1979;76:19671971. The mitochondrial genomes of members of the superclass Hexapoda (generally referred to as the 'insects') are typically approximately 15 kilobases (kb) in length and encode 37 genes, including 13 protein coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs). [Introduction to Go! mtDB: Human Mitochondrial Genome Database, a resource for population This database is dedicated to collecting, sorting and sharing basic information regarding mollusks, especially their mitochondrial genome information. See this image and copyright information in PMC. Boore JL, Collins TM, Stanton D, Daehler LL, Brown WM: Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Park J, Lee S, Choi J, Ahn K, Park B, Park J, Kang S, Lee YH: Fungal Cytochrome P450 Database. Cookies policy. The Phyloviewer (http://www.phyloviewer.org/) provides four phylogenetic analysis programs (ClustalW, DNAPARS/PROTPARS, DNAML/PROML, and PHYML [2931]) via a common interface to support phylogenetic studies based on the mitochondrial gene/genome sequences archived in IMGD. S, Sternorrhyncha; A, Auchenorrhyncha; H, Heteroptera. The site is secure. The https:// ensures that you are connecting to the Find information about mitochondrial proteins. Guo W, Liu Y, Su L, Guo S, Xie F, Ji X, Zhou K, Guo X, Gu X, Xing J. Mol Oncol. Calls below 1% heteroplasmy were completely removed. Your privacy choices/Manage cookies we use in the preference centre. Nucleic Acids Res. The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). doi: 10.1093/nar/gkl780. The pipeline described above was run on individual samples using the Terra platform. Ad hoc retrieval systems have been devised for some of the above listed databases keeping into account their peculiarities. In particular, members of Diptera and Coleoptera account for 26 (20.00%) and 12 (9.23%) mitochondrial genomes, respectively, reflecting active researches on these orders [39, 40]. . The IMGD archives sequences and taxonomical information from more than 25,000 hexapod species. Bethesda, MD 20894, Web Policies This site needs JavaScript to work properly. This internal algorithm estimates contamination by examining haplogroup markers that should show 100% alternative alleles (i.e., are fully homoplasmic) but are observed at high heteroplasmy instead (85-99.8% alternate alleles). Some of these are listed below. Zhang G, Zhang S, Chen W, Qiu W, Wu H, Wang J, Luo J, Gu X, Cotton RG. The closed red circle indicates the average mitochondrial genome size and the blue and red bars present the largest and smallest genome sizes, respectively (see also Table 2 and Table 3). The middleware platform manages not only BLAST, tRNAScan-SE, and mFold but also six phylogenetic tools managed by Phyloviewer (http://www.phyloviewer.org/). Search for gene sequence, RNA secondary structure and biochemical and taxonomic information about organelles. For example, more than 1,200 metazoan mitochondrial genomes have already been sequenced completely [7, 8]. NUMTs: Nuclear sequences of mitochondrial origin (termed NUMTs) are derived from pieces of mtDNA that have integrated into the nuclear genome over the course of human evolution. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. In IMGD, 132 completely or nearly-completely sequenced mitochondrial genomes and 113,985 mitochondrial gene sequences from 25,747 species were archived. The gene order browser implemented in IMGD was designed for efficient graphical presentation of PCGs, tRNAs, and rRNAs in the mitochondrial genome. Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake 2007 Feb;134(Pt 2):153-67. doi: 10.1017/S0031182006001429. 10.1016/j.ympev.2008.01.026. Mitochondrial Cardiomyopathy: The Roles of mt-tRNA Mutations. If the functional region is a protein coding gene, also listed is the codon number, the codon position, the amino acid state in CRS and for the variant, whether the change is synonymous or not. The mitochondrial genome: structure, transcription, translation and Search for information on the predicted and experimentally confirmed protein complement of mitochondria from the model plant Arabidopsis thaliana. All alleles at certain problematic sites were filtered out or flagged. Of special interest to medical researchers and population geneticists evaluating specific positions is a complete list of (currently 3311) mitochondrial polymorphisms among these sequences. 