Abstract Detail

Genomics / Proteomics

Sigel, Erin [1], Der, Joshua [2], DE PAMPHILIS, CLAUDE W [2], Pryer, Kathleen [1].

Time after time: Comparing homeolog expression patterns between two independent origins of the allotetraploid fern Polypodium hesperium.

Polyploidy, or whole genome duplication, is an important evolutionary mechanism contributing to speciation and diversification in plants. Following polyploidy events, many genetic and epigenetic modifications can occur, leading to differential expression of duplicated gene copies (i.e. homeologs). Gene expression patterns in allopolyploids (the result of hybridization between two or more distinct species) are particularly intriguing because they unite two or more divergent genomes within a single nucleus. Many naturally formed allopolyploids are known to form recurrently, resulting in taxa composed of multiple, independently-derived lineages. This raises the question: Do recurrent origins of a natural allopolyploid yield similar gene expression patterns? Here we present our preliminary analysis of next-generation RNA-Seq data to assess and compare homeolog expression in two independent origins of the western North American allotetraploid fern Polypodium hesperium, a member of the iconic and well-studied Polypodium vulgare species complex. We provide an overview of the bioinformatics and phylogenetic tools used to annotate transcriptome assemblies, identify the parental origin of homeologs of low-copy nuclear genes, and determine relative homeolog expression Because the two hybrid origin lineages of P. hesperium show reciprocal maternity, we also examine whether we can identify a bias in the homoeolog expressed or, potentially, homeolog loss, based on the maternal progenitor. This study provides a much-needed comparison to the majority of allotetraploid gene expression studies that are dominated by angiosperms, synthesized polyploids, and model organisms.

Broader Impacts:

1 - Duke University, Department of Biology, Box 90338, Durham, NC, 27708, USA
2 - Penn State University, Department of Biology, 201 Life Sciences Building, University Park, PA, 16802, USA, 814-777-7820

Keywords:
fern
hybrid
next generation sequencing
polyploidy
Phylogenomics
Polypodium
reticulation
RNA-Seq
allopolyploidy.

Presentation Type: Oral Paper:Papers for Topics
Session: 24
Location: Newberry/Riverside Hilton
Date: Tuesday, July 30th, 2013
Time: 10:15 AM
Number: 24002
Abstract ID:651
Candidate for Awards:None