MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in 10 Years

Area of Science:

• Marine Biology
• Genomics
• Bioinformatics

Background:

• MitoFish, MitoAnnotator, and MiFish Pipeline are established resources for fish mitochondrial genome (mitogenome) data and analysis.
• Existing platforms receive significant global traffic but require performance and functionality enhancements.

Purpose of the Study:

• To present essential updates to the MitoFish Suite, improving its reference datasets, search capabilities, annotation speed, eDNA analysis, and comparative functions.
• To enhance the overall intuitiveness, effectiveness, and reliability of the online platforms.

Main Methods:

• Enrichment of reference datasets for fish mitogenomes.
• Implementation of enhanced searching functionalities.
• Optimization of genome annotation and eDNA analysis pipelines, including sequencing error denoising.
• Addition of a multisample comparative analysis feature.

Main Results:

• Substantially faster genome annotation and eDNA analysis.
• Improved accuracy through sequencing error denoising.
• Enhanced data accessibility and searchability.
• New capabilities for multisample comparative analysis.

Conclusions:

• The updated MitoFish Suite offers a more intuitive, effective, and reliable platform for fish mitogenome research and eDNA metabarcoding.
• These improvements aim to further support the global scientific community in fish biodiversity and conservation studies.