2001. A database for comparative analysis of mitochondrial genomes and arrangements within metazoan. The human reference genome assembly and sequence information that is represented in the RefSeq collection is identical to the sequence data available in databases maintained by the International Nucleotide Sequence Database Collaboration ( INSDC ) including NCBI's GenBank database. Catalano D, Licciulli F, Turi A, Grillo G, Saccone C, D'Elia D. BMC Bioinformatics. To take a glance, please visit a sample page ( Anguilla japonica) . McGinnis S, Madden TL: BLAST: at the core of a powerful and diverse set of sequence analysis tools. mitoSomatic: a tool for accurate identification of mitochondrial DNA somatic mutations without paired controls. Mol Phylogenet Evol. MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces cerevisiae. 10.1111/j.1365-2958.2007.05918.x. 10.1038/376163a0. The IMGD archives 132 hexapod mitochondrial genomes and 113,985 GenBank accessions of partially sequenced mitochondrial genes, consisting of 102,430 PCGs, 19,452 rRNAs, and 17,944 tRNAs, from 25,747 species belonging to 33 orders (Table 1). Rapid evolution of animal mitochondrial DNA. 2008, 92 (6): 966-972. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. An official website of the United States government. The mitochondrial genome, contained in the subcellular mitochondrial network, encodes a small number of peptides pivotal for cellular energy production. Considering that more than 4,800 insect mitogenomes are actually present in Genbank databases, mining mitochondrial genomes from transcriptomes has the potential to increase the number of insects. Google Scholar. USA. 10.1093/bioinformatics/btl021. BMC Genomics. The Mollusca mitochondrial database (MODB) was established for the Life and Health Big Data Center of Yantai University. The different databases, some of which are structured using commercial packages (Microsoft Access, File Maker Pro) while others use a flat-file format, have been integrated under ORACLE. At this time, owing to an increase in the number of published complete human mitochondrial genome sequences, it became necessary to provide a web-based database of human whole genome and complete coding region sequences. government site. 10.1006/mpev.2001.1028. Three different methods of drawing phylogenetic trees (NJ, MP, and ML) are currently available. 791/5565 The P. lobata and P. cf. Gene translocations and inversions were detected in the following 12 orders: Collembola, Archaeognatha, Zygentoma, Hemiptera, Thysanoptera, Psocoptera, Phthiraptera, Neuroptera, Hymenoptera, Orthoptera, Lepidoptera, and Diptera. Bookshelf PubMedGoogle Scholar. O'Brien EA, Zhang Y, Yang L, Wang E, Marie V, Lang BF, Burger G: GOBASEa database of organelle and bacterial genome information. 1998, 392 (6677): 667-668. statement and Roe AD, Sperling FA: Patterns of evolution of mitochondrial cytochrome c oxidase I and II DNA and implications for DNA barcoding. This database is dedicated to collecting, sorting and sharing basic information regarding mollusks, especially their mitochondrial genome information. The vast majority of variant calls (98%) are homoplasmic or near homoplasmic, whereas 2% are heteroplasmic. Google Scholar. Specifically, we excluded samples with low or high mtDNA copies/cell or with evidence of mtDNA contamination. MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish Twenty-four biotypes of Bemisia tabaci (Hemiptera: Aleyrodidae), which could not be distinguished by morphological characteristics, were resolved [13]. 10.1016/S0959-437X(98)80035-X. ATP6 and 8 (ATP synthase subunit 6 and 8); COX13 (cytochrome c oxidase subunits IIII); CYTB (cytochrome b); ND16 (NADH dehydrogenase subunits 16); ND4L (NADH dehydrogenase subunit 4L) (see also Table 4). Find information about the proteins involved in mitosis. (B) MP tree built based on 88 COI sequences from 70 Phthirapteran species using DNAPARS, is shown. Fish mitochondrial genome (mitogenome) data form a fundamental basis for revealing vertebrate evolution and hydrosphere ecology. 2008, 9 (1): 402-10.1186/1471-2164-9-402. All other annotations with LOFTEE remain unchanged, and caution should be taken to interpret the annotations in the context of the mitochondrial genome. 1996 - 2023 Health Sciences Library System, University of Pittsburgh. This article is published under license to BioMed Central Ltd. 10.1016/S0968-0004(00)01773-4. IMGD: an integrated platform supporting comparative genomics and Genet. Species-driven User Interface (SUI) optimized for collecting data based on taxa. The .gov means its official. AMPDB -- the Arabidopsis Mitochondrial Protein Database, ARWEN -- a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences, GOBASE -- A database of mitochondrial and chloroplast information, HMPD -- Human mitochondrial protein database, HvrBase++ -- a phylogenetic database for primate species, MAPU -- Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes, MITOMAP -- a human mitochondrial genome