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Open Access Research article

A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers

Nathalie Pavy1*, Betty Pelgas12, Jérôme Laroche3, Philippe Rigault14, Nathalie Isabel12 and Jean Bousquet1

Author Affiliations

1 Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec G1V 0A6, Canada

2 Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 Rue du PEPS, CP 10380, Succ. Sainte-Foy, Québec, Québec G1V 4C7, Canada

3 Bioinformatics Platform, Institute for Systems and Integrative Biology, Université Laval, Québec, Québec G1V 0A6, Canada

4 Gydle Inc., 1363 Avenue Maguire, Québec, Québec G1T 1Z2, Canada

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BMC Biology 2012, 10:84  doi:10.1186/1741-7007-10-84

Published: 26 October 2012

Additional files

Additional file 1:

Composite spruce gene linkage map. This composite linkage map consisted of 1,801 genes, including 1,743 genes from white spruce and 58 genes from black spruce, positioned onto the 12 linkage groups corresponding to the 12 spruce chromosomes. Genes highlighted in grey were positioned on both spruce genomes and genes written in red were positioned only onto the black spruce composite map [82]. All other genes were positioned on the white spruce composite map. Genetic distances are indicated in cM (Kosambi) at the left of each linkage group. For magnification, zoom into the figure.

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Additional file 2:

Parameters of expanded main gene linkage map for white spruce.

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Additional file 3:

Parameters of the composite genus-level spruce gene linkage map.

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Additional file 4:

Gene position along the spruce chromosomes, accessions, sequence and annotation.

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Additional file 5:

Gene ontology distribution. Gene ontology terms assigned to the 1,801 mapped spruce genes at the level 3 of the (A) molecular functions and (B) biological processes. Only categories including five genes or more are represented.

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Additional file 6:

Gene families and number of genes mapped on the spruce genome for each family.

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Additional file 7:

Over-representation of gene ontology classes in the gene-rich regions based on Fisher exact tests.

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Additional file 8:

Over-representation of gene ontology classes in the gene arrays based on Fisher exact tests.

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Additional file 9:

Cluster of co-localizing genes: annotation and expression. We collected expression data from a transcriptomic database covering eight tissues and including mature xylem, juvenile xylem, phelloderm (including phloem), young needles, vegetative buds, megagametophytes, adventitious roots and embryogenic cells [30]. A level of expression was assigned to each tissue and to each gene represented on a microarray. Correlation tests were performed based on the level of expression. Co-expression was declared if the P-value was lower than 0.01 (**) or 0.05 (*).

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Additional file 10:

Conservation between the chromosomes from Picea and Pinus taeda or Pinus pinaster.

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Additional file 11:

Coordinates and annotation of the conserved genes found on homoeologous Picea and Pinus chromosomes.

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Additional file 12:

Unrooted majority-rule bootstrap trees obtained with the neighbour-joining (NJ) and the maximum parsimony (MP) methods for 157 gene families of seed plants.

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