Annotated Bioinformatic Pipelines for Genome Assembly and Annotation of Mitochondrial Genomes

被引：0

作者：

Winn, Jessica C. ^{[1
]}

Bester-van der Merwe, Aletta E. ^{[1
]}

Maduna, Simo N. ^{[1
,2
]}

机构：

[1] Stellenbosch Univ, Dept Genet, Mol Breeding & Biodivers Grp, Stellenbosch, Western Cape, South Africa

[2] Norwegian Inst Bioecon Res, Dept Ecosyst Barents Reg, Svanhovd Res Stn, Svanvik, Norway

来源：

BIO-PROTOCOL | 2025年 / 15卷 / 05期

基金：

新加坡国家研究基金会;

关键词：

Comparative mitogenomics; Hybrid assembly; Intramitochondrial recombination; Next-generation sequencing; TANDEM DUPLICATION; EVOLUTION; ACCURATE; REPEATS; PROGRAM;

D O I：

10.21769/BioProtoc.5231

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：28

共 56 条

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