Tree Genetics & Genomes

, Volume 3, Issue 1, pp 61–70 | Cite as

Conserved ortholog sets in forest trees

  • Konstantin V. Krutovsky
  • Christine G. Elsik
  • Marta Matvienko
  • Alex Kozik
  • David B. NealeEmail author
Original Paper


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.


COS Cryptomeria japonica EST Ortholog Picea glauca Pinus taeda Populus trichocarpa Pseudotsuga menziesii Unique transcript 



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.

Supplementary material

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)
11295_2006_52_MOESM8_ESM.xls (9.8 mb)
Table 1S contigs ESTs ID (XLS 10230 kb)
11295_2006_52_MOESM9_ESM.xls (9.4 mb)
Table 2S COS summary (XLS 9884 kb)
11295_2006_52_MOESM10_ESM.xls (46 kb)
Table 3S 26 COS annotation (XLS 46 kb)
11295_2006_52_MOESM11_ESM.xls (514 kb)
Table 4S 753 COS trees (XLS 526 kb)


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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Konstantin V. Krutovsky
    • 1
  • Christine G. Elsik
    • 2
  • Marta Matvienko
    • 3
  • Alex Kozik
    • 4
  • David B. Neale
    • 5
    • 6
    Email author
  1. 1.Department of Forest ScienceTexas A&M UniversityCollege StationUSA
  2. 2.Department of Animal ScienceTexas A&M UniversityCollege StationUSA
  3. 3.Allometra, LLCDavisUSA
  4. 4.Genome CenterUniversity of CaliforniaDavisUSA
  5. 5.Department of Plant SciencesUniversity of CaliforniaDavisUSA
  6. 6.Institute of Forest Genetics, Pacific Southwest Research StationUS Department of Agriculture Forest ServiceDavisUSA

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