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Genome sequence of the Brown Norway rat yields insights into mammalian evolutionRat Genome Sequencing Project ConsortiumNature200442849352115057822

Richard A. Gibbs, +226 more
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Abstract
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality ‘draft’ covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

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Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets

TL;DR: In a four-genome analysis of 3' UTRs, approximately 13,000 regulatory relationships were detected above the estimate of false-positive predictions, thereby implicating as miRNA targets more than 5300 human genes, which represented 30% of the gene set.
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Ewan Birney, +320 more
- 14 Jun 2007 - 
TL;DR: Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

TL;DR: A comprehensive search for conserved elements in vertebrate genomes is conducted, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu rubripes), using a two-state phylogenetic hidden Markov model (phylo-HMM).
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

LaDeana W. Hillier, +174 more
- 09 Dec 2004 - 
TL;DR: A draft genome sequence of the red jungle fowl, Gallus gallus, provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes.
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Genome sequence, comparative analysis and haplotype structure of the domestic dog

Kerstin Lindblad-Toh, +241 more
- 08 Dec 2005 - 
TL;DR: A high-quality draft genome sequence of the domestic dog is reported, together with a dense map of single nucleotide polymorphisms (SNPs) across breeds, to shed light on the structure and evolution of genomes and genes.
References
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Robert H. Waterston, +222 more
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TL;DR: The results of an international collaboration to produce a high-quality draft sequence of the mouse genome are reported and an initial comparative analysis of the Mouse and human genomes is presented, describing some of the insights that can be gleaned from the two sequences.