Trimitomics: An efficient pipeline for mitochondrial assembly from transcriptomic reads in nonmodel species

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Mitochondrial genomes are valuable for phylogenetic, population, and molecular biology studies.
• Their unique genetic features make them suitable for degraded samples and recent speciation events.
• Next-generation sequencing, particularly Illumina, has increased transcriptomic data availability.

Purpose of the Study:

• To develop a robust pipeline for recovering mitochondrial genomes from RNA-sequencing resources.
• To demonstrate the pipeline's efficacy across diverse invertebrate phyla.
• To facilitate mitochondrial genome assembly from recalcitrant samples.

Main Methods:

• Development of a computational pipeline for mitochondrial genome recovery.
• Application of the pipeline to RNA-sequencing data from eight nonmodel invertebrates.
• Validation of the pipeline's ability to retrieve protein-coding and ribosomal genes.

Main Results:

• The pipeline reliably recovers mitochondrial gene complements from various transcriptomic datasets.
• Complete mitochondrial genome sequences were obtained with sufficient sequencing depth.
• The method proved particularly effective for poriferan data, overcoming challenges posed by microbial symbionts.

Conclusions:

• The developed pipeline simplifies mitochondrial genome assembly from RNA-sequencing data.
• It enables the recovery of valuable mitochondrial data from previously sequenced and future transcriptomic experiments.
• This tool will enhance research in phylogenetics, population genetics, and molecular biology, especially for difficult-to-study organisms.