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Complete mitochondrial genomes from transcriptomes: assessing pros and cons of data mining for assembling new

Giobbe Forni1, Guglielmo Puccio1, Thomas Bourguignon2,3

  • 1Department of Biological, Geological and Environmental Sciences - University of Bologna, via Selmi 3, 40126, Bologna, Italy.

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Summary

This study demonstrates that mitochondrial genomes can be reliably reconstructed from RNA sequencing data. This approach effectively utilizes vast transcriptome resources to expand the availability of organelle genome data.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Thousands of eukaryotic transcriptomes are available, primarily for nuclear gene expression studies.
  • Organelle genome assembly from transcriptomes is an underutilized but promising application of this data.

Purpose of the Study:

  • To evaluate the reliability of reconstructing complete mitochondrial genomes from RNA-Seq data.
  • To assess factors influencing the accuracy and completeness of transcriptome-derived mitochondrial genomes.

Main Methods:

  • Reconstruction of mitochondrial genomes from RNA-Seq experiments in Reticulitermes termites.
  • Manual filling of gaps corresponding to tRNAs.
  • Comparison of transcriptome-derived mitogenomes with existing conspecific mitogenomes.

Main Results:

  • Complete mitochondrial molecules were successfully assembled, with minor manual gap filling.
  • The first mitogenome for Reticulitermes banyulensis was reconstructed.
  • Assembly accuracy was independent of transcriptome size, read length, and sequencing design.
  • Transcriptome-derived mitogenomes showed high similarity to genome-sequenced counterparts (0-3.5% divergence).
  • Phylogenetic analysis using transcriptome-derived data yielded congruent results.

Conclusions:

  • RNA sequencing data is a viable source for reconstructing accurate and complete mitochondrial genomes.
  • This method can significantly increase the number of available organelle genomes by leveraging existing transcriptome datasets.