MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics

Allio, Rémi; Schomaker-Bastos, Alex; Romiguier, Jonathan; Prosdocimi, Francisco; Nabholz, Benoît; Delsuc, Frédéric

doi:10.1111/1755-0998.13160

Cited by 1,219 publications

(259 citation statements)

References 102 publications

Supporting

Mentioning

257

Contrasting

Order By: Relevance

“… 2017 ) and MitoFinder v.1.3 (Allio et al. 2020 ) from a randomly sampled subset of total genomic reads (1,905,901 paired end). Both methods recovered one identical, circular mtDNA contig of the entire mitochondrial genome.…”

mentioning

confidence: 99%

Mitochondrial genome of the freshwater annelid Manayunkia occidentalis (Sabellida: Fabriciidae)

Ekin

Rouse

2020

Mitochondrial DNA Part B

View full text Add to dashboard Cite

mentioning

confidence: 99%

Mitochondrial genome of the freshwater annelid Manayunkia occidentalis (Sabellida: Fabriciidae)

Ekin

Rouse

2020

Mitochondrial DNA Part B

View full text Add to dashboard Cite

“…2019 ; this study), and even as by-products of restriction site-associated DNA ( Terraneo et al. 2018 a, 2018 b) or hybrid-capture ( Allio et al. 2020 ; Quek et al.…”

mentioning

confidence: 74%

Mitogenomes Reveal Alternative Initiation Codons and Lineage-Specific Gene Order Conservation in Echinoderms

Quek

Chang

et al. 2020

Molecular Biology and Evolution

View full text Add to dashboard Cite

The mitochondrial genetic code is much more varied than the standard genetic code. The invertebrate mitochondrial code, for instance, comprises six initiation codons, including five alternative start codons. However, only two initiation codons are known in the echinoderm and flatworm mitochondrial code, the canonical ATG and alternative GTG. Here, we analysed 23 Asteroidea mitogenomes, including 10 newly-sequenced species, and unambiguously identified at least two other start codons, ATT and ATC, both of which also initiate translation of mitochondrial genes in other invertebrates. These findings underscore the diversity of the genetic code and expand upon the suite of initiation codons among echinoderms to avoid erroneous annotations. Our analyses have also uncovered the remarkable conservation of gene order among asteroids, echinoids and holothuroids, with only an interchange between two gene positions in asteroids over approximately 500 million years of echinoderm evolution.

show abstract

“…The remaining reads were aligned to the reference genome of Photobacterium mandapamensis, isolated from the light organ of Siphamia tubifer (Urbanczyk et al, 2011) with BWA-MEM (Li 2013). Unaligned sequences were then processed with MitoFinder (Allio et al, 2020) using the reference mitochondrial genome of the Banggai cardinalfish Pterapogon kauderni (Matias and Hereward 2018). All cardinalfish cytochrome oxidase subunit 1 (COI) gene sequences that were recovered aligned using MUSCLE (Edgar 2004) and a maximum likelihood analysis was carried out with raxml-ng (Kozlovet al., 2019) using the evolutionary model TIM2+F+I+G4 which had the lowest BIC score as predicted by IQtree (Nguyen et al, 2015) and 1,000 bootstraps to infer the phylogenetic relationships between host species.…”

Section: Methodsmentioning

confidence: 99%

Museum genomics illuminate the high specificity of a bioluminescent symbiosis across a genus of reef fish

Gould

Fritts-Penniman

Gaisiner

2020

Preprint

View full text Add to dashboard Cite

Symbiotic relationships between bioluminescent bacteria and fishes have evolved multiple times across hundreds of fish taxa, but relatively little is known about the specificity of these associations and how conserved they have been through time. This study describes the degree of specificity of a bioluminescent symbiosis between cardinalfishes in the genus Siphamia and luminous bacteria in the Vibrio family. Primarily using museum specimens, we investigate the co-divergence of host and symbiont and test for patterns of divergence that correlate with both biogeography and time. Contrary to expectations, we determined that the light organ symbionts of all 14 Siphamia species examined belong to one genetic clade of Photobacterium mandapamensis (Clade II), indicating that the association is highly specific and conserved across the host genus. Thus, we did not find evidence of codivergence among hosts and symbionts. We did observe that symbionts hosted by individuals sampled from colder water regions were more divergent, containing more than three times as many single nucleotide polymorphisms than the rest of the symbionts. Overall our findings indicate that the symbiosis between Siphamia fishes and P. mandapamensis Clade II has been highly conserved across a broad geographic range and through time, despite the facultative nature of the bacterial symbiont. These results suggest that this bioluminescent symbiosis could have played a key role in the evolution of the host genus and that there are conserved mechanisms regulating its specificity that have yet to be defined.

show abstract

MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics

Abstract: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Cited by 1,219 publications

References 102 publications

Mitochondrial genome of the freshwater annelid Manayunkia occidentalis (Sabellida: Fabriciidae)

Mitochondrial genome of the freshwater annelid Manayunkia occidentalis (Sabellida: Fabriciidae)

Mitogenomes Reveal Alternative Initiation Codons and Lineage-Specific Gene Order Conservation in Echinoderms

Museum genomics illuminate the high specificity of a bioluminescent symbiosis across a genus of reef fish

Contact Info

Product

Resources

About