy under active investigation are how do polyploids utilize their duplicated complements of genes, and what are the emergent properties, or recurring outcomes, of genome duplication? Here, we address these questions by quantifying gene expression at the level of individual homoeologues in three related but independent allotetraploids in Glycine subgenus Glycine. We used RNA-Seq to profile the leaf transcriptomes of 2-5 accessions each of the three allotetraploids and their four diploid progenitors under two growth conditions (unstressed and excess light). Additionally, for one tetraploid and its diploid progenitors we profiled root transcriptomes. We reconstructed diploid consensus sequences for each diploid progenitor species, and mapped tetraploid reads to these sequences to quantify homoeologue expression for >20,000 genes per tetraploid species. By examining homoeologue usage within and among tetraploid species, we are able to distinguish individual- and species-specific responses from responses that are apparently conserved across polyploidy events (emergent properties). We are also using homoeologue expression to infer patterns of gene retention and loss. Retention of homoeologue expression indicates that very few homoeologues have been lost from the genomes of these polyploids in < 0.5 MY since their origins. This contrasts with the extensive gene loss observed in older polyploids (including the closely related soybean [G. max]), and suggests that the exponential decay in gene content inferred from these older events is not initiated immediately following duplication. We further discuss homoeologue expression patterns in Glycine allopolyploids in light of theories that attempt to explain patterns of biased or unbiased gene loss (fractionation) from homoeologous genomes of polyploids.

1 - Reed College, Plant Biology, 3203 SE Woodstock Blvd., Portland, OR, 97202, USA
2 - Cornell University, Section of Plant Biology, School of Integrative Plant Science, 412 Mann Library Building, Ithaca, NY, 14853-4301, USA
3 - Reed College, Biology, Portland, OR, 97202, USA
4 - Cornell University, Section of Plant Breeding & Genetics, School of Integrative Plant Science, 240 Emerson Hall, Ithaca, NY, 14853-4301, USA

Keywords:
polyploidy
Homoeologue-specific expression
RNA-seq
gene duplication
Gene loss.

Presentation Type: Oral Paper
Session: 27, Genomics & Proteomics II
Location: 105/Savannah International Trade and Convention Center
Date: Tuesday, August 2nd, 2016
Time: 2:30 PM
Number: 27005
Abstract ID:393
Candidate for Awards:None