database, MiCroKit -- MIdbody, CentROsome and KIneTochore database, MitoDat - Mendelian Inheritance and the Mitochondrion, MitoDrome -- A database of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion, MitoGenesisDB -- Mitochondrial Spatio-Temporal Expression Database, MitoP2 -- An Integrated Database on Mitochondrial Proteins in Yeast, Man, mouse, and Neurospora, MitoProteome -- Mitochondrial Protein Sequence Database and Annotation System, Mitome -- dynamic and interactive database for comparative mitochondrial genomics in metazoan animals, OGRe -- A relational database for comparative analysis of mitochondrial genomes, Organelle DB -- a cross-species database of protein localization and function, PeroxisomeDB -- a database for the peroxisomal proteome, functional genomics and disease, Yeast Deletion Project and Proteomics of Mitochondria Database, mtDB -- Human Mitochondrial Genome Database, a resource for population genetics and medical sciences, plprot -- a comprehensive proteome database for different plastid types, OBRC: Online Bioinformatics Resources Collection, DNA Sequence Databases and Analysis Tools, Gene Mutations, Genetic Variations and Diseases, Microarray, SAGE, and other Gene Expression, Other Databases and Tools (Literature Mining, Lab Protocols, Medical Topics, and others), Protein Sequence Databases and Analysis Tools. CAS Heteroplasmic variants: Unlike nuclear variants, which are called as either heterozygous or homozygous, mtDNA variants are called at all heteroplasmy levels using a specialized mitochondria mode of the GATK MuTect2 variant caller (a variant caller that was originally designed to call somatic variants in tumor samples). The SUI helps the users of IMGD search hexapod taxa using the 'Species search' and supports the addition and deletion of selected insect species via the 'Species cart' function, which is similar to the cart functions commonly used on online shopping sites (Figure 3). 6, 7 However, the sequences are highly fragmented because contigs are enormous in number (2,545-88,884) and short . At this time, owing to an increase in the number of published complete human mitochondrial genome sequences, it became necessary to provide a web-based database of human whole genome and complete coding region sequences. 2003, 61 (1): 3-67. 10.1006/mpev.1998.0580. Boykin LM, Shatters RG, Rosell RC, McKenzie CL, Bagnall RA, De Barro P, Frohlich DR: Global relationships of Bemisia tabaci (Hemiptera: Aleyrodidae) revealed using Bayesian analysis of mitochondrial COI DNA sequences. https://doi.org/10.1186/1471-2164-10-148, DOI: https://doi.org/10.1186/1471-2164-10-148. 8600 Rockville Pike al., BioRxiv, October 8, 2019. 10.1093/molbev/msn198. The closed red circle indicates the average GC content, and the blue and red bars present the maximum and minimum GC contents, respectively. Downloads for mtDNA variants are provided separately from the nuclear variants. 2008, 24 (7): 1024-1025. Dowton M: Relationships among the cyclostome braconid (Hymenoptera: Braconidae) subfamilies inferred from a mitochondrial tRNA gene rearrangement. 2007, 50 (2): 188-202. MitoZoa is a relational database collecting curated metazoan entries of complete or nearly complete mitochondrial genomes (mtDNA), specifically designed to assist comparative studies of mitochondrial genome-level features in a given taxon or in congeneric species of Metazoa. Sci. Mitochondria are small structures in cells that generate energy for the cell to use, and are hence referred to as the "powerhouses" of the cell. Expanding the functional human mitochondrial DNA database by the - PNAS 10.1016/j.ympev.2006.03.007. VEP annotations are provided using the VEP annotation pipeline for nuclear variants with the following modification: the VEP distance parameter was set to 0 to avoid upstream and downstream annotations. BLAST [26], tRNAScan-SE [27], and mFold [28] were also incorporated into IMGD. Moreover, based on the database of widely sequenced mitochondrial genes, an insect species identification system based on multiple loci can be developed. Genome rearrangements and vertebrate mitochondrial genome evolution Traditionally, vertebrate mitochondria have been considered to have a "conserved gene order" from primitive vertebrates (fish . Nucleic Acids Res. Gene. CAS 2002, 19 (8): 1385-1389. Article Waeschenbach A, Telford MJ, Porter JS, Littlewood DT: The complete mitochondrial genome of Flustrellidra hispida and the phylogenetic position of Bryozoa among the Metazoa. MitoFish: Mitochondrial Genome Database of Fish Would you like email updates of new search results? Additionally, three phylogenetic analysis tools, including ClustalW, PHYML, and PHYLIP [2931], were