Reads in a haystack: extracting complete mitogenome sequences hidden in baculovirus datasets

Area of Science:

• Genomics and Molecular Biology
• Entomology
• Bioinformatics

Background:

• The complete mitochondrial genome (mitogenome) of Thaumatotibia leucotreta, a significant economic pest, was previously unavailable.
• Availability of mitogenome sequences is crucial for developing molecular techniques for pest identification and population monitoring.

Purpose of the Study:

• To determine if next-generation sequencing (NGS) datasets for entomopathogenic viruses contain host mitochondrial DNA reads.
• To assemble and analyze the complete mitogenome of Thaumatotibia leucotreta from viral NGS data.

Main Methods:

• Analysis of 28 NGS datasets generated for Cryptophlebia leucotreta granulovirus (CrleGV).
• Bioinformatic assembly of complete mitogenomes from sufficient host DNA reads within the datasets.
• Identification of all standard mitochondrial genes (protein-coding, tRNAs, rRNAs) and phylogenetic analysis.

Main Results:

• Three NGS datasets yielded sufficient reads for the assembly of complete Thaumatotibia leucotreta mitogenomes.
• All 13 protein-coding genes, 22 tRNAs, and 2 rRNAs were identified, consistent with other Grapholitini tribe members.
• Phylogenetic analysis placed the sequences within the Olethreutinae subfamily and Thaumatotibia leucotreta clade.
• Analysis revealed up to 75 single nucleotide variations (SNVs) among the assembled Thaumatotibia leucotreta mitogenomes.

Conclusions:

• The study successfully generated complete mitogenome sequences for Thaumatotibia leucotreta using existing viral NGS data.
• This methodology demonstrates a viable approach for generating novel lepidopteran mitogenome sequences from related baculovirus NGS datasets.
• The obtained mitogenome data can facilitate the development of advanced molecular tools for pest management and population studies.