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Title: Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification

Author
item AMYOTTE, STEFAN - University Of Western Ontario
item TAN, XIAOPING - North Carolina State University
item PENNERMAN, KAYLA - North Carolina State University
item DEL MAR JIMENEZ, MARIA - Pennsylvania State University
item Klosterman, Steven
item MA, LI-JUN - University Of Massachusetts
item DOBINSON, KATHERINE - Agri Food - Canada
item VERONESE, PAOLA - North Carolina State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/30/2012
Publication Date: 7/16/2012
Citation: Amyotte, S.G., Tan, X., Pennerman, K., Del Mar Jimenez-Gasco, M., Klosterman, S.J., Ma, L., Dobinson, K.F., Veronese, P. 2012. Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification. Biomed Central (BMC) Genomics. 13:314.

Interpretive Summary: Verticillium dahliae is a soilborne fungus that causes the disease known as Verticillium wilt on many types of plants. Transposons are mobile DNA sequences, also sometimes referred to as “jumping DNA” that are present in most organisms, including V. dahliae. Since transposons are capable of moving or transposing to new positions in the genetic make-up of an organism, these elements and can have a multifaceted effect on the genome of the host organism. In this study, the transposable elements (TEs) were characterized in V. dahliae and related Verticillium species. These analyses indicate that certain strains of V. dahliae contain more of some types of TEs and that certain types of TEs are lacking in some strains. The results also reveal that particular regions of the genome of V. dahliae are enriched in sequences encoding TEs. Because the distribution of TEs is patchy within the species of Verticillium, identification of TEs and their characterization in V. dahliae may reveal targets for fungal diagnostics. In the broader sense, the results indicate that TEs have played a role in generating genetic diversity within and among Verticillium species.

Technical Abstract: Verticillium dahliae (Vd) and Verticillium albo-atrum (Va) are cosmopolitan soil fungi causing very disruptive vascular diseases on a wide range of crop plants. To date, no sexual stage has been identified in either microorganism suggesting that somatic mutation is a major force in generating genetic diversity. Whole genome comparative analysis of the recently sequenced strains VdLs.17 and VaMs.102 revealed that non-random insertions of transposable elements (TEs) have contributed to the generation of four lineage-specific (LS) regions in VdLs.17. We present here a detailed analysis of Class I retrotransposons and Class II “cut-and-paste” DNA elements detected in the sequenced Verticillium genomes. We report also of their distribution in other Vd and Va isolates from various geographic origins. In VdLs.17, we identified and characterized 56 complete retrotransposons of the Gypsy-, Copia- and LINE-like types, as well as 34 full-length elements of the “cut-and-paste” superfamilies Tc1/mariner, Activator and Mutator. While Copia and Tc1/mariner were present in multiple identical copies, Activator and Mutator sequences were highly divergent. Most elements comprised complete ORFs, had matching ESTs and showed active transcription in response to stress treatment. Noticeably, we found evidences of repeat-induced point mutation (RIP) only in some of the Gypsy retroelements. While Copia-, Gypsy- and Tc1/mariner-like transposons were prominent, a large variation in presence of the other types of mobile elements was detected in the other Verticillium spp. strains surveyed. In particular, neither complete nor defective “cut-and-paste” TEs were found in VaMs.102. Copia-, Gypsy- and Tc1/mariner-like transposons are the most wide-spread TEs in the phytopathogens V. dahliae and V. albo-atrum. In VdLs.17, we identified several retroelements and “cut-and-paste” transposons still potentially active. Some of these elements have undergone diversification and subsequent selective amplification after introgression into the fungal genome. Others, such as the ripped Copias, have been potentially acquired by horizontal transfer. The observed biased TE insertion in gene-rich regions within an individual genome (VdLs.17) and the “patchy” distribution among different strains point to the mobile elements as major generators of Verticillium intra- and inter-specific genomic variation.