ArticleGenome biology2021
Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed, 143 citations in OpenAlex.
- Genome Assemblies for Seven Families of Birds From the Global South.Molecular ecology resources · 2026Article
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- Chromosome-level genome assembly of the sand martin (Riparia riparia).Scientific data · 2026Article
- The complete mitogenome of Tylomelania sp. 'Poso A' (Caenogastropoda: Pachychilidae) from Lake Poso assembled from long-read sequencing data.Molecular biology reports · 2026Article
- High-quality de novo genome assembly for the Galápagos endemic lava gull using Oxford Nanopore Technologies.G3 (Bethesda, Md.) · 2026Article
- Rapid genome modifications including chromosomal fusions and large-scale inversions are key features in Arctic codfish species.Genome biology · 2026Article
- Mitochondrial genomic variations shed light on the phylogeny and biogeography of the Phrynocephalus guttatus species group (Reptilia: Agamidae) in arid Central Asia.BMC genomics · 2026Article
- Long-read sequencing reveals that the mitochondrial genome of an individualCurrent research in parasitology & vector-borne diseases · 2026Article
- Evolutionary patterns of the mitochondrial control region in vertebrates: A large-scale comparative analysis.PloS one · 2026Article
- Routine mitochondrial recombination drives rapid concerted evolution of duplicated control regions in a wild fish.Heredity · 2026Article
- The complete mitochondrial genome of the parasitoidMitochondrial DNA. Part B, Resources · 2026Article
- Structural evolution of the whole mitochondrial genome and phylogenetic inference in snakes (Squamata: Serpentes), including the undescribed mitogenome of the Brazilian endemic and critically endangered pitviper Bothrops insularis.Genetics and molecular biology · 2026Article
- Pipeasm: a tool for automated large chromosome-scale genome assembly and evaluation.Bioinformatics advances · 2026Article
- Mitochondrial genome assembly of the Peruvian Paso horse through PacBio long-read sequencing.Scientific reports · 2025Article
- Complete Mitochondrial Genomes ofAnimals : an open access journal from MDPI · 2025Article
- Coexisting With Humans: Genomic and Behavioral Consequences in a Small and Isolated Bear Population.Molecular biology and evolution · 2025Article
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- The Complete Mitochondrial Genome ofGenes · 2025Article
- Analysis of the Entire Mitogenome of the Threatened Freshwater StingrayInternational journal of molecular sciences · 2025Article
24 more citing papers are in PubMed but not listed here.
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Authors and funding
41 authors at 14 institutions in 6 countries.
Funding
Abstract
backgroundModern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.
resultsAs part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization.
conclusionsOur results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.