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Reference-guided assembly of four diverse Arabidopsis thaliana genomes

Schneeberger, Korbinian ; Ossowski, Stephan ; Ott, Felix ; Klein, Juliane D ; Wang, Xi ; Lanz, Christa ; Smith, Lisa M ; Cao, Jun ; Fitz, Joffrey ; Warthmann, Norman ; Henz, Stefan R ; Huson, Daniel H ; Weigel, Detlef

Proceedings of the National Academy of Sciences - PNAS, 2011-06, Vol.108 (25), p.10249-10254 [Periódico revisado por pares]

United States: National Academy of Sciences

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Título:
Reference-guided assembly of four diverse Arabidopsis thaliana genomes
Autor: Schneeberger, Korbinian ; Ossowski, Stephan ; Ott, Felix ; Klein, Juliane D ; Wang, Xi ; Lanz, Christa ; Smith, Lisa M ; Cao, Jun ; Fitz, Joffrey ; Warthmann, Norman ; Henz, Stefan R ; Huson, Daniel H ; Weigel, Detlef
Assuntos: Algorithms ; Arabidopsis - genetics ; Arabidopsis thaliana ; Base Sequence ; Biological Sciences ; Comparative analysis ; Data processing ; DNA ; Flowers & plants ; Genes ; Genetic loci ; Genetic variation ; Genome, Plant ; Genomes ; Human genome ; Libraries ; Nucleotide sequence ; nucleotide sequences ; Polymorphism, Genetic ; Ribonucleic acid ; RNA ; Scaffolds ; Sequence Alignment ; Sequence Analysis, DNA ; Sequencing ; Shotguns ; Velvet
É parte de: Proceedings of the National Academy of Sciences - PNAS, 2011-06, Vol.108 (25), p.10249-10254
Notas: http://dx.doi.org/10.1073/pnas.1107739108
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Contributed by Detlef Weigel, May 16, 2011 (sent for review November 18, 2010)
1K.S. and S.O. contributed equally to this work.
Author contributions: K.S., S.O., D.H.H., and D.W. designed research; C.L., L.M.S., J.C., and N.W. performed research; K.S., S.O., F.O., J.D.K., X.W., J.F., and S.R.H. analyzed data; and K.S., S.O., and D.W. wrote the paper.
Descrição: We present whole-genome assemblies of four divergent Arabidopsis thaliana strains that complement the 125-Mb reference genome sequence released a decade ago. Using a newly developed reference-guided approach, we assembled large contigs from 9 to 42 Gb of Illumina short-read data from the Landsberg erecta (Ler-1), C24, Bur-0, and Kro-0 strains, which have been sequenced as part of the 1,001 Genomes Project for this species. Using alignments against the reference sequence, we first reduced the complexity of the de novo assembly and later integrated reads without similarity to the reference sequence. As an example, half of the noncentromeric C24 genome was covered by scaffolds that are longer than 260 kb, with a maximum of 2.2 Mb. Moreover, over 96% of the reference genome was covered by the reference-guided assembly, compared with only 87% with a complete de novo assembly. Comparisons with 2 Mb of dideoxy sequence reveal that the per-base error rate of the reference-guided assemblies was below 1 in 10,000. Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. Genome assemblies, raw reads, and further information are accessible through http://1001genomes.org/projects/assemblies.html.
Editor: United States: National Academy of Sciences
Idioma: Inglês

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Reference-guided assembly of four diverse Arabidopsis thaliana genomes

Schneeberger, Korbinian ; Ossowski, Stephan ; Ott, Felix ; Klein, Juliane D ; Wang, Xi ; Lanz, Christa ; Smith, Lisa M ; Cao, Jun ; Fitz, Joffrey ; Warthmann, Norman ; Henz, Stefan R ; Huson, Daniel H ; Weigel, Detlef

United States: National Academy of Sciences

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