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Functional & Integrative Genomics

, Volume 9, Issue 1, pp 27–42 | Cite as

Non-LTR retrotransposons in fungi

  • Olga Novikova
  • Victor Fet
  • Alexander Blinov
Review

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.

Keywords

Fungi Non-LTR retrotransposons Horizontal transmission Ribonuclease H 

Notes

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).

Supplementary material

10142_2008_93_MOESM1_ESM.doc (88 kb)
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)
10142_2008_93_MOESM2_ESM.doc (177 kb)
Table S2 Novel non-LTR retrotransposons from fungi detected in this study and their accession numbers. (Word file). (DOC 177 KB)
10142_2008_93_MOESM3_ESM.doc (215 kb)
Table S3 Novel non-LTR retrotransposons from fungi detected in this study, their copy number, and putative structure. (Word file). (DOC 215 KB)
10142_2008_93_MOESM4_ESM.doc (106 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)
10142_2008_93_MOESM5_ESM.pdf (20 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)
10142_2008_93_MOESM6_ESM.pdf (53 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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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.Institute of Cytology and GeneticsNovosibirskRussia
  2. 2.Marshall UniversityHuntingtonUSA

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