The genome of a songbird

Warren, Wesley C.; Clayton, David F.; Ellegren, Hans; Arnold, Arthur P.; Hillier, LaDeana W.; Künstner, Axel; Searle, Steve; White, Simon; Vilella, Albert J.; Fairley, Susan; Heger, Andreas; Kong, Lesheng; Ponting, Chris P.; Jarvis, Erich D.; Mello, Claudio V.; Minx, Pat; Lovell, Peter V.; Velho, Tarciso A. F.; Ferris, Margaret; Balakrishnan, Christopher N.; Sinha, Saurabh; Blatti, Charles; London, Sarah E.; Li, Yun; Lin, Ya-Chi; George, Julia M.; Sweedler, Jonathan V.; Southey, Bruce R.; Gunaratne, Preethi H.; Watson, Michael; Nam, Kiwoong; Backström, Niclas; Smeds, Linnéa; Nabholz, Benoît; Itoh, Yuichiro; Whitney, Osceola; Pfenning, Andreas R.; Howard, Jason T.; Volker, Martin A.; Skinner, Benjamin M.; Griffin, Darren K.; Liang, Ye; McLaren, William; Flicek, Paul; Quesada, Vı́ctor; Velasco, Gloria; López-Otín, Carlos; Puente, Xosé S.; Olender, Tsviya; Lancet, Doron; Smit, Arian F. A.; Hubley, Robert; Konkel, Miriam K.; Walker, Jerilyn A.; Batzer, Mark A.; Gu, Wanjun; Pollock, David D.; Chen, Lin; Cheng, Ze; Eichler, Evan E.; Stapley, Jessica; Slate, Jon; Ekblom, Robert; Birkhead, Tim R.; Burke, Terry; Burt, David W.; Scharff, Constance; Adam, Iris; Richard, Hugues; Sultan, Marc; Солдатов, А. В.; Lehrach, Hans; Edwards, Scott V.; Yang, Shiaw-Pyng; Li, XiaoChing; Graves, Tina; Fulton, Lucinda A.; Nelson, Joanne O.; Chinwalla, Asif T.; Hou, Shunfeng; Mardis, Elaine R.; Wilson, Richard K.

doi:10.1038/nature08819

Cited by 790 publications

(989 citation statements)

References 34 publications

Supporting

Mentioning

950

Contrasting

Unclassified

Order By: Relevance

“…(d) Interpretation of SNP genotype data SNP markers were identified from transcriptome sequencing using Roche 454 Life Sciences massive parallel sequencing technology of pools of unrelated zebra finches (Warren et al 2010), as described in Backström et al (2010). They were mapped by BLAST analysis onto the zebra finch genome (Warren et al 2010) and markers were selected to cover all assembled chromosomes with an approximately even density.…”

Section: Methodsmentioning

confidence: 99%

“…They were mapped by BLAST analysis onto the zebra finch genome (Warren et al 2010) and markers were selected to cover all assembled chromosomes with an approximately even density. SNP genotyping was performed using the Illumina GoldenGate assay on an Illumina BeadStation 500GX, at the Uppsala University SNP Technology Platform (http:// www.medsci.uu.se/molmed/snpgenotyping/index.htm).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Trisomy and triploidy are sources of embryo mortality in the zebra finch

Forstmeier

Ellegren

2010

Proc. R. Soc. B.

Self Cite

View full text Add to dashboard Cite

Hatching failure is a surprisingly common phenomenon given that natural selection constantly works against it. In birds, an average of about 10 per cent of eggs across species fail to hatch, often owing to the death of embryos. While embryo mortality owing to inbreeding is both well-documented and evolutionarily plausible, this is not true for other sources of mortality. In fact, the basis for hatching failure in natural populations remains largely unexplained. Here, we demonstrate that embryo mortality in captive zebra finches (Taeniopygia guttata) follows from chromosomal aneuploidy or polyploidy. As part of microsatellite genotyping of a captive breeding population, we found 12 individuals (3.6%) with three alleles among 331 embryos that had died during development, while there were no such cases observed among 1210 adult birds. Subsequent genotyping of 1920 single nucleotide polymorphism markers distributed across the genome in birds with three alleles at microsatellite loci, and in greater than 1000 normal birds, revealed that the aberrant karyotypes involved cases of both trisomies and triploidy. Cases of both maternally and paternally inherited trisomies resulted from non-disjunction during meiosis. Maternally inherited cases of triploidy were attributable to failure of meiosis leading to diploid eggs, while paternally inherited triploidy could have arisen either from diploid sperm or from dispermy. Our initial microsatellite screening set only had the power to detect less than 10 per cent of trisomies and by extrapolation, our data therefore tentatively suggest that trisomy might be a major cause of embryo mortality in zebra finches.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Trisomy and triploidy are sources of embryo mortality in the zebra finch

Forstmeier

Ellegren

2010

Proc. R. Soc. B.

