The Douglas-Fir genome sequence reveals specialization of the photosynthetic apparatus in Pinaceae

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

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)3157-3167
Number of pages11
JournalG3: Genes, Genomes, Genetics
Volume7
Issue number9
DOIs
StatePublished - Sep 1 2017

Keywords

  • Annotation
  • Conifer
  • Genome assembly
  • Gymnosperm
  • Mega-genome
  • Shade tolerance

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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