Published preprint: Mitochondrial rRNA contamination
Last week, a preprint describing a study which I have played a small part in was posted on bioRxiv. This paper (1) uses the Metaxa2 database (2) to tease out how much of an effect mitochondrial rRNA sequences have on studies of bacterial diversity in corals. And it turns out that it matters… a lot. Importantly, by supplementing the taxonomic databases with diverse mitochondrial rRNA sequences from the Metaxa2 database, ~97% of unique unclassified sequences could be resolved as mitochondrial, without increasing the level of misannotation in mock communities. Thus the study not only points to a problem, but also to its solution! You can read it all here.
- Sonnet D, Brown T, Bengtsson-Palme J, Padilla-Gamiño J, Zaneveld JR: The Organelle in the Room: Under-annotated Mitochondrial Reads Bias Coral Microbiome Analysis. bioRxiv, 431501 (2021). doi: 10.1101/2021.02.23.431501 [Link]
- Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources, 15, 6, 1403–1414 (2015). doi: 10.1111/1755-0998.12399 [Paper link]
Published paper: The Calanus glacialis mitogenome
Mitochondrial DNA Part B today published a mitochondrial genome announcement paper (1) in which I was involved in doing the assemblies and annotating them. The paper describes the mitogenome of Calanus glacialis, a marine planktonic copepod, which is a keystone species in the Arctic Ocean. The mitogenome is 20,674 bp long, and includes 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. While this is of course note a huge paper, we believe that this new resource will be of interest in understanding the structure and dynamics of C. glacialis populations. The main work in this paper has been carried out by Marvin Choquet at Nord University in Bodø, Norway. So hats off to him for great work, thanks Marvin! The paper can be read here.
- Choquet M, Alves Monteiro HJ, Bengtsson-Palme J, Hoarau G: The complete mitochondrial genome of the copepod Calanus glacialis. Mitochondrial DNA Part B, 2, 2, 506–507 (2017). doi: 10.1080/23802359.2017.1361357 [Paper link]