Open Access Research article

An initial comparative map of copy number variations in the goat (Capra hircus) genome

Luca Fontanesi1*, Pier Luigi Martelli2, Francesca Beretti13, Valentina Riggio3, Stefania Dall'Olio1, Michela Colombo1, Rita Casadio2, Vincenzo Russo1 and Baldassare Portolano3

Author Affiliations

1 DIPROVAL, Sezione di Allevamenti Zootecnici, University of Bologna, Via F.lli Rosselli 107, 42123 Reggio Emilia, Italy

2 Biocomputing Group, Computational Biology Network, Dept. of Biology, University of Bologna, Via San Giacomo 9/2, 40126 Bologna, Italy

3 Dept. S.En.Fi.Mi.Zo., Sezione di Produzioni Animali, University of Palermo, Viale delle Scienze - Parco d'Orleans, 90128 Palermo, Italy

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BMC Genomics 2010, 11:639  doi:10.1186/1471-2164-11-639

Published: 17 November 2010

Additional files

Additional file 1:

List of CNVs identified in the analysed goats. The Excel file reports the chromosome, the nucleotides position of the CNV start and end (referred to the Btau_4.0 genome assembly), the size of the CNV in bp, the number of valid probes in the CNV (additional probes are included in CNV considering the position between two contiguous regions without 0.175 log2 value; see Methods for the definition of CNV), log2 mean of the probes in the CNV (see Methods), the type of CNV (gain/loss), the goat sample (C = Camosciata delle Alpi; G = Girgentana; MG = Murciano-Granadina; S = Saanaen; numbers after the breed symbols indicate the different animals used in the aCGH experiment), and the goat breed.

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Additional file 2:

List of CNVRs obtained by merging overlapping CNVs across animals. The Excel file reports the progressive CNVR number, the chromosome, the nucleotides position of the CNVR start and end (referred to the Btau_4.0 genome assembly), the size of the CNVR in bp, the number of valid probes in the CNVR (additional probes are included in CNVR considering the position between two contiguous regions without 0.175 log2 value; see Methods for the definition of CNVR), the type of CNVR (gain/loss), the frequency of CNVR in the analysed goat panel, the goat breed (C = Camosciata delle Alpi; G = Girgentana; MG = Murciano-Granadina; S = Saanaen), and the goat subject (numbers after the breed symbols indicate the different animals used in the aCGH experiment).

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Additional file 3:

Extension of CNVRs in the different chromosomes. Proportion of the CNVRs identified in goat compared to the dimension of the bovine chromosomes.

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Additional file 4:

List of cattle CNVRs reported in four other experiments [49-52]and overlapping with goat CNVRs. CNVRs identified in cattle have been merged from the four reported experiments [49-52]. Progressive CNVR number has been assigned using the complete list. CNVRs are indicated with nucleotide positions (begin and end) on the Btau_4.0 version. Information reported for the four different experiments includes the progressive number and in parenthesis the chromosome number and the nucleotide positions (start and end). The goat CNVRs are reported.

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Additional file 5:

Tables reporting the P values for the overlapping between goat and cattle CNVRs and among the four CNVR datasets available in cattle. Table S1 reports the results obtained comparing the goat CNVRs with the cattle CNVRs. Table S2 reports the results obtained comparing the different cattle datasets.

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Additional file 6:

Primers and PCR conditions used to validate goat CNVRs. The table includes the goat CNVRs number, the corresponding bovine chromosome, gene symbol, amplified gene fragment data (including Ensembl number), sequence of the PCR primers, length of the amnplified fragment and PCR conditions.

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Additional file 7:

Semiquantitative fluorescent multiplex-PCR (SQF-PCR) results obtained for different goats. The averaged SQF-PCR ratio normalized against the reference Camosciata delle Alpi goat is reported for the goats of the aCGH panel and for additional goats (additional panel) for the validated CNVs.

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Additional file 8:

Gene Ontology (GO) annotation of genes included in goat CNVRs. Ensembl cattle transcripts located in goat CNVRs have been annotated using GO for Biological process, Cellular component, and Molecular function.

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Additional file 9:

PANTHER annotation of genes included in goat CNVRs. Ensembl cattle transcripts located in goat CNVRs have been annotated using PANTHER.

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Additional file 10:

Gene ontology (GO) categories significantly overrepresented in goat CNVRs at different False Discovery Rate (FDR) levels. GO categories were Molecular function, Biological process, and Cellular component.

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Additional file 11:

PANTHER categories significantly overrepresented in goat CNVRs. PANTHER annotation has been obtained for the whole cattle genome.

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Additional file 12:

List of goat CNVRs with human orthologous genes. EntrezGene ID and gene name are reported for human orthologous genes. The file includes genes already mapped in goat and genes for which mutations in human cause or are associated with human genetic diseases (data have been retrieved from OMIM database, May 2010).

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