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This article is part of the supplement: IUFRO Tree Biotechnology Conference 2011: From Genomes to Integration and Delivery

Open Access Poster presentation

Identification of potential transcriptionally active Copia LTR retrotransposons in Eucalyptus

Helena Marcon12, Douglas Domingues1 and Celso Marino1

Author Affiliations

1 Departamento de Genética, UNESP, Botucatu, São Paulo, Brazil

2 IAPAR, Londrina, Paraná, Brazil

BMC Proceedings 2011, 5(Suppl 7):P164  doi:10.1186/1753-6561-5-S7-P164

The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1753-6561/5/S7/P164


Published:13 September 2011

© 2011 Marcon et al; licensee BioMed Central Ltd.

This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Background

Long Terminal Repeat retrotransposons (LTR-RTs) represent the most abundant genomic component in all plant genomes thus far investigated. They are transposable elements that replicate through a “copy/paste” mechanism that relies on reverse transcription and integration of a RNA intermediate. Plant LTR-RTs can be divided in two major superfamilies: Copia and Gypsy[1]. LTR-RTs have impact on genome size variation, as well as in the expression of adjacent genes in their host genomes, providing a “genomic plasticity” [2]. Their transcription was believed to be extremely repressed in plants. However, despite their potential mutagenic and deleterious effects, LTR-RTs were proven to be transcriptionally active in several plant species [3].

Eucalyptus is one of the most commercially important forest genus in the world, due to their superior growth, broad adaptability and multipurpose wood properties. Most molecular studies in Eucalyptus are focused on cellulose production and wood development, and there are few works on genome composition, structure and evolution. Pinus and Populus, the tree genera with most available genomic resources, have several works analyzing their repertoire of LTR-RTs [i. e 4, 5], but only one study characterized LTR-RTs in Eucalyptus[6], with no detailed manual checking or phylogenetic analysis. Here, we used FOREST database as a starting point to identify transcriptionally active Copia LTR-RTs in Eucalyptus, that were further analyzed regarding their in silico expression, evolutionary diversity, and distribution in public genomic databases.

Methods

A previous survey with 88 CopiaLTR-RTs from diverse plants defined six major common evolutionary Copialineages [7]. The 22 Arabidopsis thaliana families analyzed in that study were used as queries to the identify EucalyptusEST sequences related to Copiaelements in FORESTS database [8], by tBLASTx (e-value >1e-50). Sequences were then analyzed in RepBase [9] to confirm their similarity to Copia LTR-RTs. EucalyptusESTs with >200bp of copia-like retrotransposon fragments were used to identify complete copies in Eucalyptusgrandis genome v 1.0 in a BLASTn search (identity >80%; in a region >250bp). We picked up 10000bp surrounding the aligned region, that were analyzed using LTR-Finder [10] and LTR_STRUC [11]. Full-length LTR-RTs were then used as queries in GenBank to retrieve related EucalyptusEST sequences (>200bp; >80% identity). Phylogenetic analyses using the reverse transcriptase of these elements (alignment in MUSCLE, Maximimum Likelihood method, bootstrap 1000 replicates) were done using MEGA 5.01 [12].

Results

Stem, calli and seedlings were the cDNA libraries from FOREST database with most EST sequences, in this Copia LTR-RT search. We identified 20 consensus sequences (total: 36 ESTs) from 3 tissues, roots, leaves and flower-buds. We also identified 29 ESTs in GenBank from xylem, root apex and cold-stressed plants (Table 1). Using EST data, we identified six full-length retrotransposons families that had different copy number in the Eucalyptus genome, estimated by BLAST searches (cutoff 1e-50). Copy number ranged from 24 to 262 (Table 1). Phylogenetic analyses showed that they are members of the Ale, Angela, GMR and Ivana evolutionary lineages (figure 1). Ale was the evolutionary lineage encompassing families with highest and lowest copy number (Table 1).

Table 1. Overall features of LTR-RTs analyzed.

Conclusion

In summary, the present data demonstrate the potential impact of future studies about functional and genomic analysis of LTR-RTs in Eucalyptus. This is the first characterization of full-length Copia LTR-RTs families in Eucalyptus genome with potential transcriptional activity, giving insights about phylogenetic diversity and copy number variation of retrotransposons in this tree.

thumbnailFigure 1. Phylogenetic tree of Copia LTR-RTs elements. Based on Du and collaborators (2010).

Acknowledgements

HSM was supported by a fellowship from Coordenadoria de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and CNPq.

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