Evidence of distinct gene functional patterns in GC-poor and GC-rich isochores in Bos taurus |
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Authors: | S Arhondakis M Milanesi T Castrignanò S Gioiosa A Valentini G Chillemi |
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Institution: | 1. Bioinformatics and Computational Science (BioCoS), Boniali 11-19, Chania, 73134 Crete, Greece;2. Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, 16050-680 R. Clóvis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil;3. SCAI – Super Computing Applications and Innovation Department, CINECA, Rome, Italy;4. Department for Innovation in Biological, Agro-food and Forest Systems, DIBAF, University of Tuscia, via S. Camillo de Lellis s.n.c, 01100 Viterbo, Italy |
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Abstract: | Vertebrate genomes are mosaics of megabase-size DNA segments with a fairly homogeneous base composition, called isochores. They are divided into five families characterized by different guanine-cytosine (GC) levels and linked to several functional and structural properties. The increased availability of fully sequenced genomes allows the investigation of isochores in several species, assessing their level of conservation across vertebrate genomes. In this work, we characterized the isochores in Bos taurus using the ARS-UCD1.2 genome version. The comparison of our results with the well-studied human isochores and those of other mammals revealed a large conservation in isochore families, in number, average GC levels and gene density. Exceptions to the established increase in gene density with the increase in isochores (GC%) were observed for the following gene biotypes: tRNA, small nuclear RNA, small nucleolar RNA and pseudogenes that have their maximum number in H2 and H1 isochores. Subsequently, we assessed the ontology of all gene biotypes looking for functional classes that are statistically over- or under-represented in each isochore. Receptor activity and sensory perception pathways were significantly over-represented in L1 and L2 (GC-poor) isochores. This was also validated for the horse genome. Our analysis of housekeeping genes confirmed a preferential localization in GC-rich isochores, as reported in other species. Finally, we assessed the SNP distribution of a bovine high-density SNP chip across the isochores, finding a higher density in the GC-rich families, reflecting a potential bias in the chip, widely used for genetic selection and biodiversity studies. |
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Keywords: | bovine DNA chip cow genome composition isochores olfactory receptor |
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