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dc.contributor.authorUliano-Silva, M
dc.contributor.authorFerreira, JGRN
dc.contributor.authorKrasheninnikova, K
dc.contributor.authorBlaxter, M
dc.contributor.authorMieszkowska, N
dc.contributor.authorHall, N
dc.contributor.authorHolland, P
dc.contributor.authorDurbin, R
dc.contributor.authorRichards, T
dc.contributor.authorKersey, P
dc.contributor.authorHollingsworth, P
dc.contributor.authorWilson, W
dc.contributor.authorTwyford, A
dc.contributor.authorGaya, E
dc.contributor.authorLawniczak, M
dc.contributor.authorLewis, O
dc.contributor.authorBroad, G
dc.contributor.authorMartin, F
dc.contributor.authorHart, M
dc.contributor.authorBarnes, I
dc.contributor.authorFormenti, G
dc.contributor.authorAbueg, L
dc.contributor.authorTorrance, J
dc.contributor.authorMyers, EW
dc.contributor.authorDurbin, R
dc.contributor.authorBlaxter, M
dc.contributor.authorMcCarthy, SA
dc.date.accessioned2023-11-28T13:50:42Z
dc.date.available2023-11-28T13:50:42Z
dc.date.issued2023-07-18
dc.identifier.issn1471-2105
dc.identifier.issn1471-2105
dc.identifier.other288
dc.identifier.urihttps://pearl.plymouth.ac.uk/handle/10026.1/21756
dc.description.abstract

Background PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous genomes. In eukaryotes the mitochondrial genome is sequenced alongside the nuclear genome often at very high coverage. A dedicated tool for mitochondrial genome assembly using HiFi reads is still missing.

Results MitoHiFi was developed within the Darwin Tree of Life Project to assemble mitochondrial genomes from the HiFi reads generated for target species. The input for MitoHiFi is either the raw reads or the assembled contigs, and the tool outputs a mitochondrial genome sequence fasta file along with annotation of protein and RNA genes. Variants arising from heteroplasmy are assembled independently, and nuclear insertions of mitochondrial sequences are identified and not used in organellar genome assembly. MitoHiFi has been used to assemble 374 mitochondrial genomes (368 Metazoa and 6 Fungi species) for the Darwin Tree of Life Project, the Vertebrate Genomes Project and the Aquatic Symbiosis Genome Project. Inspection of 60 mitochondrial genomes assembled with MitoHiFi for species that already have reference sequences in public databases showed the widespread presence of previously unreported repeats.

Conclusions MitoHiFi is able to assemble mitochondrial genomes from a wide phylogenetic range of taxa from Pacbio HiFi data. MitoHiFi is written in python and is freely available on GitHub (https://github.com/marcelauliano/MitoHiFi). MitoHiFi is available with its dependencies as a Docker container on GitHub (ghcr.io/marcelauliano/mitohifi:master).

dc.format.extent288-
dc.format.mediumElectronic
dc.languageen
dc.publisherSpringer Science and Business Media LLC
dc.subjectDToL
dc.subjectDocker
dc.subjectHeteroplasmy
dc.subjectHiFi
dc.subjectLong reads
dc.subjectMitoHiFi
dc.subjectMitogenome
dc.subjectPython
dc.subjectSingularity
dc.subjectGenome, Mitochondrial
dc.subjectPhylogeny
dc.subjectRNA
dc.subjectEukaryota
dc.subjectSequence Analysis, DNA
dc.subjectHigh-Throughput Nucleotide Sequencing
dc.titleMitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
dc.typejournal-article
dc.typeJournal Article
plymouth.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/37464285
plymouth.issue1
plymouth.volume24
plymouth.publication-statusPublished online
plymouth.journalBMC Bioinformatics
dc.identifier.doi10.1186/s12859-023-05385-y
plymouth.organisational-group|Plymouth
plymouth.organisational-group|Plymouth|Faculty of Science and Engineering
plymouth.organisational-group|Plymouth|Faculty of Science and Engineering|School of Biological and Marine Sciences
plymouth.organisational-group|Plymouth|REF 2021 Researchers by UoA
plymouth.organisational-group|Plymouth|Users by role
plymouth.organisational-group|Plymouth|Users by role|Academics
plymouth.organisational-group|Plymouth|REF 2021 Researchers by UoA|UoA07 Earth Systems and Environmental Sciences
plymouth.organisational-group|Plymouth|REF 2028 Researchers by UoA
plymouth.organisational-group|Plymouth|REF 2028 Researchers by UoA|UoA07 Earth Systems and Environmental Sciences
dc.publisher.placeEngland
dcterms.dateAccepted2023-06-13
dc.date.updated2023-11-28T13:50:36Z
dc.rights.embargodate2023-12-6
dc.identifier.eissn1471-2105
rioxxterms.versionofrecord10.1186/s12859-023-05385-y


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