Third report on chicken genes and chromosomes


Publication of the chicken genome sequence in 2004 (International Chicken Genome Sequencing Consortium 2004) highlighted the beginning of a revolution in avian genomics. Progression of DNA sequencing technologies and data handling capabilities has also meant that genome sequencing and assembly is now a relatively simple, fast and inexpensive procedure. The success seen with the chicken genome was soon followed by the completion of the zebra finch genome (Warren et al., 2010), an important model for neurobiology (Clayton et al., 2009), again based on Sanger sequencing. In recent years the rapid advances in Next Generation Sequencing (NGS) technologies, hardware and software have meant that many more genomes can now be sequenced faster and cheaper than ever before (Metzker, 2010). The first avian genome to be sequenced by NGS methods was the turkey (Dalloul et al., 2010), which was also integrated with genetic and physical maps thus providing an assembly of high quality, even at the chromosome level. Recently, NGS has been used to sequence the genomes of a further 42 avian species, as part of the G10K initiative (Genome 10K Community of Scientists, 2009). In addition there have also been 15 other genome assemblies recently published, each with a focus on a unique aspect of avian biology, including the Japanese Quail (domestication; Kawahara-Miki et al., 2013), Puerto Rican parrot (speciation; Oleksyk et al., 2012), Scarlet Macaw (speech, intelligence and longevity; Seabury et al., 2013), Medium and Large Ground Finches (speciation; Parker et al., 2012; Rands et al., 2013), Collared and Pied flycatchers (speciation; Ellegren et al., 2012), Peregrine and Saker Falcons (predatory lifestyle; Zhan et al., 2013), rock pigeon (domestication; Shapiro et al., 2013), the Ground tit (adaptation to high altitude; Cai et al., 2013) and the Northern Bobwhite (population history; Halley et al., 2014). Through November 2014 there are currently 57 avian genome sequences completed, either published or in press (Table 1). A new project, B10K (, proposes sequencing all avian genomes; this would include all 40 orders, 231 families, 2,268 genera and 10,476 species of birds. The chicken genome remains the best described genome and is used as a reference upon which the annotations of other assemblies are based. Assembly and annotation of the genome continues to improve. However, gaps and unaligned regions remain (particularly for some of the smallest micro-chromosomes), which can cause practical problems in the analysis and annotation of important loci, especially for those representing gene families. Other approaches, such as long reads generated by Pacific Biosciences (PacBio) sequencing, chromosome sorting and optical maps are being used to resolve these assembly issues (Warren and Burt, personal communications). Specific genome features also require further study; for example, non-coding RNAs, annotation of rare transcripts, confirmation of alternatively spliced transcripts, mapping of transcription start sites and identification of conserved regions. One method by which some of these goals can be achieved is through analysis of transcriptomic sequence data, or ‘RNAseq’ data.

In Cytogenetic and Genome Research