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J Fungi (Basel). 2018 Jan 19;4(1). pii: E13. doi: 10.3390/jof4010013.

Analysis of Transposable Elements in Coccidioides Species.

Author information

1
Departments of Pathology and Medicine, School of Medicine, University of California, San Diego, CA 92037, USA. tkirkland@ucsd.edu.
2
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland. musze@ibb.waw.pl.
3
Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, USA. jason.stajich@ucr.edu.

Abstract

Coccidioides immitis and C. posadasii are primary pathogenic fungi that cause disease in immunologically-normal animals and people. The organism is found exclusively in arid regions of the Southwestern United States, Mexico, and South America, but not in other parts of the world. This study is a detailed analysis of the transposable elements (TE) in Coccidioides spp. As is common in most fungi, Class I and Class II transposons were identified and the LTR Gypsy superfamily is the most common. The minority of Coccidioides Gypsy transposons contained regions highly homologous to polyprotein domains. Phylogenetic analysis of the integrase and reverse transcriptase sequences revealed that many, but not all, of the Gypsy reverse transcriptase and integrase domains clustered by species suggesting extensive transposition after speciation of the two Coccidiodies spp. The TEs were clustered and the distribution is enriched for the ends on contigs. Analysis of gene expression data from C. immitis found that protein-coding genes within 1 kB of hAT or Gypsy TEs were poorly expressed. The expression of C. posadasii genes within 1 kB of Gypsy TEs was also significantly lower compared to all genes but the difference in expression was smaller than C. immitis. C. posadasii orthologs of C. immitis Gyspsy-associated genes were also likely to be TE-associated. In both C. immitis and C. posadasii the TEs were preferentially associated with genes annotated with protein kinase gene ontology terms. These observations suggest that TE may play a role in influencing gene expression in Coccidioides spp. Our hope is that these bioinformatic studies of the potential TE influence on expression and evolution of Coccidioides will prompt the development of testable hypotheses to better understand the role of TEs in the biology and gene regulation of Coccidioides spp.

KEYWORDS:

Coccidioides spp.; fungus; genomics; transcriptome; transposable elements

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