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Peer-reviewedCC BY-NC 4.0Journal of Heredity

Chromosome-level genome assemblies of Southern pygmy perch (Nannoperca australis) and Yarra pygmy perch (N. obscura) reveal several miniaturization genes

  • Jonathan Sandoval-Castillo
  • Luciano B Beheregaray
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Abstract

Freshwater biodiversity is declining at alarming rates, and the biological characteristics of small freshwater fishes make them particularly vulnerable to habitat degradation and fragmentation. Pygmy perches are small Australian fishes whose populations have recently undergone rapid declines due to human-induced pressures. They also exhibit paedomorphic miniaturization, an evolutionary phenomenon whose consequences for the persistence and diversification of freshwater fishes remain unclear. Genomic resources for pygmy perches would significantly enhance both conservation efforts and evolutionary research. Here, we describe chromosome-level genome assemblies for the Southern pygmy perch (Nannoperca australis) and the Yarra pygmy perch (N. obscura). We provide evidence for high synteny among percichthyid genomes and for positive selection on size- and growth-related genes in the pygmy perch lineage. The N. australis and N. obscura assemblies are 675.7 and 653.9 Mbp in length, with scaffold N50 values of 26.98 and 26.22 Mbp, respectively. Each assembly comprises 24 pseudo-chromosomes and 890 or 1,476 contigs, with repeat contents of 22.3% and 28.1%. We predicted 26,390 and 24,654 protein-coding genes, and BUSCO completeness scores for Teleostei genes were 96.9% and 96.5%, respectively, for N. australis and N. obscura. Their genomes are comparable in quality to the best currently available percichthyid assemblies. These genomic resources will support conservation management efforts and provide a foundation for comparative studies on the adaptive significance of miniaturization.

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Cite

BibTeXRIS
BibTeX
@article{sandovalcastillo2026chromosomelevel,
  title = {{Chromosome-level genome assemblies of Southern pygmy perch (Nannoperca australis) and Yarra pygmy perch (N. obscura) reveal several miniaturization genes}},
  author = {Jonathan Sandoval-Castillo and Luciano B Beheregaray},
  journal = {Journal of Heredity},
  year = {2026},
  month = jul,
  doi = {10.1093/jhered/esag054},
  url = {https://doi.org/10.1093/jhered/esag054},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - Chromosome-level genome assemblies of Southern pygmy perch (Nannoperca australis) and Yarra pygmy perch (N. obscura) reveal several miniaturization genes
AU  - Jonathan Sandoval-Castillo
AU  - Luciano B Beheregaray
PY  - 2026
DA  - 2026/07/10
JO  - Journal of Heredity
DO  - 10.1093/jhered/esag054
UR  - https://doi.org/10.1093/jhered/esag054
AB  - Freshwater biodiversity is declining at alarming rates, and the biological characteristics of small freshwater fishes make them particularly vulnerable to habitat degradation and fragmentation. Pygmy perches are small Australian fishes whose populations have recently undergone rapid declines due to human-induced pressures. They also exhibit paedomorphic miniaturization, an evolutionary phenomenon whose consequences for the persistence and diversification of freshwater fishes remain unclear. Genomic resources for pygmy perches would significantly enhance both conservation efforts and evolutionary research. Here, we describe chromosome-level genome assemblies for the Southern pygmy perch (Nannoperca australis) and the Yarra pygmy perch (N. obscura). We provide evidence for high synteny among percichthyid genomes and for positive selection on size- and growth-related genes in the pygmy perch lineage. The N. australis and N. obscura assemblies are 675.7 and 653.9 Mbp in length, with scaffold N50 values of 26.98 and 26.22 Mbp, respectively. Each assembly comprises 24 pseudo-chromosomes and 890 or 1,476 contigs, with repeat contents of 22.3% and 28.1%. We predicted 26,390 and 24,654 protein-coding genes, and BUSCO completeness scores for Teleostei genes were 96.9% and 96.5%, respectively, for N. australis and N. obscura. Their genomes are comparable in quality to the best currently available percichthyid assemblies. These genomic resources will support conservation management efforts and provide a foundation for comparative studies on the adaptive significance of miniaturization.
SN  - 0022-1503
SN  - 1465-7333
ER  -