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G3 (Bethesda). 2017 Sep 7;7(9):3157-3167. doi: 10.1534/g3.117.300078.

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

Author information

1
Department of Plant Sciences, University of California, Davis, California 95616 dbneale@ucdavis.edu.
2
Department of Plant Sciences, University of California, Davis, California 95616.
3
Department of Evolution and Ecology, University of California, Davis, California 95616.
4
Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742.
5
Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205.
6
Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269.
7
Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas 77843.
8
Pacific Northwest Research Station, United States Forest Service, Corvallis, Oregon 97331.
9
Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112.
10
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218.
11
Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218.
12
Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205.

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.

KEYWORDS:

annotation; conifer; genome assembly; gymnosperm; mega-genome; shade tolerance

PMID:
28751502
PMCID:
PMC5592940
DOI:
10.1534/g3.117.300078
[Indexed for MEDLINE]
Free PMC Article

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