Robust termite phylogenies built using transposable element composition and insertion eve

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F25%3A00641740" target="_blank" >RIV/60077344:_____/25:00641740 - isvavai.cz</a>

Výsledek na webu

<a href="https://www.sciencedirect.com/science/article/abs/pii/S0960982225013272?via%3Dihub" target="_blank" >https://www.sciencedirect.com/science/article/abs/pii/S0960982225013272?via%3Dihub</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.cub.2025.10.019" target="_blank" >10.1016/j.cub.2025.10.019</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Robust termite phylogenies built using transposable element composition and insertion eve

Popis výsledku v původním jazyce

Phylogenetic trees are typically reconstructed using conserved sequence alignments.1,2 Other genomic elements, such as transposable elements (TEs), make up a large fraction of eukaryotic genomes3 but are ignored for phylogenetic reconstruction, despite potentially containing phylogenetic information,4,5 which could be used to resolve nodes that remain contentious. Here, we reconstructed accurate phylogenetic trees of 45 termites and two cockroaches using two types of characters derived from the TE landscape: (1) genome-wide presence and absence of 37,966 TE families and (2) presence/absence data of 37,966 TE families in the flanking regions of orthologous ultraconserved elements (UCEs), which was a proxy for TE insertions. The topologies of our TE-based phylogenetic trees were largely congruent with phylogenetic trees inferred from alignments of UCEs and single-copy orthologous genes, only differing for a few nodes variably reconstructed in other phylogenetic analyses. Notably, trees based on genome-wide TE family composition were more accurate than trees inferred from mitochondrial genome alignments, and trees based on TE family composition in regions flanking UCEs achieved comparable accuracy with trees inferred from single-copy orthologous gene alignments. Our results demonstrate that the TE landscape is phylogenetically informative, representing an additional set of markers for robust phylogenetic reconstructions, with potential use to resolve ambiguous nodes in the tree of life.

Název v anglickém jazyce

Robust termite phylogenies built using transposable element composition and insertion eve

Popis výsledku anglicky

Phylogenetic trees are typically reconstructed using conserved sequence alignments.1,2 Other genomic elements, such as transposable elements (TEs), make up a large fraction of eukaryotic genomes3 but are ignored for phylogenetic reconstruction, despite potentially containing phylogenetic information,4,5 which could be used to resolve nodes that remain contentious. Here, we reconstructed accurate phylogenetic trees of 45 termites and two cockroaches using two types of characters derived from the TE landscape: (1) genome-wide presence and absence of 37,966 TE families and (2) presence/absence data of 37,966 TE families in the flanking regions of orthologous ultraconserved elements (UCEs), which was a proxy for TE insertions. The topologies of our TE-based phylogenetic trees were largely congruent with phylogenetic trees inferred from alignments of UCEs and single-copy orthologous genes, only differing for a few nodes variably reconstructed in other phylogenetic analyses. Notably, trees based on genome-wide TE family composition were more accurate than trees inferred from mitochondrial genome alignments, and trees based on TE family composition in regions flanking UCEs achieved comparable accuracy with trees inferred from single-copy orthologous gene alignments. Our results demonstrate that the TE landscape is phylogenetically informative, representing an additional set of markers for robust phylogenetic reconstructions, with potential use to resolve ambiguous nodes in the tree of life.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10616 - Entomology

Projekt

<a href="/cs/project/GM23-08010M" target="_blank" >GM23-08010M: Trajektorie evoluce genomů u konvergentních organismů</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2025

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Current Biology

ISSN

0960-9822

e-ISSN

1879-0445

Svazek periodika

35

Číslo periodika v rámci svazku

22

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

10

Strana od-do

5626-5632

Kód UT WoS článku

001625425500017

EID výsledku v databázi Scopus

2-s2.0-105022178854