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Non-LTR retrotransposons in fungi

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Abstract

Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. Fungi have small genomes, usually with limited amounts of repetitive DNA. In silico approach has been used to survey the non-LTR elements in 57 fungal genomes. More than 100 novel non-LTR retrotransposons were found, which belonged to five diverse clades. The present survey identified two novel clades of fungal non-LTR retrotransposons. The copy number of non-LTR retroelements varied widely. Some of the studied species contained a single copy of non-LTR retrotransposon, whereas others possessed a great number of non-LTR retrotransposon copies per genome. Although evolutionary relationships of most elements are congruent with phylogeny of host species, a new case of possible horizontal transfer was found between Eurotiomycetes and Sordariomycetes.

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Acknowledgements

The sequence data for P. chrysosporium, L. bicolor, T. reesei, A. niger, and P. stipitis were produced by the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/). Preliminary sequence data for Ascosphaera apis was obtained from Baylor College of Medicine Human Genome Sequencing Center website at http://www.hgsc.bcm.tmc.edu. Preliminary sequence data for Alternaria brassicicola were obtained from Genome Sequencing Center at Washington University Medical School (http://genome.wustl.edu/index.cgi).

This work was supported in part by state contract 10002-251/П-25/155-270/200404-082 and Siberian Branch of the Russian Academy of Sciences (project No. 10.4).

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Correspondence to Olga Novikova.

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Table S1

List of species, genomes of which were analyzed in silico in the present study and the sources of genomic sequences. (Word file). (DOC 88.5 KB)

Table S2

Novel non-LTR retrotransposons from fungi detected in this study and their accession numbers. (Word file). (DOC 177 KB)

Table S3

Novel non-LTR retrotransposons from fungi detected in this study, their copy number, and putative structure. (Word file). (DOC 215 KB)

Table S4

Amino acid divergences of 11 cellular proteins from A. niger, A. fumigatus, A. oryzae, F. oxysporum, and C. globosum. (Word file). (DOC 106 KB)

Fig. S1

The percentage of non-LTR retrotransposons sequences in investigated fungal genomes plotted against the genome size. (Adobe Reader file). (PDF 20.3 KB)

Fig. S2

The 50% consensus tree of the Bayesian inference based on RT amino acid sequences of non-LTR retrotransposons including newly described elements from fungi. Posterior probabilities are indicated. (Adobe Reader file). (PDF 52.9 KB)

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Novikova, O., Fet, V. & Blinov, A. Non-LTR retrotransposons in fungi. Funct Integr Genomics 9, 27–42 (2009). https://doi.org/10.1007/s10142-008-0093-8

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