Self Cite

View full text Add to dashboard Cite

show abstract

“…[6,12 -15]), which is probably because it was assumed that, owing to their small olfactory bulbs [16], olfaction is an unimportant sensory mode. However, the total number of olfactory receptor genes in passerines such as canaries (Serinus canaria) and blue tits (Cyanistes caeruleus) is as high as in procellariformes [17], and zebra finches (Taeniopygia guttata) have an extensive repertoire of olfactory receptor-like gene sequences [18]. The circumstances in which passerines make use of these faculties, however, have not been well identified.…”

Section: Introductionmentioning

confidence: 99%

Odour-based natal nest recognition in the zebra finch (Taeniopygia guttata), a colony-breeding songbird

Caspers

Krause

2010

Biol. Lett.

View full text Add to dashboard Cite

Passerine birds have an extensive repertoire of olfactory receptor genes. However, the circumstances in which passerine birds use olfactory signals are poorly understood. The aim of this study is to investigate whether olfactory cues play a role in natal nest recognition in fledged juvenile passerines. The natal nest provides fledglings with a safe place for sleeping and parental food provisioning. There is a particular demand in colony-breeding birds for fledglings to be able to identify their nests because many pairs breed close to each other. Olfactory orientation might thus be of special importance for the fledglings, because they do not have a visual representation of the nest site and its position in the colony when leaving the nest for the first time. We investigated the role of olfaction in nest recognition in zebra finches, which breed in dense colonies of up to 50 pairs. We performed odour preference tests, in which we offered zebra finch fledglings their own natal nest odour versus foreign nest odour. Zebra finch fledglings significantly preferred their own natal nest odour, indicating that fledglings of a colony breeding songbird may use olfactory cues for nest recognition.

show abstract

“…With new methods for obtaining reduced-representation libraries of the genome (for example, restriction digest-based methods, Miller et al, 2007 andultraconserved elements, Faircloth et al, 2012) for many individuals, phylogeographic studies may contain thousands of loci with dozens of individuals sampled. In songbirds, strong patterns of interchromosomal synteny (Kawakami et al, 2014), the published genome of the Zebra Finch (Taeniopygia guttata; Warren et al, 2010) and thousands of genetic markers across the genome allow the opportunity to investigate not only phylogeographic structure in a clade well known for its high levels of geographic differentiation (Manthey et al, 2011a), but also diversity and differentiation across chromosomes (Manthey and Spellman, 2014).…”

Section: Introductionmentioning

confidence: 99%

Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana

2015

View full text Add to dashboard Cite

With methods for sequencing thousands of loci for many individuals, phylogeographic studies have increased inferential power and the potential for applications to new questions. In songbirds, strong patterns of inter-chromosomal synteny, the published genome of a songbird and the ability to obtain thousands of genetic loci for many individuals permit the investigation of differentiation between and diversity within lineages across chromosomes. Here, we investigate patterns of differentiation and diversity in Certhia americana, a widespread North American songbird, using next-generation sequencing. Additionally, we reassess previous phylogeographic studies within the group. Based on~30 million sequencing reads and more than 16 000 single-nucleotide polymorphisms in 41 individuals, we identified a strong positive relationship between genetic differentiation and chromosome size, with a negative relationship between genetic diversity and chromosome size. A combination of selection and drift may explain these patterns, although we found no evidence for selection. Because the observed genomic patterns are very similar between widespread, allopatric clades, it is unlikely that selective pressures would be so similar across such different ecological conditions. Alternatively, the accumulation of fixed differences between lineages and loss of genetic variation within lineages due to genetic drift alone may explain the observed patterns. Due to relatively higher recombination rates on smaller chromosomes, larger chromosomes would, on average, accumulate fixed differences between lineages and lose genetic variation within lineages faster, leading to the patterns observed here in C. americana.

show abstract

The genome of a songbird

Cited by 790 publications

References 34 publications

Trisomy and triploidy are sources of embryo mortality in the zebra finch

Trisomy and triploidy are sources of embryo mortality in the zebra finch

Odour-based natal nest recognition in the zebra finch (Taeniopygia guttata), a colony-breeding songbird

Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana

Contact Info

Product

Resources

About