Abstract Detail

Phylogenomics

Birkenholz, Jude [1], Fishbein, Mark [1], Straub, Shannon [2].

Evolution of nuclear ribosomal DNA in Asclepias (milkweeds): Patterns of intragenomic polymorphisms and copy number variation.

Nuclear Ribosomal DNA (nrDNA) has been a widely used genetic marker for estimating phylogenetic relationships. Recent studies have found unexpected levels of intragenomic polymorphisms and copy number variation which could suggest that nrDNA’s use in phylogenetic studies might be error prone. The genus Asclepias was previously found to have significant intragenomic variation at the species level and potentially between individuals of the same species. To further assess patterns of nrDNA sequence evolution, I assembled the 35S nrDNA cistron of 901 individuals representing 87 species of the genus Asclepias using Illumina 150bp paired-end reads. I used Geneious Prime to both assemble my sequences and variant call them at 4 varying levels of stringency. To estimate nrDNA copy number, I mapped the read pools to 706, Asclepias specific, single-copy genes and then divided the average coverage of each sample’s nrDNA cistron by the average coverage of its single-copy gene assembly. Preliminary results show widespread intragenomic polymorphic variation both within and between species. I found that closely related species tended to share similar polymorphic sites with a small number of sites being polymorphic across multiple clades. Nuclear Ribosomal copy numbers shows even greater variation both interspecifically and intraspecifically in majority of species. Taken together these results highlight that nrDNA genes harbor greater variation that was previously thought and changes in nrDNA copy number are a defining feature in nrDNA sequence evolution. This further suggests that nrDNA’s use as a phylogenetic marker needs to be reassessed as more is learned about its evolution.

1 - Oklahoma State University, Dept Of Plant Biology, Ecology & Evolution, 301 Physical Science, Stillwater, OK, 74078, United States
2 - Hobart and William Smith Colleges, Biology, 300 Pulteney Street, Geneva, NY, 14456, USA

Keywords:
ribosomal DNA
convergent evolution
phylogenomics
gene family.

Presentation Type: Poster
Number: PPL011
Abstract ID:950
Candidate for Awards:None