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Title: Comparative Transcriptomics Among Four White Pine Species

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 inmore » conifers were investigated.« less
Authors:
 [1] ; ORCiD logo [1] ; ORCiD logo [1] ;  [1] ;  [2] ;  [3] ;  [3] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7] ;  [8] ;  [1] ;  [9] ;  [9] ;  [10] ;  [11] ;  [9]
  1. Univ. of Connecticut, Storrs, CT (United States). Dept. of Ecology and Evolutionary Biology
  2. Univ. of California, Davis, CA (United States). Dept. of Plant Pathology
  3. US Dept. of Agriculture (USDA)-Forest Service, Pacific Southwest Research Station, Placerville, CA (United States). Inst. of Forest Genetics
  4. Univ. of Colorado, Boulder, CO (United States). Dept. of Ecology and Evolutionary Biology
  5. US Dept. of Agriculture (USDA)-Forest Service, Pacific Southwest Research Station, Davis, CA (United States)
  6. US Dept. of Agriculture (USDA)., Corvallis, OR (United States). Agricultural Research Service, Horticultural Crop Research Unit
  7. Utah State Univ., Logan, UT (United States). Dept. of Biology
  8. US Dept. of Agriculture (USDA)-Forest Service, Pacific Southwest Research Station, Corvallis, OR (United States)
  9. Univ. of California, Davis, CA (United States). Dept. of Plant Sciences
  10. Univ. of California, Merced, CA (United States). Sierra Nevada Research Inst.
  11. Univ. of California, Merced, CA (United States). Sierra Nevada Research Inst.; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
G3
Additional Journal Information:
Journal Volume: 8; Journal Issue: 5; Journal ID: ISSN 2160-1836
Publisher:
Genetics Society of America
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; DE NOVO TRANSCRIPTOME ASSEMBLY; WHITE PINES; FIVE-NEEDLE PINES; WPBR; PINUS MONTICOLA; PINUS FLEXILIS; PINUS ALBICAULIS; PINUS LAMBERTIANA
OSTI Identifier:
1460314

Baker, Ethan A. G., Wegrzyn, Jill L., Sezen, Uzay U., Falk, Taylor, Maloney, Patricia E., Vogler, Detlev R., Delfino-Mix, Annette, Jensen, Camille, Mitton, Jeffry, Wright, Jessica, Knaus, Brian, Rai, Hardeep, Cronn, Richard, Gonzalez-Ibeas, Daniel, Vasquez-Gross, Hans A., Famula, Randi A., Liu, Jun-Jun, Kueppers, Lara M., and Neale, David B.. Comparative Transcriptomics Among Four White Pine Species. United States: N. p., Web. doi:10.1534/g3.118.200257.
Baker, Ethan A. G., Wegrzyn, Jill L., Sezen, Uzay U., Falk, Taylor, Maloney, Patricia E., Vogler, Detlev R., Delfino-Mix, Annette, Jensen, Camille, Mitton, Jeffry, Wright, Jessica, Knaus, Brian, Rai, Hardeep, Cronn, Richard, Gonzalez-Ibeas, Daniel, Vasquez-Gross, Hans A., Famula, Randi A., Liu, Jun-Jun, Kueppers, Lara M., & Neale, David B.. Comparative Transcriptomics Among Four White Pine Species. United States. doi:10.1534/g3.118.200257.
Baker, Ethan A. G., Wegrzyn, Jill L., Sezen, Uzay U., Falk, Taylor, Maloney, Patricia E., Vogler, Detlev R., Delfino-Mix, Annette, Jensen, Camille, Mitton, Jeffry, Wright, Jessica, Knaus, Brian, Rai, Hardeep, Cronn, Richard, Gonzalez-Ibeas, Daniel, Vasquez-Gross, Hans A., Famula, Randi A., Liu, Jun-Jun, Kueppers, Lara M., and Neale, David B.. 2018. "Comparative Transcriptomics Among Four White Pine Species". United States. doi:10.1534/g3.118.200257. https://www.osti.gov/servlets/purl/1460314.
@article{osti_1460314,
title = {Comparative Transcriptomics Among Four White Pine Species},
author = {Baker, Ethan A. G. and Wegrzyn, Jill L. and Sezen, Uzay U. and Falk, Taylor and Maloney, Patricia E. and Vogler, Detlev R. and Delfino-Mix, Annette and Jensen, Camille and Mitton, Jeffry and Wright, Jessica and Knaus, Brian and Rai, Hardeep and Cronn, Richard and Gonzalez-Ibeas, Daniel and Vasquez-Gross, Hans A. and Famula, Randi A. and Liu, Jun-Jun and Kueppers, Lara M. and Neale, David B.},
abstractNote = {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.},
doi = {10.1534/g3.118.200257},
journal = {G3},
number = 5,
volume = 8,
place = {United States},
year = {2018},
month = {3}
}