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TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species
BACKGROUND: Long terminal repeat retrotransposons (LTR-RTs) are major components of plant genomes. Common LTR-RTs contain the palindromic dinucleotide 5′-‘TG’–‘CA’-3′ motif at the ends. Thus, further analyses of non-canonical LTR-RTs with non-palindromic motifs will enhance our understanding of thei...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5659011/ https://www.ncbi.nlm.nih.gov/pubmed/29093758 http://dx.doi.org/10.1186/s13100-017-0098-8 |
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author | Yin, Hao Wu, Xiao Shi, Dongqing Chen, Yangyang Qi, Kaijie Ma, Zhengqiang Zhang, Shaoling |
author_facet | Yin, Hao Wu, Xiao Shi, Dongqing Chen, Yangyang Qi, Kaijie Ma, Zhengqiang Zhang, Shaoling |
author_sort | Yin, Hao |
collection | PubMed |
description | BACKGROUND: Long terminal repeat retrotransposons (LTR-RTs) are major components of plant genomes. Common LTR-RTs contain the palindromic dinucleotide 5′-‘TG’–‘CA’-3′ motif at the ends. Thus, further analyses of non-canonical LTR-RTs with non-palindromic motifs will enhance our understanding of their structures and evolutionary history. RESULTS: Here, we report two new LTR-RT subfamilies (TGTT and AACA) with atypical dinucleotide ends of 5′-‘TG’–‘TT’-3′, and 5′-‘AA’–‘CA’-3′ in pear, apple, peach and mei. In total, 91 intact LTR-RTs were identified and classified into four TGTT and four AACA families. A structural annotation analysis showed that the four TGTT families, together with AACA1 and AACA2, belong to the Copia-like superfamily, whereas AACA3 and AACA4 appeared to be TRIM elements. The average amplification time frames for the eight families ranged from 0.05 to 2.32 million years. Phylogenetics coupled with sequence analyses revealed that the TGTT1 elements of peach were horizontally transferred from apple. In addition, 32 elements from two TGTT and three AACA families had detectable transcriptional activation, and a qRT-PCR analysis indicated that their expression levels varied dramatically in different species, organs and stress treatments. CONCLUSIONS: Two novel LTR-RT subfamilies that terminated with non-palindromic dinucleotides at the ends of their LTRs were identified in four Rosaceae species, and a deep analysis showed their recent activity, horizontal transfer and varied transcriptional levels in different species, organs and stress treatments. This work enhances our understanding of the structural variation and evolutionary history of LTR-RTs in plants and also provides a valuable resource for future investigations of LTR-RTs having specific structures in other species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13100-017-0098-8) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5659011 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-56590112017-11-01 TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species Yin, Hao Wu, Xiao Shi, Dongqing Chen, Yangyang Qi, Kaijie Ma, Zhengqiang Zhang, Shaoling Mob DNA Research BACKGROUND: Long terminal repeat retrotransposons (LTR-RTs) are major components of plant genomes. Common LTR-RTs contain the palindromic dinucleotide 5′-‘TG’–‘CA’-3′ motif at the ends. Thus, further analyses of non-canonical LTR-RTs with non-palindromic motifs will enhance our understanding of their structures and evolutionary history. RESULTS: Here, we report two new LTR-RT subfamilies (TGTT and AACA) with atypical dinucleotide ends of 5′-‘TG’–‘TT’-3′, and 5′-‘AA’–‘CA’-3′ in pear, apple, peach and mei. In total, 91 intact LTR-RTs were identified and classified into four TGTT and four AACA families. A structural annotation analysis showed that the four TGTT families, together with AACA1 and AACA2, belong to the Copia-like superfamily, whereas AACA3 and AACA4 appeared to be TRIM elements. The average amplification time frames for the eight families ranged from 0.05 to 2.32 million years. Phylogenetics coupled with sequence analyses revealed that the TGTT1 elements of peach were horizontally transferred from apple. In addition, 32 elements from two TGTT and three AACA families had detectable transcriptional activation, and a qRT-PCR analysis indicated that their expression levels varied dramatically in different species, organs and stress treatments. CONCLUSIONS: Two novel LTR-RT subfamilies that terminated with non-palindromic dinucleotides at the ends of their LTRs were identified in four Rosaceae species, and a deep analysis showed their recent activity, horizontal transfer and varied transcriptional levels in different species, organs and stress treatments. This work enhances our understanding of the structural variation and evolutionary history of LTR-RTs in plants and also provides a valuable resource for future investigations of LTR-RTs having specific structures in other species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13100-017-0098-8) contains supplementary material, which is available to authorized users. BioMed Central 2017-10-27 /pmc/articles/PMC5659011/ /pubmed/29093758 http://dx.doi.org/10.1186/s13100-017-0098-8 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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. |
spellingShingle | Research Yin, Hao Wu, Xiao Shi, Dongqing Chen, Yangyang Qi, Kaijie Ma, Zhengqiang Zhang, Shaoling TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species |
title | TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species |
title_full | TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species |
title_fullStr | TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species |
title_full_unstemmed | TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species |
title_short | TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species |
title_sort | tgtt and aaca: two transcriptionally active ltr retrotransposon subfamilies with a specific ltr structure and horizontal transfer in four rosaceae species |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5659011/ https://www.ncbi.nlm.nih.gov/pubmed/29093758 http://dx.doi.org/10.1186/s13100-017-0098-8 |
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