Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences

[NathanS]

Давно уже небыло новостей по митоДНК, а PhyloTree застряло на Build 17 с февраля 2016.
Авторы этой статьи сделали новый анализ мито-геномов, в частности доступных в GenBank.
Они предлагают новое обновленное мито-дерево с сохранением терминиологии Build 17 и добавляют новые группы через *
5 лет ждали новостей

Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences
Arne Dür, Nicole Huber and Walther Parson
Int J Mol Sci. 2021 Jun; 22(11): 5747.

Abstract

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.

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Mitochondrial haplogroup names were developed in the 1990s [5], and a systematically organized catalogue was established in 2009 by Phylotree(mt) ([6]; http://phylotree.org, accessed on 5 May 2021). This freely accessible resource was curated until February 2016, when its last build (17) was released. This version used 24,275 mitochondrial DNA (mtDNA) sequences (=mitogenomes), resulting in a tree with 5435 different haplogroup defining motifs.

... previous work has been performed to enhance the haplogroup estimation by extending the data basis of full mitogenome sequences, e.g., by adding 14,990 GenBank sequences [4]. In this study, we further refine this approach by compiling a database of 26,011 vetted full mitogenomes and by using this database to refine the Phylotree haplogroup motifs.

The reanalysis of the mitogenome sequences that define the current haplogroup nomenclature system of Phylotree(mt) (PT17) led to an increase of discernable subhaplogroups of 18% and 30% for the mitogenome and the CR, respectively. Although the haplogroup nomenclature was not changed, but extended by using the * symbol, its effect on improved alignment and haplogrouping is significant. We note that we deliberately decided to stick to the established haplogroup nomenclature system to avoid confusion in future studies.