The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F18%3A73591960" target="_blank" >RIV/61989592:15310/18:73591960 - isvavai.cz</a>
Result on the web
<a href="https://www.sciencedirect.com/science/article/pii/S1055790317304281" target="_blank" >https://www.sciencedirect.com/science/article/pii/S1055790317304281</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1016/j.ympev.2018.07.008" target="_blank" >10.1016/j.ympev.2018.07.008</a>
Alternative languages
Result language
angličtina
Original language name
The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera
Original language description
A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of > 3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10616 - Entomology
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2018
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
MOLECULAR PHYLOGENETICS AND EVOLUTION
ISSN
1055-7903
e-ISSN
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Volume of the periodical
128
Issue of the periodical within the volume
1
Country of publishing house
US - UNITED STATES
Number of pages
11
Pages from-to
1-11
UT code for WoS article
000446022200001
EID of the result in the Scopus database
2-s2.0-85050543241