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Conserved ortholog sets in forest trees

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Abstract

Putative single-copy genes and conserved ortholog sets (COS) were identified in model plant species thale cress (Arabidopsis thaliana), rice (Oryza sativa ssp. japonica), and poplar [black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw)] and used to find putative COS in four conifers (the Coniferales order). Using expressed sequence tag sequences, unique transcript sets were assembled in loblolly pine (Pinus taeda L.), white spruce [Picea glauca (Moench) Voss], Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii], and sugi [Cryptomeria japonica (Thunberg ex Linnaeus f.) D. Don]. They were compared with COS sets identified in three model plant species using comparative sequence analysis. Almost half of the single-copy genes in herbaceous species (Arabidopsis and rice) had additional copies and homologs in poplar and conifers. The identified tentative COS sets have many applications in evolutionary genomics studies, phylogenetic analysis, and comparative mapping.

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Acknowledgments

We thank Glenn Howe and Dana Howe (Oregon State University, USA) for providing additional Douglas-fir EST sequences and Stephen DiFazio (West Virginia University, Morgantown, WV, USA) for the poplar predicted protein set. We also thank Santiago C. González-Martínez (Center of Forest Research, Madrid, Spain), Glenn Howe, Jean Bousquet (Université Laval, Canada) and anonymous reviewers for thorough reviewing of the manuscript and useful recommendations that greatly helped us improve the paper. Funding for this project was provided by the USDA Plant Genome National Research Initiative (grant no. 00-35300-9316) and the Pacific Southwest Research Station, the USDA Forest Service within the American Forest & Paper Association Agenda 2020 program. Trade names and commercial products or enterprises are mentioned solely for information and no endorsement by the USDA is implied.

Author information

Authors and Affiliations

  1. Department of Forest Science, Texas A&M University, College Station, TX, 77843-2135, USA

    Konstantin V. Krutovsky

  2. Department of Animal Science, Texas A&M University, College Station, TX, 77843-2471, USA

    Christine G. Elsik

  3. Allometra, LLC, Davis, CA, 95616, USA

    Marta Matvienko

  4. Genome Center, University of California, Davis, CA, 95616, USA

    Alex Kozik

  5. Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA

    David B. Neale

  6. Institute of Forest Genetics, Pacific Southwest Research Station, US Department of Agriculture Forest Service, Davis, CA, 95616, USA

    David B. Neale

Authors
  1. Konstantin V. Krutovsky
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  2. Christine G. Elsik
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  3. Marta Matvienko
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  4. Alex Kozik
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  5. David B. Neale
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Corresponding author

Correspondence to David B. Neale.

Additional information

Communicated by S. Aitken

Electronic supplementary material

Below is the link to the electronic supplementary material.

These files are unfortunately not in the Publisher's archive anymore:

  • C_japonica_55-COS-genes-shared-with-ARP (FASTA 38 kb)

  • P_glauca_359-COS-genes-shared-with-ARP (FASTA 355 kb)

  • P_menziesii_90-COS-genes-shared-with-ARP (FASTA 56 kb)

  • P_taeda_216-COS-genes-shared-with-ARP (FASTA 175 kb)

  • P_trichocarpa-753-COS-genes-shared-with-ARP (FASTA 338 kb)

  • Poplar-9605-single-copy-genes-locat-annot (FASTA 3290 kb)

  • rice-12004-single-hits (FASTA 3849 kb)

Table 1S

contigs ESTs ID (XLS 10230 kb)

Table 2S

COS summary (XLS 9884 kb)

Table 3S

26 COS annotation (XLS 46 kb)

Table 4S

753 COS trees (XLS 526 kb)

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Krutovsky, K.V., Elsik, C.G., Matvienko, M. et al. Conserved ortholog sets in forest trees. Tree Genetics & Genomes 3, 61–70 (2006). https://doi.org/10.1007/s11295-006-0052-2

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  • DOI: https://doi.org/10.1007/s11295-006-0052-2

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