The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae. Issue 9 (1st September 2017)

• Record Type: Journal Article
• Authors: 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
• Is Part Of: G3. Volume 7:Issue 9(2017)
• Page Start: 3157
• Page End: 3167
• Publication Date: 2017-09-01
• Subjects: gymnosperm -- mega-genome -- conifer -- genome assembly -- shade tolerance -- annotation; Genetics -- Research -- Periodicals; Genomics -- Periodicals; Genetics; Genomics; Genes; Genetics -- Research; Genomics; Electronic journals; Periodical; Periodicals; Fulltext; Internet Resources; Periodicals; 572.8
• DOI: 10.1534/g3.117.300078
• Languages: English
• ISSNs: 2160-1836

Abstract

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.