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Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia)

By Carson Holt, Michael Campbell, David A. Keays, Nathaniel Edelman, Aurélie Kapusta, Emily Maclary, Eric T. Domyan, Alexander Suh, Wesley C. Warren, Mark Yandell, M. Thomas P. Gilbert, and Michael D. Shapiro

 Shapiro Lab, Department of Biology, University of Utah

Intensive selective breeding of the domestic rock pigeon (Columba livia) has resulted in more than 350 breeds that display extreme differences in morphology and behavior (Levi 1986; Domyan and Shapiro 2017). The large phenotypic differences among different breeds make them a useful model for studying the genetic basis of radical phenotypic changes, which are more typically found among different species rather than within a single species.

In genetic and genomic studies of C. livia, linkage analysis is important for identifying genotypes associated with specific phenotypic traits of interest (Domyan and Shapiro 2017); however, short scaffold sizes in the Cliv_1.0 draft reference assembly (Shapiro et al. 2013) hinder computationally-based comparative analyses. Short scaffolds also make it more difficult to identify structural changes, such as large insertions or deletions, that are responsible for traits of interest (Domyan et al. 2014; Kronenberg et al. 2015). 

Here we present the Cliv_2.1 reference assembly and an updated gene annotation set. The new assembly greatly improves scaffold length over the previous draft reference assembly, and updated gene annotations show improved concordance with both transcriptome and protein homology evidence.

Read the full article as it appears in G3.

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