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opencc-by-4.0Sep 2019View details →

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

MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics Rémi Allio1, Alex Schomaker-Bastos2,&dagger;, Jonathan Romiguier1, Francisco Prosdocimi2, Benoit Nabholz1, and Frédéric Delsuc1 1Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France. 2Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil. &dagger; In Memoriam (08/01/2015)   Correspondence Rémi Allio Email: <a href="mailto:remi.allio@umontpelier.fr">remi.allio@umontpellier.fr</a> Frédéric Delsuc Email: <a href="mailto:frederic.delsuc@umontpellier.fr">frederic.delsuc@umontpellier.fr</a>   Running head Mitochondrial signal from UCE capture data   Abstract Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routinely inferring phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA is rarely assembled and used in conjunction with nuclear markers in capture-based studies. Here, we developed MitoFinder, a user-friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries. As a case study, we used ants (Formicidae) for which 501 UCE libraries have been sequenced whereas only 29 mitogenomes are available. We compared the efficiency of four different assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. Using MitoFinder, we show that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA. Mitogenomic signal was successfully extracted from all 501 UCE libraries allowing confirming species identification using COI barcoding. Moreover, our automated procedure retrieved 296 cases in which the mitochondrial genome was assembled in a single contig, thus increasing the number of available ant mitogenomes by an order of magnitude. By leveraging the power of metagenomic assemblers, MitoFinder provides an efficient tool to extract complementary mitogenomic data from UCE libraries, allowing testing for potential mito-nuclear discordance. Our approach is potentially applicable to other sequence capture methods, transcriptomic data, and whole genome shotgun sequencing in diverse taxa.   Figures & Tables Figure 1. Conceptualization of the pipeline used to assemble and extract UCE and mitochondrial signal from ultraconserved element sequencing data. Figure 2. Comparison of the efficiency of the assemblers in terms of: A) computational time, B) number of potentially mitochondrial contigs identified, and C) number of mitochondrial genes annotated. Violin plots reflect the data distribution with a horizontal line indicating the median. Note that for the three metagenomic assemblers, 5 CPUs were used compared to 35 CPUs for Trinity. Plots were obtained using PlotsOfData (Postma & Goedhart 2019). Figure 3. Phylogenomic relationships of ants (Formicidae). AA) Mito-nuclear phylogenetic differences among subfamily relationships based on the UCE and mtDNA supermatrices obtained with the assembler MetaSPAdes assembler. Clades corresponding to subfamilies were collapsed. Inter-subfamily relationships with UFBS < 95% were collapsed. Non-maximal node support values are reported. B) The topology obtained reflects the results of phylogenetic analyses based on the amino acid mitochondrial supermatrix (using MetaSPAdes as assembler). Histograms reflect the percent of UCEs (light grey) and mitochondrial genes (dark grey) recovered for each species. Illustrative pictures (*): Diacamma sp. (Ponerinae; top left), Formica sp. (Formicinae; top right), and Messor barbarus (Myrmicinae; bottom right). Table 1. Summary statistics on assembly results according to the assembler used. The values are averages over the 501 assemblies, except for the assembly time, which is a median value. The two tables report specific statistics for A) ultraconserved elements data, and B) mitochondrial data. Note that 35 CPUs were used for Trinity whereas 5 CPUs were used for other assemblers. Table 2. Statistical comparison between the performances of the different assemblers. Statistical significance was estimated with a paired non parametric test (paired wilcoxon test). *** = p<0.001; ** = p<0.01; * = p<0.05; NS = p>0.05; and (+)/(-) is the result of the comparison between the row and the column.   Appendices Appendix S1. List of the 501 UCE libraries (SRA accessions) and associated metadata. Appendix S2. Summary statistics on mitochondrial signal recovered per species and depending on the assembler used. The table provides the number of contigs and genes recovered with MitoFinder and the size of each annotated gene. Appendix S3. Summary statistics of barcoding analyses. Detailed results for both BOLDsystem and Megablast analyses are provided for each CO1 recovered with MitoFinder using MetaSPAdes. Appendix S4. Detailed results of tree distance analyses realized with Dquad (Ranwez, Criscuolo, & Douzery 2010). Trees obtained with each assembler with mitochondrial amino acid supermatrix, mitochondrial nucleotide supermatrix, and UCE nucleotide supermatrix were compared with each others. Appendix S5. List of Genbank accession numbers for newly generated mitchondrial contigs.   Zenodo supplementary files Assembly_results.tar.gz Contains all contigs obtained for each species with the different assemblers implemented in MitoFinder. MitoFinder_annotations.tar.gz Contains MitoFinder annotations for each species. (based on the contigs obtained with MetaSPAdes) UCE_results.tar.gz Contains all annotated UCE obtained for each species after UCE identification with PHYLUCE. (MetaSPAdes) Final_mtDNA_alignments.tar.gz Contains the final mitochondrial gene alignments. (MetaSPAdes) Final_UCE_alignments.tar.gz Contains the final UCE alignments. (MetaSPAdes) Final_mtDNA_matrices.tar.gz Contains the final mi  tochondrial supermatrices (AA and NT) used for the phylogenetic analyses. (MetaSPAdes) Metaspades_final_UCE_matrix.phy The final UCE supermatrix used for the phylogenetic analyses. (MetaSPAdes)

