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. 2023 Jun 1;13(6):jkad088.
doi: 10.1093/g3journal/jkad088.

An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca)

Valentina Peona  1 , Octavio Manuel Palacios-Gimenez  1   2   3 , Dave Lutgen  4   2   5 , Remi André Olsen  6 , Niloofar Alaei Kakhki  2 , Pavlos Andriopoulos  7 , Vasileios Bontzorlos  8 , Manuel Schweizer  9   4 , Alexander Suh  1   10 , Reto Burri  5   4   3
Affiliations

An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca)

Valentina Peona et al. G3 (Bethesda). .

Abstract

Pervasive convergent evolution and in part high incidences of hybridization distinguish wheatears (songbirds of the genus Oenanthe) as a versatile system to address questions at the forefront of research on the molecular bases of phenotypic and species diversification. To prepare the genomic resources for this venture, we here generated and annotated a chromosome-scale assembly of the Eastern black-eared wheatear (Oenanthe melanoleuca). This species is part of the Oenanthe hispanica complex that is characterized by convergent evolution of plumage coloration and high rates of hybridization. The long-read-based male nuclear genome assembly comprises 1.04 Gb in 32 autosomes, the Z chromosome, and the mitogenome. The assembly is highly contiguous (contig N50, 12.6 Mb; scaffold N50, 70 Mb), with 96% of the genome assembled at the chromosome level and 95.5% benchmarking universal single-copy orthologs (BUSCO) completeness. The nuclear genome was annotated with 18,143 protein-coding genes and 31,333 mRNAs (annotation BUSCO completeness, 98.0%), and about 10% of the genome consists of repetitive DNA. The annotated chromosome-scale reference genome of Eastern black-eared wheatear provides a crucial resource for research into the genomics of adaptation and speciation in an intriguing group of passerines.

Keywords: Oenanthe hispanica complex; Oenanthe melanoleuca; birds; open-habitat chats; repeat content; transcriptome; transposable elements.

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Conflict of interest statement

Conflicts of interest statement The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Eastern black-eared wheatear (O. melanoleuca). The species sports a white-throated (left; Agii Pantes, Greece, June 2022) and a black-throated phenotype (right; Lesvos, Greece, May 2017) in males. © Reto Burri.
Fig. 2.
Fig. 2.
Circular sketch map of the O. melanoleuca mitogenome assembly. The outer circle shows coding sequences, rRNAs, and tRNAs. The black track on the middle circle indicates GC content. On the inner circle, positive and negative GC skews in nucleotide composition are indicated.
Fig. 3.
Fig. 3.
Repeat annotation landscapes. a) Pie chart summarizing the TE content annotated in the genome assembly. b) TE landscape. The divergence between interspersed repeat copies and their consensus sequences is shown on the X-axis as genetic distance calculated using the Kimura 2-parameter distance. The percentage of the genome assembly occupied by transposable elements is shown on the Y-axis. c) Satellite DNA landscape. The divergence between the satellite DNA consensus sequences and sequences annotated in the short-read library is shown on the X-axis as genetic distance calculated using the Kimura 2-parameter distance. The percentage of the genome (short reads) annotated as satellite DNA is shown on the Y-axis.
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