Genome Report:De novogenome assembly and annotation for the Taita white-eye (Zosterops silvanus)

Abstract

The Taita White-eye (Zosterops silvanus) is an endangered songbird endemic to the Taita Hills of Southern Kenya, where it is confined to small areas of fragmented forest.With diversification rates exceeding those reported in most other vertebrates, White-eyes are a prime example of a 'great speciator'. Nevertheless, we still know surprisingly little about the genomic underpinnings leading to this extraordinary fast radiation. Here, we present a draft genome assembly (ZSil_MB_1.0) for the Taita White-eye generated from a blood sample of a wild, female bird captured in the Taita Hills, Kenya. By performing a de novo assembly with linked-reads and annotation of the assembly with the MAKER pipeline, we generated a 1.069 Gb assembly with a scaffold N50 of 1.105 Mb and an L50 of 244. After quality evaluation of the assembly, we identified 92.1% of BUSCOs complete or fragmented, indicating that our de novo assembly is of high quality. This new assembly provides a genomic resource for future studies into the evolutionary and comparative genomics of this rapidly diversifying group of birds.

Hybridization may aid evolutionary rescue of an endangered East African passerine

“…In addition to the above‐mentioned indicators (mixed feeding flocks, high genetic diversity in Z. silvanus , general tendency of Zosterops to hybridize), new genomic analyses show a recent increase in the effective population size of Z. silvanus , which may be indicative of hybridization with Z. flavilateralis (see the Supplementary Material for details; cf. Engler et al, 2020 ). Hence, our findings will serve as a hypothesis for follow‐up genomic analyses once both genomes are adequately described.…”

Genome assemblies of three closely related leaf beetle species (Galerucella spp.)

“…First, for each genome, we generated one initial evidence-based annotation using both protein and transcriptome data sources. Protein databases came from the UniProt Swiss-Prot database (downloaded on 2019-11; 561,356 proteins) ( Engler et al 2020 ), as well a subset of manually selected proteins (uniport request: taxonomy: “Coleoptera [7041],” existence: “Inferred from homology [3],” 161,853 proteins). In addition to protein resources, transcriptome data containing 57,255 transcripts from G. pusilla were used as evidence for all three genomes ( Yang et al 2020 ).…”

Genome assemblies of three closely related leaf beetle species (Galerucellaspp)

“…First, for each genome, we generated one initial evidence-based annotation using both protein and transcriptome data sources. Protein databases came from the Uniprot Swiss-Prot database (downloaded on 2019-11; 561,356 proteins) (Engler et al 2020), as well a subset of manually selected proteins (uniport request: taxonomy: "Coleoptera [7041]", existence:…”