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The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

  • Author(s): Neale, David B;
  • McGuire, Patrick E;
  • Wheeler, Nicholas C;
  • Stevens, Kristian A;
  • Crepeau, Marc W;
  • Cardeno, Charis;
  • Zimin, Aleksey V;
  • Puiu, Daniela;
  • Pertea, Geo M;
  • Sezen, U Uzay;
  • Casola, Claudio;
  • Koralewski, Tomasz E;
  • Paul, Robin;
  • Gonzalez-Ibeas, Daniel;
  • Zaman, Sumaira;
  • Cronn, Richard;
  • Yandell, Mark;
  • Holt, Carson;
  • Langley, Charles H;
  • Yorke, James A;
  • Salzberg, Steven L;
  • Wegrzyn, Jill L
  • et al.
Abstract

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms.

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