A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus).

Camilla Lo Cascio Sætre,Alan Tracey,William Chow,Fabrice Eroukhmanoff,Rose Thorogood,Katja Rönkä,Kerstin Howe,Sarah Pelan,James Torrance,Ole K Tørresen,Edward Kluen,Kjetill S Jakobsen,Bonnie Fraser

doi:10.1093/gbe/evab212

Camilla Lo Cascio Sætre, Alan Tracey + Show 11 more

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https://doi.org/10.1093/gbe/evab212

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Abstract

The reed warbler (Acrocephalus scirpaceus) is a long-distance migrant passerine with a wide distribution across Eurasia. This species has fascinated researchers for decades, especially its role as host of a brood parasite, and its capacity for rapid phenotypic change in the face of climate change. Currently, it is expanding its range northwards in Europe, and is altering its migratory behavior in certain areas. Thus, there is great potential to discover signs of recent evolution and its impact on the genomic composition of the reed warbler. Here, we present a high-quality reference genome for the reed warbler, based on PacBio, 10×, and Hi-C sequencing. The genome has an assembly size of 1,075,083,815 bp with a scaffold N50 of 74,438,198 bp and a contig N50 of 12,742,779 bp. BUSCO analysis using aves_odb10 as a model showed that 95.7% of BUSCO genes were complete. We found unequivocal evidence of two separate macrochromosomal fusions in the reed warbler genome, in addition to the previously identified fusion between chromosome Z and a part of chromosome 4A in the Sylvioidea superfamily. We annotated 14,645 protein-coding genes, and a BUSCO analysis of the protein sequences indicated 97.5% completeness. This reference genome will serve as an important resource, and will provide new insights into the genomic effects of evolutionary drivers such as coevolution, range expansion, and adaptations to climate change, as well as chromosomal rearrangements in birds.

Highlights

The ecology and evolution of the reed warbler (Acrocephalus scirpaceus) has been of interest for over 40 years (Thorogood et al 2019) as it is one of the favorite host species of the broodparasitic common cuckoo (Cuculus canorus) (Davies and Brooke 1989; Stokke et al 2018)
The completeness of the assembled genome is high: of the 8,338 universal avian single-copy orthologs, we identified 7,978 complete Benchmarking Universal Single-Copy Orthologs (BUSCO) (95.7%), including 7,920 single-copy (95.0%), and 58 duplicated BUSCOs (0.7%)
We present the first assembled and annotated genome for the reed warbler A. scirpaceus

Summary

Introduction

The ecology and evolution of the reed warbler (Acrocephalus scirpaceus) has been of interest for over 40 years (Thorogood et al 2019) as it is one of the favorite host species of the broodparasitic common cuckoo (Cuculus canorus) (Davies and Brooke 1989; Stokke et al 2018). They are expanding their breeding range northwards into Fennoscandia (J€arvinen and Ulfstrand 1980; Røed 1994; Stolt 1999; Brommer et al 2012), and have generally increased their productivity following the rise in temperature (Schaefer et al 2006; Eglington et al 2015; Meller et al 2018) They are showing rapid changes in phenology (Halupka et al 2008), and migratory behavior; instead of crossing the Sahara, monitoring suggests that some reed warblers remain on the Iberian Peninsula over winter (Chamorro et al 2019). The genome will be an important resource in the study of chromosomal rearrangements in birds

Results and Discussion

Conclusion

Materials and Methods

Literature Cited