opennotspecifiedJun 2020View details →

FIGURES 7–14. 7. Ptetica cristulata Saussure, 1884 in Comparative analysis of mitogenomes among three species of Haplotropidini grasshoppers and a new species of the genus Sulcotropis (Orthoptera: Acridoidea Pamphagidae) from China

FIGURES 7–14. 7. Ptetica cristulata Saussure, 1884 ♂(after 2020 Orthoptera Species File); 8. Pyrgodera Fischer von Waldheim, 1846 ♂(after Zhang, 2019); 9. Sulcohumpacris hebeiensis Yin, Yin & Cao, 2017 ♂(after Yin et al, 2017); 10. Humphaplotropis taishanensis Xiao, Yin & Yin, 2013 ♂(after Xiao et al, 2013); 11. Sulcotropis cyanipes Yin et Chou, 1979 ♂; 12. Haplotropis heiheensis. Zhang, Li et Yin, 2020 ♂; 13. Sulcotropis cyanipes Yin et Chou, 1979 ♀; 14. Haplotropis brunneriana Saussure, 1888(after Saussure, 1888).

opencc-zeroDec 2019View details →

Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul

Background: Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by phylogeneticists is likely a product of the scarcity or unavailability of fresh tissue samples for DNA sequencing. Lack of comprehensive phylogenies result in highly discrepant taxonomic arrangements that are based exclusively on morphological data—impressively, these are the only classification schemes available for the group. Here we used high-throughput sequencing and an unprecedented sampling effort of museum specimens to provide the first comprehensive phylogenetic analysis of tree squirrels, with a special emphasis on Neotropical taxa. Results: We gathered mitochondrial genome data from 232 modern and historical samples, representing 40 out of the 43 currently recognized species of Sciurini. We found no correlation between specimen age and completeness of mitogenomes recovered for historical samples. Our phylogenetic analyses—performed with datasets differing on levels of missing data and taxa under distinctanalytical methods— strongly support the monophyly of Sciurini and consistently recovered 12 major clades within the tribe. We found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least seven lineages that might represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of pairs of mammae indicated that alternative conditions of both characters must have evolved multiple times along the evolutionary history of tree squirrels. Conclusions: We were able to obtain complete mitogenomes for samples as old as 120 years, reinforcing the potential of historical samples for phylogenetic and evolutionary inferences of elusive lineages of the tree of life. None of the taxonomic arrangements ever proposed for tree squirrels fully corresponded to our phylogenetic reconstruction, with only a few of the currently recognized genera recovered as monophyletic. By investigating the evolution of two morphological traits widely employed in the taxonomy of the group, we revealed that their homoplastic nature can help to explain the incongruence between phylogenetic results and classification schemes presented so far, and we recommend a substantial taxonomic overhaul.

opencc-by-4.0Sep 2020View details →

Mitogenomes reveal alternative initiation codons and lineage-specific gene order conservation in echinoderms

Sample information, gene alignments and concatenated matrix

opennotspecifiedDec 2020View details →

FIGURE 8 in First partial mitogenome of a new Seira Lubbock species (Collembola, Entomobryidae, Seirinae) from Cambodia reveals a possible separate lineage from the Neotropical Seirinae

