Functionally annotated Corylus assembly

This file lists all 13,690 Coryllus avellana contigs with their annotation. We considered, for each contig (col 1), the best blast hit found in the Swissprot database (col2) and in the Non-redundant nucleotide database (col3). We associated to these contigs GO terms. GO terms IDs are listed in col4 and GO terms definition is listed in col 5 (MF: Molecular function; CC: Cellular component; BP: Biological process)

Image_2_Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand.TIFF

<p>Anticipating the evolutionary responses of long-lived organisms, such as trees, to environmental changes, requires the assessment of genetic variation of adaptive traits in natural populations. To this end, high-density markers are needed to calculate genomic relatedness between individuals allowing to estimate the genetic variance of traits in wild populations. We designed a targeted capture-based, next-generation sequencing assay based on the highly heterozygous pedunculate oak (Quercus robur) reference genome, for the sequencing of 3 Mb of genic and intergenic regions. Using a mixed stand of 293 Q. robur and Q. petraea genotypes we successfully captured over 97% of the target sequences, corresponding to 0.39% of the oak genome, with sufficient depth (97×) for the detection of about 190,000 SNPs evenly spread over the targeted regions. We validated the technique by evaluating its reproducibility, and comparing the genomic relatedness of trees with their known pedigree relationship. We explored the use of the technique on other related species and highlighted the advantages and limitations of this approach. We found that 92.07% of target sequences in Q. suber and 70.36% of sequences in Fagus sylvatica were captured. We used this SNP resource to estimate genetic relatedness in the mixed oak stand. Mean pairwise genetic relatedness was low within each species with a few values exceeding 0.25 (half-sibs) or 0.5 (full-sibs). Finally, we applied the technique to a long-standing issue in population genetics of trees regarding the relationship between inbreeding and components of fitness. We found very weak signals for inbreeding depression for reproductive success and no signal for growth within both species.</p

Image_1_Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand.TIFF

<p>Anticipating the evolutionary responses of long-lived organisms, such as trees, to environmental changes, requires the assessment of genetic variation of adaptive traits in natural populations. To this end, high-density markers are needed to calculate genomic relatedness between individuals allowing to estimate the genetic variance of traits in wild populations. We designed a targeted capture-based, next-generation sequencing assay based on the highly heterozygous pedunculate oak (Quercus robur) reference genome, for the sequencing of 3 Mb of genic and intergenic regions. Using a mixed stand of 293 Q. robur and Q. petraea genotypes we successfully captured over 97% of the target sequences, corresponding to 0.39% of the oak genome, with sufficient depth (97×) for the detection of about 190,000 SNPs evenly spread over the targeted regions. We validated the technique by evaluating its reproducibility, and comparing the genomic relatedness of trees with their known pedigree relationship. We explored the use of the technique on other related species and highlighted the advantages and limitations of this approach. We found that 92.07% of target sequences in Q. suber and 70.36% of sequences in Fagus sylvatica were captured. We used this SNP resource to estimate genetic relatedness in the mixed oak stand. Mean pairwise genetic relatedness was low within each species with a few values exceeding 0.25 (half-sibs) or 0.5 (full-sibs). Finally, we applied the technique to a long-standing issue in population genetics of trees regarding the relationship between inbreeding and components of fitness. We found very weak signals for inbreeding depression for reproductive success and no signal for growth within both species.</p

Image_7_Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand.TIFF

<p>Anticipating the evolutionary responses of long-lived organisms, such as trees, to environmental changes, requires the assessment of genetic variation of adaptive traits in natural populations. To this end, high-density markers are needed to calculate genomic relatedness between individuals allowing to estimate the genetic variance of traits in wild populations. We designed a targeted capture-based, next-generation sequencing assay based on the highly heterozygous pedunculate oak (Quercus robur) reference genome, for the sequencing of 3 Mb of genic and intergenic regions. Using a mixed stand of 293 Q. robur and Q. petraea genotypes we successfully captured over 97% of the target sequences, corresponding to 0.39% of the oak genome, with sufficient depth (97×) for the detection of about 190,000 SNPs evenly spread over the targeted regions. We validated the technique by evaluating its reproducibility, and comparing the genomic relatedness of trees with their known pedigree relationship. We explored the use of the technique on other related species and highlighted the advantages and limitations of this approach. We found that 92.07% of target sequences in Q. suber and 70.36% of sequences in Fagus sylvatica were captured. We used this SNP resource to estimate genetic relatedness in the mixed oak stand. Mean pairwise genetic relatedness was low within each species with a few values exceeding 0.25 (half-sibs) or 0.5 (full-sibs). Finally, we applied the technique to a long-standing issue in population genetics of trees regarding the relationship between inbreeding and components of fitness. We found very weak signals for inbreeding depression for reproductive success and no signal for growth within both species.</p

