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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
BMC Genomics. 2009; 10: 604.
Published online Dec 14, 2009. doi:  10.1186/1471-2164-10-604
PMCID: PMC2808326
The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species
Raffaele Mazza,corresponding author#1 Francesco Strozzi,#2 Andrea Caprera,3 Paolo Ajmone-Marsan,1 and John L Williams2
1Istituto di Zootecnica, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29100 Piacenza, Italy
2IDRA Lab, Parco Tecnologico Padano, via Einstein, Loc Cascina Codazza, 26900 Lodi, Italy
3CERSA, Parco Tecnologico Padano, via Einstein, Loc Cascina Codazza, 26900 Lodi, Italy
corresponding authorCorresponding author.
#Contributed equally.
Raffaele Mazza: raffaele.mazza/at/; Francesco Strozzi: francesco.strozzi/at/; Andrea Caprera: andrea.caprera/at/; Paolo Ajmone-Marsan: paolo.ajmone/at/; John L Williams: john.williams/at/
Received July 13, 2009; Accepted December 14, 2009.
With the rapid growth in the availability of genome sequence data, the automated identification of orthologous genes between species (orthologs) is of fundamental importance to facilitate functional annotation and studies on comparative and evolutionary genomics. Genes with no apparent orthologs between the bovine and human genome may be responsible for major differences between the species, however, such genes are often neglected in functional genomics studies.
A BLAST-based method was exploited to explore the current annotation and orthology predictions in Ensembl. Genes with no orthologs between the two genomes were classified into groups based on alignments, ontology, manual curation and publicly available information. Starting from a high quality and specific set of orthology predictions, as provided by Ensembl, hidden relationship between genes and genomes of different mammalian species were unveiled using a highly sensitive approach, based on sequence similarity and genomic comparison.
The analysis identified 3,801 bovine genes with no orthologs in human and 1010 human genes with no orthologs in cow, among which 411 and 43 genes, respectively, had no match at all in the other species. Most of the apparently non-orthologous genes may potentially have orthologs which were missed in the annotation process, despite having a high percentage of identity, because of differences in gene length and structure. The comparative analysis reported here identified gene variants, new genes and species-specific features and gave an overview of the other side of orthology which may help to improve the annotation of the bovine genome and the knowledge of structural differences between species.
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