FIGURE 8. Phylogeny of Seirinae resulting from Maximum likelihood analysis of amino acid variation of 13 protein-coding mitochondrial genes using a partitioned dataset. Neotropical Seirinae is highlighted in yellow. Nodal support is shown as SHaLRT support (%) / ultrafast bootstrap support (%).

opennotspecifiedDec 2020View details →

FIGURE 4A–C in First partial mitogenome of a new Seira Lubbock species (Collembola, Entomobryidae, Seirinae) from Cambodia reveals a possible separate lineage from the Neotropical Seirinae

FIGURE 4A–C. Seira sanloemensis sp. nov.: dorsal chaetotaxy (left side); A, Th II–III; B, Abd I–III; C, Abd IV–V.

opennotspecifiedDec 2020View details →

FIGURE 5A–F in First partial mitogenome of a new Seira Lubbock species (Collembola, Entomobryidae, Seirinae) from Cambodia reveals a possible separate lineage from the Neotropical Seirinae

FIGURE 5A–F. Seira sanloemensis sp. nov.: trunk appendages; A, trochanteral organ (posterior side); B, femur III (anterior view), arrow indicates spine-like chaetae on proximal half; C, distal tibiotarsus and empodial complex III (posterior view); D, collophore (lateral view); E, manubrium ventral chaetotaxy; F, manubrial plate (dorsal view).

FIGURE 6 in Mitogenomic features of Pteronarcys sachalina (Plecoptera: Pteronarcyidae), the only salmonfly known from China

FIGURE 6. Predicted structural elements in the control region of Pteronarcys sachalina. Tandem repeats are indicated with orange boxes; stem-loop structures are depicted showing their nucleotides. Other sequences are shown as dark lines.

FIGURE 5 in Mitogenomic features of Pteronarcys sachalina (Plecoptera: Pteronarcyidae), the only salmonfly known from China

FIGURE 5. Secondary structures of tRNA genes in the mitogenome of Pteronarcys sachalina. The tRNA genes are labelled with their corresponding amino acids. Structural elements are indicated in trnV.

FIGURE 1 in Mitogenomic features of Pteronarcys sachalina (Plecoptera: Pteronarcyidae), the only salmonfly known from China

FIGURE 1. Mitochondrial map of Pteronarcys sachalina. Genes inside the circle are transcribed in a clockwise direction, whereas those on the outside are transcribed counterclockwise. Different gene types are shown as filled boxes in different colors.

FIGURE 4 in Mitogenomic features of Pteronarcys sachalina (Plecoptera: Pteronarcyidae), the only salmonfly known from China

FIGURE 4. Evolutionary rates of PCGs in Pteronarcys sachalina, Pteronarcys princeps and Pteronarcella badia.

FIGURE 2 in Mitogenomic features of Pteronarcys sachalina (Plecoptera: Pteronarcyidae), the only salmonfly known from China

FIGURE 2. Comparison of length and A+T content of Pteronarcys sachalina, Pteronarcys princeps and Pteronarcella badia.

FIGURE 7 in Mitogenomic features of Pteronarcys sachalina (Plecoptera: Pteronarcyidae), the only salmonfly known from China

FIGURE 7. The alignment of nucleotide sequences of CRs among Pteronarcys sachalina, Pteronarcys princeps and Pteronarcella badia. Sequence identity among species was indicated by colored boxes. The species tree below the alignment was constructed according to sequence similarity by DNAMAN.

FIGURE 3 in Mitogenomic features of Pteronarcys sachalina (Plecoptera: Pteronarcyidae), the only salmonfly known from China

FIGURE 3. Relative synonymous codon usage (RSCU) of PCGs in Pteronarcys sachalina, Pteronarcys princeps and Pteronarcella badia. Full codon families are indicated below the X-axis.

opencc-zeroDec 2018View details →

Data from: Fin whale (Balaenoptera physalus) mitogenomics: a cautionary tale of defining sub-species from mitochondrial sequence monophyly

The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1,676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 358 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively "trivial" aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic.

opencc-zeroDec 2017View details →

Data from: Resolving the phylogenetic position of Darwin's extinct ground sloth (Mylodon darwinii) using mitogenomic and nuclear exon data

Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first discovered its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12,880 year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient sub-fossil, likely the result of the dry and cold conditions prevailing within the cave. Accordingly, taxonomic assessment of our shotgun metagenomic data showed a very high percentage of endogenous DNA with 22% of the assembled metagenomic contigs assigned to Xenarthra. Additionally, we enriched over 15 kilobases of sequence data from seven nuclear exons, using target sequence capture designed against a wide xenarthran dataset. Phylogenetic and dating analyses of the mitogenomic dataset including all extant species of xenarthrans and the assembled nuclear supermatrix unambiguously place Mylodon darwinii as the sister-group of modern two-fingered sloths from which it diverged around 22 million years ago. These congruent results from both the mitochondrial and nuclear data support the diphyly of the two modern sloths lineages, implying the convergent evolution of their unique suspensory behaviour as an adaption to arboreality. Our results offer promising perspectives for whole genome sequencing of this emblematic extinct taxon.

opencc-zeroDec 2013View details →

Data from: Evolutionary neutrality of mtDNA introgression: evidence from complete mitogenome analysis in roe deer

Introgressive hybridization offers a unique platform for studying the molecular basis of natural selection acting on mitogenomes. Most of the mtDNA protein-coding genes are extremely conserved; however, some of the observed variations have potentially adaptive significance. Here, we evaluated whether the evolution of mtDNA in closely related roe deer species affected by widespread mtDNA introgression is neutral or adaptive. We characterized and compared 16 complete mitogenomes of European (Capreolus capreolus) and Siberian (C. pygargus) roe deer, including four of Siberian origin introgressed into European species. The average sequence divergence of species-specific lineages was estimated at 2.8% and varied across gene classes. Only 21 of 315 fixed differences identified in protein-coding genes represented nonsynonymous changes. Only three of them were determined to have arisen in the C. pygargus lineage since the time to the most recent common ancestor (TMRCA) of both Capreolus species, reflecting a decelerated evolutionary ratio. The almost four-fold higher dN/dS ratio described for the European roe deer lineage is constrained by overall purifying selection, especially pronounced in the ND4 and ND5 genes. We suggest that the highly divergent C. capreolus lineage could have maintained a capability for genomic incorporation of the well-preserved and almost ancestral type of mtDNA present in C. pygargus. Our analyses did not indicate any signs of positive selection for Siberian roe deer mtDNA, suggesting that the present widespread introgression is evolutionarily neutral.

opencc-zeroDec 2010View details →

Data from: Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny

BACKGROUND: Tunicates represent a key metazoan group as the sister-group of vertebrates within chordates. The six complete mitochondrial genomes available so far for tunicates have revealed distinctive features. Extensive gene rearrangements and particularly high evolutionary rates have been evidenced with regard to other chordates. This peculiar evolutionary dynamics has hampered the reconstruction of tunicate phylogenetic relationships within chordates based on mitogenomic data. RESULTS: In order to further understand the atypical evolutionary dynamics of the mitochondrial genome of tunicates, we determined the complete sequence of the solitary ascidian Herdmania momus. This genome from a stolidobranch ascidian presents the typical tunicate gene content with 13 protein-coding genes, 2 rRNAs and 24 tRNAs which are all encoded on the same strand. However, it also presents a novel gene arrangement, highlighting the extreme plasticity of gene order observed in tunicate mitochondrial genomes. Probabilistic phylogenetic inferences were conducted on the concatenation of the 13 mitochondrial protein-coding genes from representatives of major metazoan phyla. We show that whereas standard homogeneous amino acid models support an artefactual sister position of tunicates relative to all other bilaterians, the CAT and CAT+BP site- and time-heterogeneous mixture models place tunicates as the sister-group of vertebrates within monophyletic chordates. Moreover, the reference phylogeny indicates that tunicate mitochondrial genomes have experienced a drastic acceleration in their evolutionary rate that equally affects protein-coding and ribosomal-RNA genes. CONCLUSION: This is the first mitogenomic study supporting the new chordate phylogeny revealed by recent phylogenomic analyses. It illustrates the beneficial effects of an increased taxon sampling coupled with the use of more realistic amino acid substitution models for the reconstruction of animal phylogeny.