Annotated Bioinformatic Pipelines for Genome Assembly and Annotation of Mitochondrial Genomes
Mitochondrial genomes (mitogenomes) display relatively rapid mutation rates, low sequence recombination, high copy numbers, and maternal inheritance patterns, rendering them valuable blueprints for mapping lineages, uncovering historical migration patterns, understanding intraspecific population dyn...
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Bio-protocol LLC
2025-03-01
|
| Series: | Bio-Protocol |
| Online Access: | https://bio-protocol.org/en/bpdetail?id=5231&type=0 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850070721078755328 |
|---|---|
| author | Jessica Winn Aletta Bester-van der Merwe Simo Maduna |
| author_facet | Jessica Winn Aletta Bester-van der Merwe Simo Maduna |
| author_sort | Jessica Winn |
| collection | DOAJ |
| description | Mitochondrial genomes (mitogenomes) display relatively rapid mutation rates, low sequence recombination, high copy numbers, and maternal inheritance patterns, rendering them valuable blueprints for mapping lineages, uncovering historical migration patterns, understanding intraspecific population dynamics, and investigating how environmental pressures shape traits underpinned by genetic variation. Here, we present the bioinformatic pipeline and code used to assemble and annotate the complete mitogenomes of five houndsharks (Chondrichthyes: Triakidae) and compare them to the mitogenomes of other closely related species. We demonstrate the value of a combined assembly approach for detecting deviations in mitogenome structure and describe how to select an assembly approach that best suits the sequencing data. The datasets required to run our analyses are available on the GitHub and Dryad repositories. |
| format | Article |
| id | doaj-art-d55bce6e942e4543941a2e10abab19a0 |
| institution | DOAJ |
| issn | 2331-8325 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Bio-protocol LLC |
| record_format | Article |
| series | Bio-Protocol |
| spelling | doaj-art-d55bce6e942e4543941a2e10abab19a02025-08-20T02:47:28ZengBio-protocol LLCBio-Protocol2331-83252025-03-0115510.21769/BioProtoc.5231Annotated Bioinformatic Pipelines for Genome Assembly and Annotation of Mitochondrial GenomesJessica Winn0Aletta Bester-van der Merwe1Simo Maduna2Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, South AfricaMolecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, South AfricaMolecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape, South AfricaDepartment of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, Svanvik, NorwayMitochondrial genomes (mitogenomes) display relatively rapid mutation rates, low sequence recombination, high copy numbers, and maternal inheritance patterns, rendering them valuable blueprints for mapping lineages, uncovering historical migration patterns, understanding intraspecific population dynamics, and investigating how environmental pressures shape traits underpinned by genetic variation. Here, we present the bioinformatic pipeline and code used to assemble and annotate the complete mitogenomes of five houndsharks (Chondrichthyes: Triakidae) and compare them to the mitogenomes of other closely related species. We demonstrate the value of a combined assembly approach for detecting deviations in mitogenome structure and describe how to select an assembly approach that best suits the sequencing data. The datasets required to run our analyses are available on the GitHub and Dryad repositories.https://bio-protocol.org/en/bpdetail?id=5231&type=0 |
| spellingShingle | Jessica Winn Aletta Bester-van der Merwe Simo Maduna Annotated Bioinformatic Pipelines for Genome Assembly and Annotation of Mitochondrial Genomes Bio-Protocol |
| title | Annotated Bioinformatic Pipelines for Genome Assembly and Annotation of Mitochondrial Genomes |
| title_full | Annotated Bioinformatic Pipelines for Genome Assembly and Annotation of Mitochondrial Genomes |
| title_fullStr | Annotated Bioinformatic Pipelines for Genome Assembly and Annotation of Mitochondrial Genomes |
| title_full_unstemmed | Annotated Bioinformatic Pipelines for Genome Assembly and Annotation of Mitochondrial Genomes |
| title_short | Annotated Bioinformatic Pipelines for Genome Assembly and Annotation of Mitochondrial Genomes |
| title_sort | annotated bioinformatic pipelines for genome assembly and annotation of mitochondrial genomes |
| url | https://bio-protocol.org/en/bpdetail?id=5231&type=0 |
| work_keys_str_mv | AT jessicawinn annotatedbioinformaticpipelinesforgenomeassemblyandannotationofmitochondrialgenomes AT alettabestervandermerwe annotatedbioinformaticpipelinesforgenomeassemblyandannotationofmitochondrialgenomes AT simomaduna annotatedbioinformaticpipelinesforgenomeassemblyandannotationofmitochondrialgenomes |