Abstract
BackgroundRecent advances in genetics and genomics present unique opportunities for enhancing our understanding of mammalian biology and evolution through detailed multi-species comparative analysis of gene organization and expression. Yet, of the more than 20,000 protein coding genes found in mammalian genomes, fewer than 10% have been examined in any detail. Here we elucidate the power of data available in publicly-accessible genomic and genetic resources by querying them to evaluate Zmat2, a minimally studied gene whose human ortholog has been implicated in spliceosome function and in keratinocyte differentiation.ResultsWe find extensive conservation in coding regions and overall structure of Zmat2 in 18 mammals representing 13 orders and spanning ~ 165 million years of evolutionary development, and in their encoded proteins. We identify a tandem duplication in the Zmat2 gene and locus in opossum, but not in other monotremes, marsupials, or other mammals, indicating that this event occurred subsequent to the divergence of these species from one another. We also define a collection of Zmat2 pseudogenes in half of the mammals studied, and suggest based on phylogenetic analysis that they each arose independently in the recent evolutionary past.ConclusionsMammalian Zmat2 genes and ZMAT2 proteins illustrate conservation of structure and sequence, along with the development and diversification of pseudogenes in a large fraction of species. Collectively, these observations also illustrate how the focused identification and interpretation of data found in public genomic and gene expression resources can be leveraged to reveal new insights of potentially high biological significance.
Highlights
Recent advances in genetics and genomics present unique opportunities for enhancing our understanding of mammalian biology and evolution through detailed multi-species comparative analysis of gene organization and expression
Mammalian ZMAT2/Zmat2 genes are poorly annotated in genomic databases Human ZMAT2 is an ortholog of yeast Snu23, a zincfinger-containing protein that is a key component of the spliceosome [12], the molecular machine responsible for the removal of introns from primary gene transcripts [13]
The human ZMAT2 gene has been incompletely characterized in the Ensembl and UCSC genomic repositories
Summary
Recent advances in genetics and genomics present unique opportunities for enhancing our understanding of mammalian biology and evolution through detailed multi-species comparative analysis of gene organization and expression. Of the more than 20,000 protein coding genes found in human and in other mammalian genomes, fewer than 10% have been studied in any detail [1,2,3] This is true despite that fact that ready access to public genomic and gene-expression databases [4] means that nearly any gene is available for intensive analysis from the molecular and cellular to the individual and population levels [5,6,7,8,9,10]. Human ZMAT2 has been mapped to the spliceosome in structural biological studies [14], even this observation has not much generated interest in the protein
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