Identification of annotation artifacts concerning the chalcone synthase (CHS)

Area of Science:

• Plant molecular biology
• Bioinformatics
• Genomics

Background:

• Chalcone synthase (CHS) is a key enzyme in flavonoid biosynthesis.
• Automated annotation of plant genomes has generated numerous CHS gene entries.
• Potential inaccuracies in automatically annotated CHS gene models require investigation.

Purpose of the Study:

• To investigate apparent multiplications of chalcone synthase (CHS) domains in CHS gene models.
• To identify plant species with potentially erroneous CHS gene annotations.
• To determine the cause of observed CHS domain artifacts.

Main Methods:

• Database searches for CHS gene entries.
• Bioinformatic analysis of CHS gene models.
• Manual inspection of gene models using RNA-sequencing data.

Main Results:

• Apparent triplication of CHS domain-encoding regions was identified in CHS genes from *Macadamia integrifolia*, *Musa balbisiana*, *Musa troglodytarum*, and *Nymphaea colorata*.
• Manual review indicated these gene models are likely artificial fusions resulting from the annotation process.
• The reason for the appearance of these specific annotation artifacts remains unclear.

Conclusions:

• Automated genome annotation can produce artifacts, such as fused CHS gene models.
• Careful manual curation and validation with experimental data (e.g., RNA-seq) are crucial for accurate gene annotation.
• Further investigation is needed to understand the origin of these specific CHS annotation errors.