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Patching Holes in the Chlamydomonas Genome

View ORCID ProfileFrej Tulin and Frederick R. Cross
G3: Genes, Genomes, Genetics July 1, 2016 vol. 6 no. 7 1899-1910; https://doi.org/10.1534/g3.116.029207
Frej Tulin
The Rockefeller University, New York, New York 10065
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  • For correspondence: frej.tulin@slcu.cam.ac.ukFrederick.Cross@rockefeller.edu
Frederick R. Cross
The Rockefeller University, New York, New York 10065
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  • For correspondence: frej.tulin@slcu.cam.ac.ukFrederick.Cross@rockefeller.edu
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Abstract

The Chlamydomonas genome has been sequenced, assembled, and annotated to produce a rich resource for genetics and molecular biology in this well-studied model organism. However, the current reference genome contains ∼1000 blocks of unknown sequence (‘N-islands’), which are frequently placed in introns of annotated gene models. We developed a strategy to search for previously unknown exons hidden within such blocks, and determine the sequence, and exon/intron boundaries, of such exons. These methods are based on assembly and alignment of short cDNA and genomic DNA reads, completely independent of prior reference assembly or annotation. Our evidence indicates that a substantial proportion of the annotated intronic N-islands contain hidden exons. For most of these, our algorithm recovers full exonic sequence with associated splice junctions and exon-adjacent intronic sequence. These new exons represent de novo sequence generally present nowhere in the assembled genome, and the added sequence improves evolutionary conservation of the predicted encoded peptides.

  • transcriptome assembly
  • trinity
  • Chlamydomonas
  • Received March 15, 2016.
  • Accepted April 23, 2016.
  • Copyright © 2016 Tulin, Cross

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Volume 6 Issue 7, July 2016

G3: Genes|Genomes|Genetics: 6 (7)

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Patching Holes in the Chlamydomonas Genome

View ORCID ProfileFrej Tulin and Frederick R. Cross
G3: Genes, Genomes, Genetics July 1, 2016 vol. 6 no. 7 1899-1910; https://doi.org/10.1534/g3.116.029207
Frej Tulin
The Rockefeller University, New York, New York 10065
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Frej Tulin
  • For correspondence: frej.tulin@slcu.cam.ac.ukFrederick.Cross@rockefeller.edu
Frederick R. Cross
The Rockefeller University, New York, New York 10065
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: frej.tulin@slcu.cam.ac.ukFrederick.Cross@rockefeller.edu
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Citation

Patching Holes in the Chlamydomonas Genome

View ORCID ProfileFrej Tulin and Frederick R. Cross
G3: Genes, Genomes, Genetics July 1, 2016 vol. 6 no. 7 1899-1910; https://doi.org/10.1534/g3.116.029207
Frej Tulin
The Rockefeller University, New York, New York 10065
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Frej Tulin
  • For correspondence: frej.tulin@slcu.cam.ac.ukFrederick.Cross@rockefeller.edu
Frederick R. Cross
The Rockefeller University, New York, New York 10065
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: frej.tulin@slcu.cam.ac.ukFrederick.Cross@rockefeller.edu

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