Whole-genome sequence of the African Common Reed Frog (Hyperolius viridiflavus viridiflavus) from Ethiopia

Sep 29, 2026

Amphibians of the Afrobatrachia clade are a major component of sub-Saharan Africa’s biodiversity but remain underrepresented in genomic databases. The study reports the first whole-genome assembly of the Common Reed Frog, Hyperolius viridiflavus viridiflavus, from Ethiopia. Using PacBio HiFi sequencing and de novo assembly, the genome totals 4.4 Gb with BUSCO completeness of 84.2% and 29,809 annotated genes. Mitogenome and phylogenomic analyses confirm species distinctiveness and expand genomic resources to support systematics and conservation.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages10

Reading Time25 min

AccessFree to download

Genome Report

Introduction

G3, 2026, 16(1), jkaf257 [https://doi.org/10.1093/g3journal/jkaf257](https://doi.org/10.1093/g3journal/jkaf257) Advance Access Publication Date: 27 October 2025 Genome Report Whole-genome sequence of the African Common Reed Frog (Hyperolius viridiflavus viridiflavus) from Ethiopia Lucinda P. Lawson , 1 ,2 ,3 ,* Sandra Goutte ,4 H. Christoph Liedtke 5 1Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, United States 2Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, United States 3Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, United States 4Division of Science, New York University Abu Dhabi, PO Box: 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates 5Department of Evolution and Ecology, Doñana Biological Station (CSIC), 41092, La Cartuja Island, Seville, Spain *Corresponding author. Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, United States. [Email:lucinda.lawson@cchmc.org](Email:lucinda.lawson@cchmc.org) Amphibians of the Afrobatrachia clade represent a major component of sub-Saharan Africa’s biodiversity, yet they remain underrepresented in genomic databases. Here, we present the first whole-genome assembly of the Common Reed Frog, Hyperolius viridiflavus viridiflavus Ahl, 1931 from Ethiopia, a member of the H. viridiflavus superspecies complex. The genome was sequenced using PacBio HiFi long-read technology and assembled de novo with HiFiasm, resulting in a 4.4 Gb assembly across 10,009 contigs with an N50 of 1.09 Mb. Genome completeness had a BUSCO score of 84.2%, with 29,809 annotated genes, including 27,983 protein-coding genes and 942 long non-coding RNAs. Despite a similar estimated size, scaffolding against the chromosome-level genome of Hyperolius rigge∼ nbachi Nieden, 1910 revealed low mapping coverage (0.0654 per base across 1 Mb windows), likely due to phylogenetic divergence ( 14 Mya) and high repeat content. The complete mitochondrial genome (23,453 bp) was also assembled and annotated, revealing structural differences from closely related species. Phylogenomic analyses using 416 single-copy BUSCO genes and mitochondrial 16S sequences confirmed the distinctiveness of H. v. viridiflavus within the Hyperoliidae. As only one other Afrobatrachian genome exceeds 50% completeness in public databases ( H. riggenbachi), this genome expands the resources available for African frogs and supports future research in systematics and conservation. Further, when considering the complex taxonomy and evolutionary history of the H. viridiflavus superspecies complex, this genome can serve as a tool for species delimitation and conservation when compared to other species and subspecies within the clade. Keywords: genome assembly; Afrobatrachia; amphibian; species-complex Introduction The African Common Reed Frog, Hyperolius viridiflavus , represents a superspecies complex of ∼60 species and subspecies found throughout sub-Saharan Africa (Duméril and Bibron 1841 ; Schiøtz 1975 ; Channing and Howell 2006) . Within this complex there are a number of named species and subspecies with uncertain taxonomic status or geographical boundaries (Schiøtz 1999 ; Wieczorek et al. 2001 ; Portik et al. 2019 ; Channing 2022) . Understanding the evolution and diversification of this radiation first requires creating genomic resources, yet whole genome resources for amphibians in general are scarce (Kosch et al. 2024) . Afrobatrachia, consisting of four families that are endemic to the African continent (Arthroleptidae, Brevicipitidae, Hemisotidae, and Hyperoliidae) have been entirely absent for whole genomes prior to 2024. In comparison to other anuran lineages, Afrobatrachia are therefore undersampled despite representing more than half of the diversity of frogs on the African continent, leaving a large section of th

FAQs

What genome resources does the article provide for Hyperolius viridiflavus viridiflavus?

It provides the first whole-genome assembly for this Ethiopian Common Reed Frog, along with an assembled and annotated mitochondrial genome.

How was the genome assembly generated and evaluated for quality?

The genome was sequenced with PacBio HiFi long reads and assembled de novo using HiFiasm; completeness was assessed using BUSCO, yielding 84.2%.

How do mitochondrial and phylogenomic analyses support the study’s conclusions?

Phylogenomic analyses using single-copy BUSCO genes and mitochondrial 16S sequences confirm the distinctiveness of H. v. viridiflavus within the Hyperoliidae.

Sep 29, 2026

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