Pichia pastoris Genomic Resources: Accessibility, Recommendations, and Pitfalls

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Reliable genomic data is crucial for advancing genome engineering.
• Existing genomic databases vary in completeness and utility.
• Pichia pastoris has been reclassified into Komagataella phaffii, Komagataella pastoris, and Komagataella kurtzmanii.

Purpose of the Study:

• To provide an overview of genome references and annotations for industrially relevant Komagataella (formerly Pichia pastoris) strains.
• To offer guidance on selecting the most suitable genomic reference for specific genome engineering applications.
• To detail important databases, data types, and access methods using Komagataella phaffii CBS 7435 as a case study.

Main Methods:

• Literature review of available genomic databases and annotations.
• Comparative analysis of genomic resources for different Komagataella species.
• Demonstration of data access methods for K. phaffii CBS 7435.

Main Results:

• Identification of key genome references and annotation databases for industrial Komagataella strains.
• A guideline for choosing appropriate genomic resources based on research objectives.
• Practical examples of accessing and utilizing genomic data for K. phaffii CBS 7435.

Conclusions:

• Effective utilization of genomic resources is essential for successful genome engineering in Komagataella.
• Understanding the landscape of available databases and annotations enables informed selection of tools.
• This chapter serves as a practical guide for researchers working with these industrially important yeasts.