Comparative analyses of multi-species sequences from targeted genomic regions

Abstract

The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.

Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response

“…Thus, the gene list comprises 2832 pig sequences and 125 human sequences and the final set consists of 2957 oligonucleotides. GO annotations of the probes were retrieved using the corresponding human RefSeq IDs [63,64]. Oligonucleotides were all designed and synthesized by Operon Company.…”

Isolation, Characterization, and Evolutionary Divergence of Mouse RNase 6: Evidence for Unusual Evolution in Rodents

“…The RNase 6 gene tree reconstructed with the neighbor-joining method recapitulated expected phylogeny, indicating that the sequences obtained are orthologous. Artiodactyls and Perissodactyls are thought to be outgroups of primates and rodents (Murphy et al 2001;Thomas et al 2003). Thus, the evolutionary rate of RNase 6 in rodents can be compared with that in primates using the horse and cow sequences as outgroups.…”

In vivo characterization of a vertebrate ultraconserved enhancer

“…This has been accomplished through comparison of the human genome with the genomes of a wide-range of species from primates to fish [1][2][3][4]. The underlying success of this strategy is based on comparing sufficiently divergent genomes to distinguish neutral versus functionally constrained sequence elements [5,6].…”