Chromosome-Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution

Area of Science:

• Genomics
• Evolutionary Biology
• Ichthyology

Background:

• The percomorph fish clade Gobioidei includes over 2200 species across diverse aquatic habitats.
• Understanding the genetic basis of Gobioidei species diversification is crucial for evolutionary studies.

Purpose of the Study:

• To investigate the genomic underpinnings of species diversification in Gobioidei.
• To analyze the genome of the loach goby (Rhyacichthys aspro) as an early-diverging representative.

Main Methods:

• Genome sequencing and annotation of Rhyacichthys aspro.
• Comparative genomic analysis with nine other Gobioidei species.
• Identification and analysis of transposable elements (TEs) and genes under selection.

Main Results:

• The loach goby has the smallest genome (594 Mb) within Gobioidei.
• Genome size and TE content, especially DNA transposons, increase with species diversity.
• DNA transposon proliferation correlates with substitution rates, suggesting a role in mutation and adaptation.
• Rhyacichthys aspro exhibits unique gene profiles related to sensory systems (synaptic function), neurocranium development, and renal function, adapted for its morphology and life cycle.

Conclusions:

• Proliferation of DNA transposons is a key driver of Gobioidei diversification and adaptability.
• The loach goby genome highlights specific adaptations for survival in strong currents and an amphidromous lifestyle.
• Convergent evolution in body shape and osmoregulation is observed with other fish species.