MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics

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

doi:10.1101/685412

Cited by 73 publications

(94 citation statements)

References 80 publications

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“…As mitochondrial DNA is naturally enriched, sequencing reads of target‐enriched libraries typically include background mitochondrial sequences as byproducts. For example, Allio et al (2019) were able to extract COI barcodes and other mitochondrial genes from 501 hybrid‐capture libraries in ants (Formicidae), and Taucce et al (2018) assembled mitogenomes for five frog species (Anura) from hybrid‐capture libraries. Here, we show that mitochondrial genes other than COI could be recovered for all samples in this study (Figure S2).…”

Section: Discussionmentioning

confidence: 99%

Transcriptome‐based target‐enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

Quek

Jain

Neo

et al. 2020

Molecular Ecology Resources

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Despite the ecological and economic significance of stony corals (Scleractinia), a robust understanding of their phylogeny remains elusive due to patchy taxonomic and genetic sampling, as well as the limited availability of informative markers. To increase the number of genetic loci available for phylogenomic analyses in Scleractinia, we designed 15,919 DNA enrichment baits targeting 605 orthogroups (mean 565 ± SD 366 bp) over 1,139 exon regions. A further 236 and 62 barcoding baits were designed for COI and histone H3 genes respectively for quality and contamination checks. Hybrid capture using these baits was performed on 18 coral species spanning the presently understood scleractinian phylogeny, with two corallimorpharians as outgroup. On average, 74% of all loci targeted were successfully captured for each species. Barcoding baits were matched unambiguously to their respective samples and revealed low levels of cross‐contamination in accordance with expectation. We put the data through a series of stringent filtering steps to ensure only scleractinian and phylogenetically informative loci were retained, and the final probe set comprised 13,479 baits, targeting 452 loci (mean 531 ± SD 307 bp) across 865 exon regions. Maximum likelihood, Bayesian and species tree analyses recovered maximally supported, topologically congruent trees consistent with previous phylogenomic reconstructions. The phylogenomic method presented here allows for consistent capture of orthologous loci among divergent coral taxa, facilitating the pooling of data from different studies and increasing the phylogenetic sampling of scleractinians in the future.

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Section: Discussionmentioning

confidence: 99%

Transcriptome‐based target‐enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

Quek

Jain

Neo

et al. 2020

Molecular Ecology Resources

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“…We subsequently used a custom Python 3 script 26 to retrieve BLAST hits and did the assembly with Geneious R9 (https ://www.genei ous.com). The mtDNA of T. senegalensis was assembled using MitoFinder 27 .…”

Section: Methodsmentioning

confidence: 99%

The evolutionary history of manatees told by their mitogenomes

Souza

Freitas

Ramos

et al. 2021

Sci Rep

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The manatee family encompasses three extant congeneric species: Trichechus senegalensis (African manatee), T. inunguis (Amazonian manatee), and T. manatus (West Indian manatee). The fossil record for manatees is scant, and few phylogenetic studies have focused on their evolutionary history. We use full mitogenomes of all extant manatee species to infer the divergence dates and biogeographical histories of these species and the effect of natural selection on their mitogenomes. The complete mitochondrial genomes of T. inunguis (16,851 bp), T. senegalensis (16,882 bp), and T. manatus (16,882 bp), comprise 13 protein-coding genes, 2 ribosomal RNA genes (rRNA - 12S and 16S), and 22 transfer RNA genes (tRNA), and (D-loop/CR). Our analyses show that the first split within Trichechus occurred during the Late Miocene (posterior mean 6.56 Ma and 95% HPD 3.81–10.66 Ma), followed by a diversification event in the Plio-Pleistocene (posterior mean 1.34 Ma, 95% HPD 0.1–4.23) in the clade composed by T. inunguis and T. manatus; T. senegalensis is the sister group of this clade with higher support values (pp > 0.90). The branch-site test identified positive selection on T. inunguis in the 181st position of the ND4 amino acid gene (LRT = 6.06, p = 0.0069, BEB posterior probability = 0.96). The ND4 gene encodes one subunit of the NADH dehydrogenase complex, part of the oxidative phosphorylation machinery. In conclusion, our results provide novel insight into the evolutionary history of the Trichechidae during the Late Miocene, which was influenced by geological events, such as Amazon Basin formation.

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“…For each set of raw reads, I used the associated adapter fasta file generated by initial processing with illumiprocessor (ILLUMINACLIP:adapters.fasta:2:30:10), and omitted the LEADING, TRAILING and SLIDINGWINDOW options that are used by default in illumiprocessor . I used these adapter‐cleaned reads as input for the programme mitoFinder (Allio et al ., 2020) using the mitogenome of Vollenhovia emeryi (NCBI BioProject PRJNA278668) as a reference and MetaSpades (Nurk et al ., 2017) for assembly. I used the longest contig output from mitoFinder as input for mitoBim (Hahn et al ., 2013) to extend the contig and to assess coverage depth, as viewed in Tablet (Milne et al ., 2013).…”

Section: Methodsmentioning

confidence: 99%

Phylogenomic species delimitation in the ants of the Temnothorax salvini group (Hymenoptera: Formicidae): an integrative approach

Prebus

2020

Systematic Entomology

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The members of the Temnothorax salvini (Forel) species group are rarely collected, arboreally nesting ants of Central American forests. Previously thought to consist of two broadly dispersed species, recent collections have revealed a diversity of specimens that defy the two‐species salvini group concept, but these are difficult to distinguish from each other based solely on morphology. I contrast several model‐based approaches to species delimitation based on target‐enriched genomic data. With molecular data from thousands of ultraconserved elements (UCEs), mitochondrial genome sequences and morphometric data, I use an integrated approach to species delimitation within the salvini group. Morphometric data were analysed using cluster analysis of principal component analysis (PCA) output. I use several popular methods of molecular species delimitation, including bPTP, BPP and STACEY, using a novel approach to filtering UCE data based on posterior predictive checks of nucleotide substitution model adequacy. In addition, I use iBPP to integrate morphometric PCA data and filtered UCE data in a ‘total evidence’ analysis. I use geographical range data for an independent contrast to discriminate among competing species delimitation hypotheses. Furthermore, I investigate the evolutionary timescale and biogeographical history of the group and find that it arose roughly 13 Ma ago in habitats associated with present day mid‐to‐high elevations of the mountain complex spanning southern Mexico to northern Nicaragua. In addition, dispersal of the salvini group into the Southern Sierra Madre in Mexico, lowland habitats and the southern Central American cordilleras in Costa Rica and Panama subsequent to mountain building in southern Central America 5–8 Ma ago appears to follow a taxon‐cycle dynamic, with the lowland‐adapted T. aztecus representing the most recent expansion phase. I find that the salvini group, which previously contained two named species, is composed of nine, all of which are morphologically diagnosable a posteriori.

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MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics

Cited by 73 publications

References 80 publications

Transcriptome‐based target‐enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

Transcriptome‐based target‐enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

The evolutionary history of manatees told by their mitogenomes

Phylogenomic species delimitation in the ants of the Temnothorax salvini group (Hymenoptera: Formicidae): an integrative approach

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