integrated into IMGD to facilitate analyses across multiple species: these tools are available through the web interface supported by Phyloviewer (http://www.phyloviewer.org/; B. 1997, 25 (5): 955-964. Low or high mtDNA copy number: Samples with an estimated mtDNA copy number less than 50 were removed (N=6,505 samples) since they are prone to contamination and NUMT-derived false positive calls. Nucleic Acids Res. Wolfsberg TG, Schafer S, Tatusov RL, Tatusov TA: Organelle genome resource at NCBI. However, variations in the mitochondrial gene content and order have been utilized to elucidate evolutionary relationships among distantly-related species, on the basis of shared derived characteristics that denote the common ancestry of a given group [5]. Illustration of the location of mitochondrial DNA in human cells. mtDB: Human Mitochondrial Genome Database, a resource for population For this release we also filtered out variants with heteroplasmy < 10% in order to avoid false positives derived from contamination, sequencing errors, and NUMT misalignment. Single nucleotide polymorphisms (SNPs) in the insect mitochondrial genome sequences can support fine-scale phylogenetic analyses, as illustrated in the following examples. The Species search function supports the search of species by species name. Massively parallel sequencing of Cannabis sativa chloroplast hotspots for forensic typing. Nucleic Acids Res. (85.804%), 56/516 Single nucleotide polymorphisms (SNPs) in eight species with more than one mitochondrial genome having been sequenced (Table 4), were analyzed via the SNP Analysis Platform (http://sap.snu.ac.kr/), which is based on BLAST. 10.1093/bioinformatics/btn058. Comprehensive molecular characterization of mitochondrial genomes in Wonhoon Lee, Jongsun Park contributed equally to this work. Mol Phylogenet Evol. Federal government websites often end in .gov or .mil. 2002, 13 (2): 123-127. 2008, 9: 585-10.1186/1471-2164-9-586. Home - Genome - NCBI - National Center for Biotechnology Information IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes. Figure 3A shows an ML phylogenetic tree based on 19 completely sequenced and 5 nearly completed mitochondrial genomes in the order Hemiptera, which clearly shows two major suborder clades (Sternorrhyncha + Auchenorrhyncha and Heteroptera). (C) MP tree using 90 COI sequences from 14 Mantophasmatodean species, with Galloisiana yuasai (Grylloblattodea) as an outgroup, was drawn using DNAPARS. gnomAD v3.1 Mitochondrial DNA Variants | gnomAD browser - Broad Institute Conversely, reads genuinely arising from the mtDNA genome can be mis-aligned to the NUMTs in the reference genome. Estimates of the GC content and genome size of the 132 hexapod mitochondrial genomes. 2022 Mar;63:32-36. doi: 10.1016/j.mito.2022.01.002. Nelson LA, Wallman JF, Dowton M: Using COI barcodes to identify forensically and medically important blowflies. WebHome < MITOMAP < Foswiki Our mtDNA data include allele frequencies for heteroplasmic and homoplasmic variants, haplogroup-specific allele frequencies, predicted consequences for protein and tRNA variants, and links to mitochondrial resources. Mol Biol Evol. Entomol Abh. MITOMAP uses the mtDNA sequence as the unifying element for bringing together information on mitochondrial genome structure and function, pathogenic mutations and their clinical characteristics, population associated variation, and gene-gene interactions. Google Scholar. Google Scholar. The underrepresentation of mitochondrial gene sequences from many orders suggests that to adequately support the analysis of evolutionary relationships within the Hexapoda, these underrepresented orders require more attention. PMC The SNU Genome Browser displays SNPs/INDELs as well as PCGs, tRNAs, GC contents among the aligned genomes of Drosophila simulans KY007, KY045, and K201 strains. Characterization of the complete mitochondrial genome and phylogenetic The study of mitochondrial genetic diseases and mitochondrial DNA intraspecies diversity are key topics in several biotechnological fields. Mitochondrial DNA mutation associated with Leber's hereditary optic neuropathy. Mitochondrial genomes of parasitic arthropods: implications for studies of population genetics and evolution. Daniel MacArthur, Monkol Lek, and Vamsi Mootha provided leadership and analytical advice. Choi J, Park J, Jeon J, Chi MH, Goh J, Yoo SY, Park J, Jung K, Kim H, Park SY, Rho HS, Kim S, Kim BR, Han SS, Kang S, Lee YH: Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae. Nat Genet. Low heteroplasmic calls should be treated with caution and may be enriched with artifacts, but we want to make information on these calls available to benefit the community and allow users to put their own calls in context, such as to evaluate potential shared error modes. Search the Human Mitochondrial Protein Database (HMPDb) which provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis, function and diseases. Ellegren H: Sequencing goes 454 and takes large-scale genomics into the wild. Curr Opin Genet Dev. J Clin Med. 10.1093/nar/22.22.4673. Analyses of gene order in the 112 completely sequenced mitochondrial genomes revealed several interesting features. 