Image_4_Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand.TIFF

<p>Anticipating the evolutionary responses of long-lived organisms, such as trees, to environmental changes, requires the assessment of genetic variation of adaptive traits in natural populations. To this end, high-density markers are needed to calculate genomic relatedness between individuals allowing to estimate the genetic variance of traits in wild populations. We designed a targeted capture-based, next-generation sequencing assay based on the highly heterozygous pedunculate oak (Quercus robur) reference genome, for the sequencing of 3 Mb of genic and intergenic regions. Using a mixed stand of 293 Q. robur and Q. petraea genotypes we successfully captured over 97% of the target sequences, corresponding to 0.39% of the oak genome, with sufficient depth (97×) for the detection of about 190,000 SNPs evenly spread over the targeted regions. We validated the technique by evaluating its reproducibility, and comparing the genomic relatedness of trees with their known pedigree relationship. We explored the use of the technique on other related species and highlighted the advantages and limitations of this approach. We found that 92.07% of target sequences in Q. suber and 70.36% of sequences in Fagus sylvatica were captured. We used this SNP resource to estimate genetic relatedness in the mixed oak stand. Mean pairwise genetic relatedness was low within each species with a few values exceeding 0.25 (half-sibs) or 0.5 (full-sibs). Finally, we applied the technique to a long-standing issue in population genetics of trees regarding the relationship between inbreeding and components of fitness. We found very weak signals for inbreeding depression for reproductive success and no signal for growth within both species.</p

Corylus avellana CAV2 transcriptomic assembly

In this file, the 13,690 CAV2 contigs sequences are listed in fasta format

Table_1_Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand.PDF

<p>Anticipating the evolutionary responses of long-lived organisms, such as trees, to environmental changes, requires the assessment of genetic variation of adaptive traits in natural populations. To this end, high-density markers are needed to calculate genomic relatedness between individuals allowing to estimate the genetic variance of traits in wild populations. We designed a targeted capture-based, next-generation sequencing assay based on the highly heterozygous pedunculate oak (Quercus robur) reference genome, for the sequencing of 3 Mb of genic and intergenic regions. Using a mixed stand of 293 Q. robur and Q. petraea genotypes we successfully captured over 97% of the target sequences, corresponding to 0.39% of the oak genome, with sufficient depth (97×) for the detection of about 190,000 SNPs evenly spread over the targeted regions. We validated the technique by evaluating its reproducibility, and comparing the genomic relatedness of trees with their known pedigree relationship. We explored the use of the technique on other related species and highlighted the advantages and limitations of this approach. We found that 92.07% of target sequences in Q. suber and 70.36% of sequences in Fagus sylvatica were captured. We used this SNP resource to estimate genetic relatedness in the mixed oak stand. Mean pairwise genetic relatedness was low within each species with a few values exceeding 0.25 (half-sibs) or 0.5 (full-sibs). Finally, we applied the technique to a long-standing issue in population genetics of trees regarding the relationship between inbreeding and components of fitness. We found very weak signals for inbreeding depression for reproductive success and no signal for growth within both species.</p

Image_6_Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand.TIFF

<p>Anticipating the evolutionary responses of long-lived organisms, such as trees, to environmental changes, requires the assessment of genetic variation of adaptive traits in natural populations. To this end, high-density markers are needed to calculate genomic relatedness between individuals allowing to estimate the genetic variance of traits in wild populations. We designed a targeted capture-based, next-generation sequencing assay based on the highly heterozygous pedunculate oak (Quercus robur) reference genome, for the sequencing of 3 Mb of genic and intergenic regions. Using a mixed stand of 293 Q. robur and Q. petraea genotypes we successfully captured over 97% of the target sequences, corresponding to 0.39% of the oak genome, with sufficient depth (97×) for the detection of about 190,000 SNPs evenly spread over the targeted regions. We validated the technique by evaluating its reproducibility, and comparing the genomic relatedness of trees with their known pedigree relationship. We explored the use of the technique on other related species and highlighted the advantages and limitations of this approach. We found that 92.07% of target sequences in Q. suber and 70.36% of sequences in Fagus sylvatica were captured. We used this SNP resource to estimate genetic relatedness in the mixed oak stand. Mean pairwise genetic relatedness was low within each species with a few values exceeding 0.25 (half-sibs) or 0.5 (full-sibs). Finally, we applied the technique to a long-standing issue in population genetics of trees regarding the relationship between inbreeding and components of fitness. We found very weak signals for inbreeding depression for reproductive success and no signal for growth within both species.</p

Mapping of the Corylus avellana input sequences against the CAV2 assembly.

Alignments of the 836,641 Corylus avellana Roche sequences against the 13,690 CAV2 contigs in bam format

Image_3_Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand.TIFF

<p>Anticipating the evolutionary responses of long-lived organisms, such as trees, to environmental changes, requires the assessment of genetic variation of adaptive traits in natural populations. To this end, high-density markers are needed to calculate genomic relatedness between individuals allowing to estimate the genetic variance of traits in wild populations. We designed a targeted capture-based, next-generation sequencing assay based on the highly heterozygous pedunculate oak (Quercus robur) reference genome, for the sequencing of 3 Mb of genic and intergenic regions. Using a mixed stand of 293 Q. robur and Q. petraea genotypes we successfully captured over 97% of the target sequences, corresponding to 0.39% of the oak genome, with sufficient depth (97×) for the detection of about 190,000 SNPs evenly spread over the targeted regions. We validated the technique by evaluating its reproducibility, and comparing the genomic relatedness of trees with their known pedigree relationship. We explored the use of the technique on other related species and highlighted the advantages and limitations of this approach. We found that 92.07% of target sequences in Q. suber and 70.36% of sequences in Fagus sylvatica were captured. We used this SNP resource to estimate genetic relatedness in the mixed oak stand. Mean pairwise genetic relatedness was low within each species with a few values exceeding 0.25 (half-sibs) or 0.5 (full-sibs). Finally, we applied the technique to a long-standing issue in population genetics of trees regarding the relationship between inbreeding and components of fitness. We found very weak signals for inbreeding depression for reproductive success and no signal for growth within both species.</p