Universität zu Köln

Depotter, J. R. L., Oekmen, B., Ebert, M. K., Beckers, J., Kruse, J., Thines, M. and Doehlemann, G. . High Nucleotide Substitution Rates Associated with Retrotransposon Proliferation Drive Dynamic Secretome Evolution in Smut Pathogens. Microbiol. Spectr.. WASHINGTON: AMER SOC MICROBIOLOGY. ISSN 2165-0497

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Abstract

Transposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, Ustilago hordei, encountered a recent genome expansion. Using long reads, we assembled genomes of 6 U. hordei strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to a higher genome fraction of long terminal repeat retrotransposons (LTR-RTs). In the studied smut genomes, LTR-RTs fractions are the largest in U. hordei and are positively correlated with the mating-type locus sizes, which is up to similar to 560 kb in U. hordei. Furthermore, LTR-RTs were found to be associated with higher nucleotide substitution levels, as these occur in specific genome regions of smut species with a recent LTR-RT proliferation. Moreover, genes in genome regions with higher nucleotide substitution levels generally reside closer to LTR-RTs than other genome regions. Genome regions with many nucleotide substitutions encountered an especially high fraction of CG substitutions, which is not observed for LTR-RT sequences. The high nucleotide substitution levels particularly accelerate the evolution of secretome genes, as their more accessory nature results in substitutions that often lead to amino acid alterations. IMPORTANCE Genomic alteration can be generated through various means, in which transposable elements (TEs) can play a pivotal role. Their mobility causes mutagenesis in itself and can disrupt the function of the sequences they insert into. They also impact genome evolution as their repetitive nature facilitates nonhomologous recombination. Furthermore, TEs have been linked to specific epigenetic genome organizations. We report a recent TE proliferation in the genome of the barley covered smut fungus, Ustilago hordei. This proliferation is associated with a distinct nucleotide substitution regime that has a higher rate and a higher fraction of CG substitutions. This different regime shapes the evolution of genes in subjected genome regions. We hypothesize that TEs may influence the error-rate of DNA polymerase in a hitherto unknown fashion.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Depotter, J. R. L. UNSPECIFIED UNSPECIFIED UNSPECIFIED Oekmen, B. UNSPECIFIED UNSPECIFIED UNSPECIFIED Ebert, M. K. UNSPECIFIED UNSPECIFIED UNSPECIFIED Beckers, J. UNSPECIFIED UNSPECIFIED UNSPECIFIED Kruse, J. UNSPECIFIED UNSPECIFIED UNSPECIFIED Thines, M. UNSPECIFIED UNSPECIFIED UNSPECIFIED Doehlemann, G. UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-676357
DOI:	10.1128/spectrum.00349-22
Journal or Publication Title:	Microbiol. Spectr.
Publisher:	AMER SOC MICROBIOLOGY
Place of Publication:	WASHINGTON
ISSN:	2165-0497
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language GENOME EVOLUTION; MATING-TYPE; SEQUENCE; REVEALS; FUNGUS; ALIGNMENT; PROTEIN; SYSTEM; TOOL; ARCHITECTURE Multiple languages Microbiology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/67635