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New evidence on the relationship between Microsporidia and Fungi: a genome-wide analysis by DarkHorse software

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Microsporidia are a group of obligate intracellular eukaryotic parasites that infect a wide variety of species, including humans. Phylogenetic analysis indicates a relationship between the Microsporidia and the Fungi. However, most results are based on the analysis of relatively few genes. DarkHorse analysis involves the transformation of BLAST results into a lineage probability index (LPI) value and allows for the comparison of genes for an entire genome with those of other genomes. Thus, we can see which genes from the microsporidia score most closely based on the LPI with other eukaryotic organisms. In this analysis, we calculated the LPI for each gene from the genomes of 7 Microsporidia, Antonospora locustae, Enterocytozoon bieneusi, Encephalitozoon cuniculi, Encephalitozoon intestinalis, Nosema bombycis, Nosema ceranae, and Nematocida parisii, to analyze the genetic relationships between Microsporidia and other species. It was found that many (91%) genes were most closely correlated with genes from other microsporidial genomes and had the highest mean LPI (0.985), indicating a monophyletic origin of the Microsporidia. In a subsequent analysis, we excluded the other Microsporidia from the analysis to look for relationships before the divergence of Microsporidia, and found that 43% of the microsporidial genes scored highest with fungal genes, and a higher mean LPI was found with Fungi than with other kingdoms, suggesting that Microsporidia is closely related to Fungi at the genomic level. Microsporidial genes were functionally clustered based on the KOG (Eukaryotic COG) database, and the possible lineages for each gene family were discussed in concert with the DarkHorse results.
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Keywords: DarkHorse algorithm; Fungi; Microsporidia; Microsporidies; algorithme DarkHorse; champignons; genomics; génomique; indice de probabilité de lignée; lineage probability index

Document Type: Research Article

Affiliations: 1: College of Animal Science and Technology, Southwest University, Beibei, Chongqing 400715, People’s Republic of China. 2: Biotechnology Research Center, Southwest University, Beibei, Chongqing 400715, People’s Republic of China. 3: Potato Research Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada. 4: State Key Laboratory of Silkworm Genome Biology, Southwest University, 2 Tiansheng Road, Beibei District, Chongqing 400715, People’s Republic of China.

Publication date: January 1, 2014

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