Refined Pichia pastoris reference genome sequence

Area of Science:

• Microbiology
• Genomics
• Molecular Biology

Background:

• Komagataella phaffii (Pichia pastoris) is widely used for recombinant protein production and studying cellular processes.
• Previous genome sequences contained errors, gaps, and incorrectly annotated open reading frames (ORFs).

Purpose of the Study:

• To present a refined reference genome for Komagataella phaffii (Pichia pastoris).
• To improve the accuracy of genomic information for P. pastoris strains.

Main Methods:

• Genome and transcriptome sequencing from multiple P. pastoris strains.
• Manual curation of putative open reading frames (ORFs) using RNA-seq and LC-MS/MS data.
• Correction of sequence gaps, re-orientation of chromosomal fragments, and addition of new ORFs.

Main Results:

• Closed 12 major sequence gaps and corrected over 500 genomic positions.
• Manually curated and confirmed 5111 out of 5256 putative ORFs, reducing spliced genes from 797 to 571.
• Added new ORFs, re-oriented chromosomal fragments, and included predicted centromeres and plasmid sequences.

Conclusions:

• The refined reference genome provides a more accurate foundation for P. pastoris research.
• This improved genome sequence will facilitate future studies in recombinant protein production and cellular biology.
• The updated annotation and corrected sequences enhance the reliability of genomic analyses in P. pastoris.