Home LiteratureArticle Details

PMID: 18818371 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Sequencing of natural strains of Arabidopsis thaliana with short reads.

Genome research ·Vol. 18 ·No. 12 ·2008-12-00 ·Pages 2024-33

Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D

Abstract

Whole-genome hybridization studies have suggested that the nuclear genomes of accessions (natural strains) of Arabidopsis thaliana can differ by several percent of their sequence. To examine this variation, and as a first step in the 1001 Genomes Project for this species, we produced 15- to 25-fold coverage in Illumina sequencing-by-synthesis (SBS) reads for the reference accession, Col-0, and two divergent strains, Bur-0 and Tsu-1. We aligned reads to the reference genome sequence to assess data quality metrics and to detect polymorphisms. Alignments revealed 823,325 unique single nucleotide polymorphisms (SNPs) and 79,961 unique 1- to 3-bp indels in the divergent accessions at a specificity of >99%, and over 2000 potential errors in the reference genome sequence. We also identified >3.4 Mb of the Bur-0 and Tsu-1 genomes as being either extremely dissimilar, deleted, or duplicated relative to the reference genome. To obtain sequences for these regions, we incorporated the Velvet assembler into a targeted de novo assembly method. This approach yielded 10,921 high-confidence contigs that were anchored to flanking sequences and harbored indels as large as 641 bp. Our methods are broadly applicable for polymorphism discovery in moderate to large genomes even at highly diverged loci, and we established by subsampling the Illumina SBS coverage depth required to inform a broad range of functional and evolutionary studies. Our pipeline for aligning reads and predicting SNPs and indels, SHORE, is available for download at http://1001genomes.org.

MeSH Terms

Arabidopsis/genetics Base Sequence Chromosome Mapping Chromosomes, Plant DNA, Plant/genetics,isolation & purification Frameshift Mutation Gene Duplication Genome, Plant Molecular Sequence Data Polymorphism, Genetic Sequence Analysis, DNA/methods Sequence Deletion Sequence Homology, Nucleic Acid

Chemicals

DNA, Plant

Authors & Affiliations

6 authors, click to expand affiliations / ORCID

Ossowski Stephan

Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.

Schneeberger Korbinian

Clark Richard M

Lanz Christa

Warthmann Norman

Weigel Detlef

References (24)

24 references, click to expand

Nearly identical paralogs: implications for maize (Zea mays L.) genome evolution.
Genetics. 2007 Jan;175(1):429-39 PMID: 17110490
Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis.
Nature. 2006 Jun 22;441(7096):947-52 PMID: 16791187
Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.
Science. 2007 Jul 20;317(5836):338-42 PMID: 17641193
Recombination and linkage disequilibrium in Arabidopsis thaliana.
Nat Genet. 2007 Sep;39(9):1151-5 PMID: 17676040
Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants.
PLoS Biol. 2007 Sep;5(9):e236 PMID: 17803357
Paired-end mapping reveals extensive structural variation in the human genome.
Science. 2007 Oct 19;318(5849):420-6 PMID: 17901297
MSQT for choosing SNP assays from multiple DNA alignments.
Bioinformatics. 2007 Oct 15;23(20):2784-7 PMID: 17785349
Whole-genome sequencing and variant discovery in C. elegans.
Nat Methods. 2008 Feb;5(2):183-8 PMID: 18204455
Short read fragment assembly of bacterial genomes.
Genome Res. 2008 Feb;18(2):324-30 PMID: 18083777
Quantitative trait loci mapping in five new large recombinant inbred line populations of Arabidopsis thaliana genotyped with consensus single-nucleotide polymorphism markers.
Genetics. 2008 Apr;178(4):2253-64 PMID: 18430947
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.
Genome Res. 2008 May;18(5):802-9 PMID: 18332092
ALLPATHS: de novo assembly of whole-genome shotgun microreads.
Genome Res. 2008 May;18(5):810-20 PMID: 18340039
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Genome Res. 2008 May;18(5):821-9 PMID: 18349386
Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays.
Genome Res. 2008 Jun;18(6):918-29 PMID: 18323538
Mapping short DNA sequencing reads and calling variants using mapping quality scores.
Genome Res. 2008 Nov;18(11):1851-8 PMID: 18714091
Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis.
Plant Cell. 1999 Nov;11(11):2099-112 PMID: 10559437
EMBOSS: the European Molecular Biology Open Software Suite.
Trends Genet. 2000 Jun;16(6):276-7 PMID: 10827456
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
Nature. 2000 Dec 14;408(6814):796-815 PMID: 11130711
Large-scale identification of single-feature polymorphisms in complex genomes.
Genome Res. 2003 Mar;13(3):513-23 PMID: 12618383
Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus.
Proc Natl Acad Sci U S A. 2003 Nov 25;100 Suppl 2:14587-92 PMID: 14506289
Naturally occurring genetic variation in Arabidopsis thaliana.
Annu Rev Plant Biol. 2004;55:141-72 PMID: 15377217
Molecular population genetics and the search for adaptive evolution in plants.
Mol Biol Evol. 2005 Mar;22(3):506-19 PMID: 15525701
The pattern of polymorphism in Arabidopsis thaliana.
PLoS Biol. 2005 Jul;3(7):e196 PMID: 15907155
Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana.
Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12057-62 PMID: 17626786

