Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences

In this paper, we present a new algorithm for alignment and haplogroup estimation of mitochondrial DNA (mtDNA) sequences. Based on 26,011 vetted full mitogenome sequences, we refined the 5435 original haplogroup motifs of Phylotree Build 17 without changing the haplogroup nomenclature. We adapted 43...

Descripción completa

Detalles Bibliográficos
Autores principales: Dür, Arne, Huber, Nicole, Parson, Walther
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8198973/
https://www.ncbi.nlm.nih.gov/pubmed/34072215
http://dx.doi.org/10.3390/ijms22115747
_version_ 1783707266425290752
author Dür, Arne
Huber, Nicole
Parson, Walther
author_facet Dür, Arne
Huber, Nicole
Parson, Walther
author_sort Dür, Arne
collection PubMed
description In this paper, we present a new algorithm for alignment and haplogroup estimation of mitochondrial DNA (mtDNA) sequences. Based on 26,011 vetted full mitogenome sequences, we refined the 5435 original haplogroup motifs of Phylotree Build 17 without changing the haplogroup nomenclature. We adapted 430 motifs (about 8%) and added 966 motifs for yet undetermined subclades. In summary, this led to an 18% increase of haplogroup defining motifs for full mitogenomes and a 30% increase for the mtDNA control region that is of interest for a variety of scientific disciplines, such as medical, population and forensic genetics. The new algorithm is implemented in the EMPOP mtDNA database and is freely accessible.
format Online
Article
Text
id pubmed-8198973
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-81989732021-06-14 Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences Dür, Arne Huber, Nicole Parson, Walther Int J Mol Sci Article In this paper, we present a new algorithm for alignment and haplogroup estimation of mitochondrial DNA (mtDNA) sequences. Based on 26,011 vetted full mitogenome sequences, we refined the 5435 original haplogroup motifs of Phylotree Build 17 without changing the haplogroup nomenclature. We adapted 430 motifs (about 8%) and added 966 motifs for yet undetermined subclades. In summary, this led to an 18% increase of haplogroup defining motifs for full mitogenomes and a 30% increase for the mtDNA control region that is of interest for a variety of scientific disciplines, such as medical, population and forensic genetics. The new algorithm is implemented in the EMPOP mtDNA database and is freely accessible. MDPI 2021-05-27 /pmc/articles/PMC8198973/ /pubmed/34072215 http://dx.doi.org/10.3390/ijms22115747 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Dür, Arne
Huber, Nicole
Parson, Walther
Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences
title Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences
title_full Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences
title_fullStr Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences
title_full_unstemmed Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences
title_short Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences
title_sort fine-tuning phylogenetic alignment and haplogrouping of mtdna sequences
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8198973/
https://www.ncbi.nlm.nih.gov/pubmed/34072215
http://dx.doi.org/10.3390/ijms22115747
work_keys_str_mv AT durarne finetuningphylogeneticalignmentandhaplogroupingofmtdnasequences
AT hubernicole finetuningphylogeneticalignmentandhaplogroupingofmtdnasequences
AT parsonwalther finetuningphylogeneticalignmentandhaplogroupingofmtdnasequences

Ejemplares similares