Comparative Transcriptomics Among Four White Pine Species

G3: Genes, Genomes, Genetics

article

Ethan A. G. Baker¹  Jill L. Wegrzyn¹  Uzay U. Sezen¹  Taylor Falk¹  Patricia E. Maloney²  Detlev R. Vogler³  Annette Delfino-Mix³  Camille Jensen³  Jeffry Mitton⁴  Jessica Wright⁵  Brian Knaus⁶  Hardeep Rai⁷  Richard Cronn⁸  Daniel Gonzalez-Ibeas¹  Hans A. Vasquez-Gross⁹  Randi A. Famula⁹  Jun-Jun Liu^1,10  Lara M. Kueppers^1,11  David B. Neale⁹ 

[1] Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT,Canada;Department of Plant Pathology,University of California, Davis, CA,Canada;Department of Plant Sciences, University of California, Davis, CA,Canada;USDA-Forest Service, Pacific Southwest Research Station, Institute of Forest Genetics, Placerville, CA,Canada;Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO,Canada;USDA-Forest Service Pacific Southwest Research Station,Davis, CA,Canada;US Department of Agriculture, Agricultural Research Service, Horticultural Crop Research Unit, Corvallis, OR,Canada;Department of Biology, Utah State University, Logan, UT 84322,Canada;USDA-Forest Service Pacific Northwest Research Station, Corvallis, OR,Canada;Pacific Forestry Center, Canadian Forest Service, Natural Resources Canada, Victoria, BC,Canada;Sierra Nevada Research Institute, University of California, Merced, California 95343;Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

关键词: Keywords: de novo transcriptome assembly;    white pines;    five-needle pines;    wpbr;    Pinus monticola;    Pinus flexilis;    Pinus albicaulis;    Pinus lambertiana;   

DOI  :  10.1534/g3.118.200257

学科分类：社会科学、人文和艺术（综合）

来源: Genetics Society of America

【 摘 要 】

Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus . The populations of many Strobus species are challenged by native and introduced pathogens, native insects, and abiotic factors. RNA from the needles of western white pine ( Pinus monticola ), limber pine ( Pinus flexilis ), whitebark pine ( Pinus albicaulis) , and sugar pine ( Pinus lambertiana ) was sampled, Illumina short read sequenced, and de novo assembled. The assembled transcripts and their subsequent structural and functional annotations were processed through custom pipelines to contend with the challenges of non-model organism transcriptome validation. Orthologous gene family analysis of over 58,000 translated transcripts, implemented through Tribe-MCL, estimated the shared and unique gene space among the four species. This revealed 2025 conserved gene families, of which 408 were aligned to estimate levels of divergence and reveal patterns of selection. Specific candidate genes previously associated with drought tolerance and white pine blister rust resistance in conifers were investigated.

【 授权许可】

CC BY|CC BY-NC