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Abstract Detail



Phylogenomics

Weitemier, Kevin [1], Straub, Shannon [2], Fishbein, Mark [3], Liston, Aaron [4].

Intragenomic polymorphisms among high-copy loci: A genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae).

Despite knowledge that concerted evolution among some high-copy loci is imperfect, few studies exist investigating the extent of intragenomic polymorphisms, and much fewer that include many species. We present a bioinformatic pipeline for characterizing polymorphisms among the many copies of a high-copy locus. Results are presented for nuclear ribosomal DNA (nrDNA) across the milkweed genus, Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 members of the genus. Reads were mapped back to each individual's consensus, and at each position reads differing from the consensus were tallied using a custom perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%). Most nrDNA positions (91%) were polymorphic in at least one individual. Highly polymorphic sites existed in each individual, with higher abundance within the ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Polymorphisms among nrDNA copies are common, being found here at higher frequency than any study to date. This high and variable frequency may impact phylogenetic applications of nrDNA. This approach enables similar analyses in other taxa and high-copy regions via genome skimming.


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1 - Oregon State University, Botany And Plant Pathology, Cordley Hall 2082, Corvallis, OR, 97331, USA
2 - Oregon State University, Department Of Plant Biology, 2082 Cordley Hall, Corvallis, OR, 97331, USA
3 - Oklahoma State University, Dept Of Botany, 301 Physical Science, Stillwater, OK, 74078, USA
4 - Oregon State University, Department Of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA, 541/737-5301

Keywords:
concerted evolution
genome skimming
high-copy
intragenomic polymorphism
intra-individual site polymorphism (2ISP)
nuclear ribosomal DNA (nrDNA)
Asclepias.

Presentation Type: Poster:Posters for Topics
Session: P
Location: Eyrie/Boise Centre
Date: Monday, July 28th, 2014
Time: 5:30 PM
Number: PPL003
Abstract ID:650
Candidate for Awards:Genetics Section Poster Award


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