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SRX732706: Fishbein 5596 [OKLA]-101-CGTT
1 ILLUMINA (Illumina Genome Analyzer IIx) run: 2.2M spots, 165.5M bases, 88Mb downloads

Design: "See Straub et al. 2012, Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. American Journal of Botany 99:349?364."
Submitted by: (Listonlab)
Study: Intragenomic polymorphisms among high-copy loci: A genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae)
show Abstracthide Abstract
Despite knowledge that concerted evolution of high-copy loci is often imperfect, few studies 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).
Sample: Fishbein 5596 [OKLA]-101
SAMN03078579 • SRS721491 • All experiments • All runs
Library:
Instrument: Illumina Genome Analyzer IIx
Strategy: WGS
Source: GENOMIC
Selection: RANDOM
Layout: SINGLE
Spot descriptor:
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Runs: 1 run, 2.2M spots, 165.5M bases, 88Mb
Run# of Spots# of BasesSizePublished
SRR16121482,177,644165.5M88Mb2015-07-22

ID:
1058933

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