Cargando…
AcademH, a lineage of Academ DNA transposons encoding helicase found in animals and fungi
BACKGROUND: DNA transposons are ubiquitous components of eukaryotic genomes. Academ superfamily of DNA transposons is one of the least characterized DNA transposon superfamilies in eukaryotes. DNA transposons belonging to the Academ superfamily have been reported from various animals, one red algal...
Autor principal: | |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165386/ https://www.ncbi.nlm.nih.gov/pubmed/32328173 http://dx.doi.org/10.1186/s13100-020-00211-1 |
_version_ | 1783523466531569664 |
---|---|
author | Kojima, Kenji K. |
author_facet | Kojima, Kenji K. |
author_sort | Kojima, Kenji K. |
collection | PubMed |
description | BACKGROUND: DNA transposons are ubiquitous components of eukaryotic genomes. Academ superfamily of DNA transposons is one of the least characterized DNA transposon superfamilies in eukaryotes. DNA transposons belonging to the Academ superfamily have been reported from various animals, one red algal species Chondrus crispus, and one fungal species Puccinia graminis. Six Academ families from P. graminis encode a helicase in addition to putative transposase, while some other families encode a single protein which contains a putative transposase and an XPG nuclease. RESULTS: Systematic searches on Repbase and BLAST searches against publicly available genome sequences revealed that several species of fungi and animals contain multiple Academ transposon families encoding a helicase. These AcademH families generate 9 or 10-bp target site duplications (TSDs) while Academ families lacking helicase generate 3 or 4-bp TSDs. Phylogenetic analysis clearly shows two lineages inside of Academ, designated here as AcademH and AcademX for encoding helicase or XPG nuclease, respectively. One sublineage of AcademH in animals encodes plant homeodomain (PHD) finger in its transposase, and its remnants are found in several fish genomes. CONCLUSIONS: The AcademH lineage of TEs is widely distributed in animals and fungi, and originated early in the evolution of Academ DNA transposons. This analysis highlights the structural diversity in one less studied superfamily of eukaryotic DNA transposons. |
format | Online Article Text |
id | pubmed-7165386 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-71653862020-04-23 AcademH, a lineage of Academ DNA transposons encoding helicase found in animals and fungi Kojima, Kenji K. Mob DNA Research BACKGROUND: DNA transposons are ubiquitous components of eukaryotic genomes. Academ superfamily of DNA transposons is one of the least characterized DNA transposon superfamilies in eukaryotes. DNA transposons belonging to the Academ superfamily have been reported from various animals, one red algal species Chondrus crispus, and one fungal species Puccinia graminis. Six Academ families from P. graminis encode a helicase in addition to putative transposase, while some other families encode a single protein which contains a putative transposase and an XPG nuclease. RESULTS: Systematic searches on Repbase and BLAST searches against publicly available genome sequences revealed that several species of fungi and animals contain multiple Academ transposon families encoding a helicase. These AcademH families generate 9 or 10-bp target site duplications (TSDs) while Academ families lacking helicase generate 3 or 4-bp TSDs. Phylogenetic analysis clearly shows two lineages inside of Academ, designated here as AcademH and AcademX for encoding helicase or XPG nuclease, respectively. One sublineage of AcademH in animals encodes plant homeodomain (PHD) finger in its transposase, and its remnants are found in several fish genomes. CONCLUSIONS: The AcademH lineage of TEs is widely distributed in animals and fungi, and originated early in the evolution of Academ DNA transposons. This analysis highlights the structural diversity in one less studied superfamily of eukaryotic DNA transposons. BioMed Central 2020-04-18 /pmc/articles/PMC7165386/ /pubmed/32328173 http://dx.doi.org/10.1186/s13100-020-00211-1 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Kojima, Kenji K. AcademH, a lineage of Academ DNA transposons encoding helicase found in animals and fungi |
title | AcademH, a lineage of Academ DNA transposons encoding helicase found in animals and fungi |
title_full | AcademH, a lineage of Academ DNA transposons encoding helicase found in animals and fungi |
title_fullStr | AcademH, a lineage of Academ DNA transposons encoding helicase found in animals and fungi |
title_full_unstemmed | AcademH, a lineage of Academ DNA transposons encoding helicase found in animals and fungi |
title_short | AcademH, a lineage of Academ DNA transposons encoding helicase found in animals and fungi |
title_sort | academh, a lineage of academ dna transposons encoding helicase found in animals and fungi |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165386/ https://www.ncbi.nlm.nih.gov/pubmed/32328173 http://dx.doi.org/10.1186/s13100-020-00211-1 |
work_keys_str_mv | AT kojimakenjik academhalineageofacademdnatransposonsencodinghelicasefoundinanimalsandfungi |