MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics
\n\nRémi Allio1, Alex Schomaker-Bastos2,†, Jonathan Romiguier1, Francisco Prosdocimi2, Benoit Nabholz1, and Frédéric Delsuc1
\n\n1Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France.
\n\n2Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil.
\n\n† In Memoriam (08/01/2015)
\n\n\n\n
Correspondence
\n\nRémi Allio
\n\nEmail: remi.allio@umontpellier.fr
\n\nFrédéric Delsuc
\n\nEmail: frederic.delsuc@umontpellier.fr
\n\n\n\n
Running head
\n\nMitochondrial signal from UCE capture data
\n\n\n\n
Abstract
\n\nThanks 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.
\n\n\n\n
Figures & Tables
\n\nFigure 1. Conceptualization of the pipeline used to assemble and extract UCE and mitochondrial signal from ultraconserved element sequencing data.
\n\nFigure 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).
\n\nFigure 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).
\n\nTable 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.
\n\nTable 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.
\n\n\n\n
Appendices
\n\nAppendix S1. List of the 501 UCE libraries (SRA accessions) and associated metadata.
\n\nAppendix 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.
\n\nAppendix S3. Summary statistics of barcoding analyses. Detailed results for both BOLDsystem and Megablast analyses are provided for each CO1 recovered with MitoFinder using MetaSPAdes.
\n\nAppendix 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.
\n\nAppendix S5. List of Genbank accession numbers for newly generated mitchondrial contigs.
\n\n\n\n
Zenodo supplementary files
\n\nAssembly_results.tar.gz Contains all contigs obtained for each species with the different assemblers implemented in MitoFinder.
\n\nMitoFinder_annotations.tar.gz Contains MitoFinder annotations for each species. (based on the contigs obtained with MetaSPAdes)
\n\nUCE_results.tar.gz Contains all annotated UCE obtained for each species after UCE identification with PHYLUCE. (MetaSPAdes)
\n\nFinal_mtDNA_alignments.tar.gz Contains the final mitochondrial gene alignments. (MetaSPAdes)
\n\nFinal_UCE_alignments.tar.gz Contains the final UCE alignments. (MetaSPAdes)
\n\nFinal_mtDNA_matrices.tar.gz Contains the final mi tochondrial supermatrices (AA and NT) used for the phylogenetic analyses. (MetaSPAdes)
\n\nMetaspades_final_UCE_matrix.phy The final UCE supermatrix used for the phylogenetic analyses. (MetaSPAdes)
", "funding": [ { "award": { "acronym": "ConvergeAnt", "id": "00k4n6c32::683257", "identifiers": [ { "identifier": "https://cordis.europa.eu/projects/683257", "scheme": "url" } ], "number": "683257", "program": "H2020-EU.1.1.", "title": { "en": "An Integrative Approach to Understanding Convergent Evolution in Ant-eating Mammals" } }, "funder": { "id": "00k4n6c32", "name": "European Commission" } } ], "publication_date": "2019-09-30", "publisher": "Zenodo", "related_identifiers": [ { "identifier": "10.1101/685412", "relation_type": { "id": "iscitedby", "title": { "de": "Wird zitiert von", "en": "Is cited by" } }, "resource_type": { "id": "publication-preprint", "title": { "de": "Preprint", "en": "Preprint" } }, "scheme": "doi" } ], "resource_type": { "id": "dataset", "title": { "de": "Datensatz", "en": "Dataset" } }, "rights": [ { "description": { "en": "The Creative Commons Attribution license allows re-distribution and re-use of a licensed work on the condition that the creator is appropriately credited." }, "icon": "cc-by-icon", "id": "cc-by-4.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/licenses/by/4.0/legalcode" }, "title": { "en": "Creative Commons Attribution 4.0 International" } } ], "subjects": [ { "subject": "Mitogenomics" }, { "subject": "Next-generation sequencing" }, { "subject": "de novo assembly" }, { "subject": "Targeted enrichment" }, { "subject": "Ultraconserved elements" }, { "subject": "Barcoding" }, { "subject": "Phylogenomics" }, { "subject": "Formicidae" }, { "subject": "MitoFinder" } ], "title": "MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics" }, "parent": { "access": { "owned_by": { "user": "68307" } }, "communities": {}, "id": "3231389", "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.3231389", "provider": "datacite" } } }, "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.3231390", "provider": "datacite" }, "oai": { "identifier": "oai:zenodo.org:3231390", "provider": "oai" } }, "revision_id": 6, "stats": { "all_versions": { "data_volume": 1039891945121.0, "downloads": 1509, "unique_downloads": 1349, "unique_views": 706, "views": 766 }, "this_version": { "data_volume": 1039887462519.0, "downloads": 1503, "unique_downloads": 1344, "unique_views": 702, "views": 760 } }, "status": "published", "swh": {}, "updated": "2024-07-22T22:50:12.116004+00:00", "versions": { "index": 1, "is_latest": true } }