10.1139/G06-148. The mitochondrial genome specifies components of complexes I-IV of the electron transport chain and complex V (ATP synthase). BLAST the Human Genome Microbial Nucleotide BLAST Genome Annotation and Analysis Eukaryotic Genome Annotation Prokaryotic Genome Annotation PASC (Pairwise Sequence Comparison) External Resources GOLD - Genomes Online Database Bacteria Genomes at Sanger Ensembl You are here: NCBI > Genomes & Maps > Genome 2007, 32 (1): 40-59. Nature. Jameson D, Gibson AP, Hudelot C, Higgs PG: OGRe: a relational database for comparative analysis of mitochondrial genomes. Clipboard, Search History, and several other advanced features are temporarily unavailable. 2001 Nov;18(5):382-7. doi: 10.1002/humu.1209. (2008) [46] and violet circle presents the sequences from the study of Klass et al. MitoFish is a comprehensive and standardized fish mitochondrial genome database. An official website of the United States government. Phylogenetic analysis based on the mitochondrial gene sequences is often limited to closely related species, due to the high rate of nucleotide substitutions. 2006 Jan 24;7:36. doi: 10.1186/1471-2105-7-36. and transmitted securely. Yong-Hwan Lee or Seunghwan Lee. Mitochondrial DNA sequence variation and risk of glioma. This research was supported by Korea Ministry of Environment as "The Eco-technopia 21 project", a grant from by Agricultural R&D Promotion Center, and a grant from Biogreen21 Project (20070301034032) to S.L. It is defined for each sample as one minus the mean heteroplasmy of any haplogroup-defining variants observed with heteroplasmy (85-99.8% alternate alleles) if at least 3 such variants are present; otherwise estimated contamination is defined as one minus the mean heteroplasmy of haplogroup-defining variants with heteroplasmy 85-100%. This site needs JavaScript to work properly. 2008, 46 (1): 82-87. 2001 Dec;18(6):482-5. We would like to note that we have tested our pipeline only on WGS samples. The exonic and mitochondrial DNA was enriched by SureSelect Human All Exon v5/6 + mitochondrial probes (Agilent Technologies, Santa Clara, CA, USA) and sequenced by NovaSeq6000 or NextSeq2000 . Xi H, Park J, Ding G, Lee YH, Li Y: SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry. Am. Park et al., unpublished) and presented through the SNU Genome Browser (http://genomebrowser.snu.ac.kr/) [25]. Lee, W., Park, J., Choi, J. et al. The IMGD also provides the Object Browser, which can collect and move selected sequences in IMGD into the Favorite, a personalized virtual storage space, for further data analyses using the analysis tools in both IMGD and CFGP [24]. 10.1038/ng2002. The mtDB provides a unique resource to both medical and human population genetic researchers. Ratasingham S, Hebert PDN: BOLD: The Barcode of Life Data System http://www.barcodinglife.org. The user interface of IMGD provides the Mitochondrial Genome Browser, which is founded on the SNU Genome Browser (http://genomebrowser.snu.ac.kr/) [25], to support the browsing and comparison of mitochondrial genome sequences in both the text and graphical forms via an interactive interface, and the Partial Sequence Browser to allow for the browsing of partially sequenced mitochondrial sequences. Atlanta, Georgia, U.S.A. MitoDat - Mendelian Inheritance and the Mitochondrion . Based on the fully sequenced mitochondrial genomes in the genus Flustrellidra (Ctenostomata: Flustrellidridae), a SNP analysis was conducted to identify a suitable gene maker for distinguishing morphologically similar species [15]. 2007, 16 (9): 1957-1968. Bookshelf These regions can serve as potential molecular markers in population genetic studies of these three orders. Mitochondrial Genome - an overview | ScienceDirect Topics WL, JP, SL, and YHL designed and managed this project, JC, JP, and WL construct the IMGD sequence database and WL, JL, JC, and JP curated all sequences in IMGD. Mol Biol Evol. 10.1016/S1055-7903(02)00342-1. Park J, Park B, Jung K, Jang S, Yu K, Choi J, Kong S, Park J, Kim S, Kim H, Kim S, Kim J, Blair J, Lee K, Kang S, Lee Y-H-: CFGP: A Web-based, Comparative Fungal Genomics Platform.
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