Article Info

Journal

Genome research

Abbr.

Genome Res

ISSN

1088-9051

DOI

10.1101/gr.080200.108

Published

2008-12-00

Epub

2008-00-25

Pages

2024-33

Language

English

Region

United States

NLM ID

9518021

PMCID

PMC2593571

Subset

Databases

GENBANK

FI160450, FI160451, FI160452, FI160453, FI160454, FI160455, FI160456, FI160457, FI160458, FI160459, FI160460, FI160461, FI160462, FI160463, FI160464, FI160465, FI160466, FI160467, FI160468, FI160469, FI160470, FI160471, FI160472, FI160473, FI160474, FI160475, FI160476, FI160477, FI160478, FI160479, FI160480, FI160481, FI160482, FI160483, FI160484, FI160485, FI160486, FI160487, FI160488, FI160489, FI160490, FI160491, FI160492, FI160493, FI160494, FI160495, FI160496, FI160497, FI160498, FI160499, FI160500, FI160501, FI160502, FI160503, FI160504, FI160505, FI160506, FI160507, FI160508, FI160509, FI160510, FI160511, FI160512, FI160513, FI160514, FI160515, FI160516, FI160517, FI160518, FI160519, FI160520, FI160521, FI160522, FI160523, FI160524, FI160525, FI160526, FI160527, FI160528, FI160529, FI160530, FI160531, FI160532, FI160533, FI160534, FI160535, FI160536, FI160537, FI160538, FI160539, FI160540, FI160541, FI160542, FI160543, FI160544, FI160545, FI160546, FI160547, FI160548, FI160549, FI160550, FI160551, FI160552, FI160553, FI160554, FI160555, FI160556, FI160557, FI160558, FI160559, FI160560, FI160561, FI160562, FI160563, FI160564, FI160565, FI160566, FI160567, FI160568, FI160569, FI160570, FI160571, FI160572, FI160573, FI160574, FI160575, FI160576, FI160577, FI160578, FI160579, FI160580, FI160581, FI160582, FI160583, FI160584, FI160585, FI160586, FI160587, FI160588, FI160589, FI160590, FI160591, FI160592, FI160593, FI160594, FI160595, FI160596, FI160597, FI160598, FI160599, FI160600, FI160601, FI160602, FI160603, FI160604, FI160605, FI160606, FI160607, FI160608, FI160609, FI160610, FI160611, FI160612, FI160613, FI160614, FI160615, FI160616, FI160617, FI160618, FI160619, FI160620, FI160621, FI160622, FI160623, FI160624, FI160625, FI160626, FI160627, FI160628, FI160629, FI160630, FI160631, FI160632, FI160633, FI160634, FI160635, FI160636, FI160637

External Links

PubMed source DOI: 10.1101/gr.080200.108 PMC Full Text View journal details

Analysis Services

Sequencing of natural strains of Arabidopsis thaliana with short reads.

Contact

WeChat Official Account