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Assembly and annotation of 2 high-quality columbid reference genomes from sequencing of a Columba livia × Columba guinea F1 hybrid - PubMed

  • ️Mon Jan 01 2024

Assembly and annotation of 2 high-quality columbid reference genomes from sequencing of a Columba livia × Columba guinea F1 hybrid

Emily T Maclary et al. G3 (Bethesda). 2024.

Abstract

Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for columbids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for 2 columbid species, Columba livia and Columba guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general.

Keywords: Columba guinea; Columba livia; F1 hybrid; domestic pigeon; genome annotation; genome assembly.

© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.

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Conflict of interest statement

Conflicts of interest The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.

Genome assembly and annotation strategy. a, b) Representative images of C. livia a) and C. guinea a). C. livia photo: Sydney Stringham. C. guinea photo: Roy Lowry, CC BY 4.0, via iNaturalist.co.uk. c) Genome assembly strategy for haplotype-resolved C. livia and C. guinea genomes and annotations from an F1 hybrid.

Fig. 2.
Fig. 2.

Cliv_3 and Cgui_1 assemblies show major improvements in contiguity over Cliv_2.1.

Fig. 3.
Fig. 3.

AEDs for Cliv_3, Cgui_1, and Cliv_2.1 assemblies. Cliv_3 and Cgui_1 show significantly lower AED scores (P < 1E−15, t-test) than Cliv_2.1, indicating improved concordance between annotation models and RNA-seq data in the new annotations.

Fig. 4.
Fig. 4.

Repeat annotations differ between C. livia and C. guinea. a) Cumulative distribution plot of C. livia and C. guinea repeats. The Cgui_1 genome is enriched for longer repeat tracts. b) Distribution of repeat classifications in Cliv_3 and Cgui_1 assemblies.

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References

    1. Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC. 2019. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 20(1):224. doi:10.1186/s13059-019-1829-6. - DOI - PMC - PubMed
    1. B10K consortium . 2019. Columbina picui genome assembly. GenBank. GCA_013397635.1.
    1. Bao W, Kojima KK, Kohany O. 2015. Repbase update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 6(1):11. doi:10.1186/s13100-015-0041-9. - DOI - PMC - PubMed
    1. Baptista LF, Trail PW, Horblit HM. 1997. Handbook of the Birds of the World. Barcelona: Lynx Edicions. (J del Hoyo, A Elliott, & J Sargatal, Eds).
    1. Beijing Genomics Institute. 2012. Whole genome sequencing of rock pigeon. NCBI Sequence Read Archive. SRS346866.

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