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Sci Data. 2017 Oct 10;4:170149. doi: 10.1038/sdata.2017.149.

Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus.

Pirita Paajanen, Jan Strauss, Cock van Oosterhout, Mark McMullan, Matthew D Clark, Thomas Mock

Affiliations

  1. Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
  2. European Molecular Biology Laboratory (EMBL) Hamburg, c/o German Electron Synchrotron (DESY), Notkestra├če 85, 22607 Hamburg, Germany.
  3. School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
  4. Earlham Institute, Norwich Research Park, Norwich NR4 7HU, UK.

PMID: 28994819 PMCID: PMC5634323 DOI: 10.1038/sdata.2017.149

Abstract

The genome of the cold-adapted diatom Fragilariopsis cylindrus is characterized by highly diverged haplotypes that intersperse its homozygous genome. Here, we describe how a combination of PacBio DNA and Illumina RNA sequencing can be used to resolve this complex genomic landscape locally into the highly diverged haplotypes, and how to map various environmentally controlled transcripts onto individual haplotypes. We assembled PacBio sequence data with the FALCON assembler and created a haplotype resolved annotation of the assembly using annotations of a Sanger sequenced F. cylindrus genome. RNA-seq datasets from six different growth conditions were used to resolve allele-specifc gene expression in F. cylindrus. This approach enables to study differential expression of alleles in a complex genomic landscape and provides a useful tool to study how diverged haplotypes in diploid organisms are used for adaptation and evolution to highly variable environments.

References

  1. Bioinformatics. 2015 Jan 15;31(2):166-9 - PubMed
  2. Genome Res. 1998 Mar;8(3):195-202 - PubMed
  3. Elife. 2013 Jul 02;2:e01114 - PubMed
  4. PLoS One. 2011;6(12):e28012 - PubMed
  5. Genome Res. 2009 Sep;19(9):1639-45 - PubMed
  6. Nat Methods. 2016 Dec;13(12 ):1050-1054 - PubMed
  7. Nature. 2017 Jan 26;541(7638):536-540 - PubMed
  8. Bioinformatics. 2009 Aug 15;25(16):2078-9 - PubMed
  9. Bioinformatics. 2005 May 1;21(9):1859-75 - PubMed
  10. Nat Protoc. 2006;1(2):581-5 - PubMed
  11. Bioinformatics. 2009 Jul 15;25(14):1754-60 - PubMed
  12. Genome Res. 2003 Jan;13(1):91-6 - PubMed

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