A proof-of-principle study: Species identification based on mitochondrial 12S rRNA gene using QNome nanopore...

Area of Science:

• Genetics
• Bioinformatics
• Forensic Science

Background:

• Accurate species identification is vital for criminal investigations and biodiversity conservation.
• DNA barcoding, particularly using the mitochondrial 12S rRNA gene, offers a reliable method due to its genetic characteristics.
• Nanopore sequencing technologies present new opportunities for rapid and portable species identification.

Purpose of the Study:

• To evaluate the applicability of the mitochondrial 12S rRNA gene for species identification using QNome nanopore sequencing.
• To develop and validate an automated species identification pipeline (ClassIdent) for QNome sequencing data.
• To assess the accuracy and efficiency of the developed pipeline in identifying animal species.

Main Methods:

• Collected 12S rRNA gene reference sequences for 120 species from Genbank.
• Developed ClassIdent, an open-source pipeline for species identification based on QNome nanopore sequencing.
• Sequenced 60 animal samples and analyzed results using ClassIdent for read assignment and consensus sequence generation.

Main Results:

• The ClassIdent pipeline successfully identified 53 out of 60 tested samples to the correct species.
• An average of 95.66% of sequencing reads were assigned to reference sequences with 99.11% similarity.
• Generated consensus sequences showed high accuracy (99.34% similarity) compared to Sanger sequences.

Conclusions:

• The study demonstrates the potential of combining the 12S rRNA gene with QNome nanopore sequencing for effective species identification.
• The ClassIdent pipeline offers a robust and automated solution for species identification from nanopore sequencing data.
• Future research should explore additional DNA barcoding markers and whole mitochondrial genome sequencing for enhanced identification capabilities.