Abstract Detail

Genomics / Proteomics

Weitemier, Kevin [1], Straub, Shannon C.K. [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 of high-copy loci is often imperfect, studies that investigate the extent of intragenomic polymorphisms and comparisons across a large number of species are rarely made. We present a bioinformatic pipeline for characterizing polymorphisms within an individual among 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 samples representing 90 species of Asclepias. 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, with polymorphic sites being less frequent in subunit regions and loops. Highly polymorphic sites existed in each individual, with highest abundance in the “noncoding” ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date. The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone. The new analytical approach provided here is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming).

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1 - Oregon State University, Botany And Plant Pathology, Cordley Hall 2082, Corvallis, OR, 97331, USA
2 - Hobart and William Smith Colleges, Department of Biology, 300 Pulteney St., Geneva, NY, 14456, United States
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:
Asclepias
Concerted evolution
Genome skimming
High-copy
Intragenomic polymorphism
Partial SNP (pSNP)
nuclear ribosomal DNA
nrDNA
Intra-individual site polymorphism
2ISP
ITS.

Presentation Type: Oral Paper:Papers for Topics
Session: 39
Location: Salon 19/20/The Shaw Conference Centre
Date: Tuesday, July 28th, 2015
Time: 10:45 AM
Number: 39007
Abstract ID:961
Candidate for Awards:Margaret Menzel Award