The genome of a songbird. Nature

The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.
Nature (Impact Factor: 41.46). 04/2010; 464(7289):757-62. DOI: 10.1038/nature08819
Source: PubMed

ABSTRACT The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.

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Available from: Niclas Backstrom, Sep 28, 2015
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    • "CR1 retroelements are the most abundant, dominant group of TEs in some of the major lineages of amniotes (Shedlock et al. 2007). This applies to the genomes of birds (Hillier et al. 2004; Warren et al. 2010), crocodilians (Green et al. 2014), turtles (Shaffer et al. 2013), and snakes (Castoe et al. 2013), whereas mammalian genomes exhibit dominance of L1 or L2 LINEs (Lander et al. 2001; Mikkelsen et al. 2007; Warren et al. 2008) and the anole lizard genome contains various nearly equally dominant TEs (i.e., CR1 LINEs, L1 LINEs, L2 LINEs, LTR retroposons, DNA transposons) (Novick et al. 2009; Alfö ldi et al. 2011; Tollis and Boissinot 2011). "
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    ABSTRACT: Chicken repeat 1 (CR1) retroposons are Long INterspersed Elements (LINEs) that are ubiquitous within amniote genomes and constitute the most abundant family of transposed elements in birds, crocodilians, turtles, and snakes. They are also present in mammalian genomes, where they reside as numerous relics of ancient retroposition events. Yet, despite their relevance for understanding amniote genome evolution, the diversity and evolution of CR1 elements has never been studied on an amniote-wide level. We reconstruct the temporal and quantitative activity of CR1 subfamilies via presence/absence analyses across crocodilian phylogeny and comparative analyses of twelve crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our large-scale phylogenetic analysis of amniote CR1 subfamilies suggest the presence of at least seven ancient CR1 lineages in the amniote ancestor; and amniote-wide analyses of CR1 successions and quantities reveal differential retention (presence of ancient relics or recent activity) of these CR1 lineages across amniote genome evolution. Interestingly, birds and lepidosaurs retained the fewest ancient CR1 lineages among amniotes and also exhibit smaller genome sizes. Our study is the first to analyze CR1 evolution in a genome-wide and amniote-wide context and the data strongly suggest that the ancestral amniote genome contained myriad CR1 elements from multiple ancient lineages, and remnants of these are still detectable in the relatively stable genomes of crocodilians and turtles. Early mammalian genome evolution was thus characterized by a drastic shift from CR1 prevalence to dominance and hyperactivity of L2 LINEs in monotremes and L1 LINEs in therians.
    Genome Biology and Evolution 12/2014; 7(1). DOI:10.1093/gbe/evu256 · 4.23 Impact Factor
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    • "Among amniote vertebrates, birds possess among the smallest genomes and the lowest levels of repetitive elements [1]–[3]. These two characteristics make their genomes relatively inexpensive to sequence and also make mapping and assembling genomic sequencing reads computationally more tractable. "
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    ABSTRACT: As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.
    PLoS ONE 09/2014; 9(9):e106649. DOI:10.1371/journal.pone.0106649 · 3.23 Impact Factor
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    • "Gossmann et al. GBE defined high-, low-, and very low-recombination regions (Backströ m et al. 2010; Warren et al. 2010, see Materials and Methods). Genes in high-recombination regions show a reduction regarding their median o value when compared with either very low-or low-recombination regions (MWU, P = 0.001 and P = 0.002, respectively), which is consistent with the pattern found above. "
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    ABSTRACT: Determining the rate of protein evolution and identifying the causes of its variation across the genome are powerful ways to understand forces that are important for genome evolution. By using a multi-tissue transcriptome data set from great tit (Parus major), we analysed patterns of molecular evolution between two passerine birds, great tit and zebra finch (Taeniopygia guttata), using the chicken genome (Gallus gallus) as an outgroup. We investigated whether a special feature of avian genomes, the highly variable recombinational landscape, modulates the efficacy of natural selection through the effects of Hill-Robertson interference, which predicts that selection should be more effective in removing deleterious mutations and incorporating beneficial mutations in high-recombination regions than in low-recombination regions. In agreement with these predictions, genes located in low-recombination regions tend to have a high proportion of neutrally evolving sites and relaxed selective constraint on sites subject to purifying selection, whereas genes that show strong support for past episodes of positive selection appear disproportionally in high-recombination regions. There is also evidence that genes located in high-recombination regions tend to have higher gene expression specificity than those located in low-recombination regions. Furthermore, more compact genes (i.e., those with fewer/shorter introns or shorter proteins) evolve faster than less compact ones. In sum, our results demonstrate that transcriptome sequencing is a powerful method to answer fundamental questions about genome evolution in non-model organisms.
    Genome Biology and Evolution 07/2014; 6(8). DOI:10.1093/gbe/evu157 · 4.23 Impact Factor
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