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United States Department of Agriculture

Agricultural Research Service

Research Project: CONTROL OF TOXIC ENDOPHYTIC FUNGI WITH BACTERIAL ENDOPHYTES AND REGULATION OF BACTERIAL METABOLITES FOR NOVEL USES IN FOOD SAFETY

Location: Toxicology and Mycotoxin Research

Title: Comparative genomic survey, exon-intron annotation and phylogenetic analysis of NAT-homologous sequences in archaea, protists, fungi, viruses, and invertebrates

Authors
item Glenn, Anthony
item Karagianni, Eleni -
item Ulndreaj, Antigona -
item Boukouvala, Sotiria -

Submitted to: Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: May 1, 2010
Publication Date: September 3, 2010
Citation: Glenn, A.E., Karagianni, E.P., Ulndreaj, A., Boukouvala, S. 2010. Comparative genomic survey, exon-intron annotation and phylogenetic analysis of NAT-homologous sequences in archaea, protists, fungi, viruses, and invertebrates. In: Proceedings of the 5th International Workshop on the Arylamine N-Acetyltransferases, September 1-3, 2010, Paris, France. p. 15.

Technical Abstract: We have previously published extensive genomic surveys [1-3], reporting NAT-homologous sequences in hundreds of sequenced bacterial, fungal and vertebrate genomes. We present here the results of our latest search of 2445 genomes, representing 1532 (70 archaeal, 1210 bacterial, 43 protist, 97 fungal, 76 animal, 36 plant) species. We describe the first NAT homologues in protists, many fungi and invertebrates, as well as in one archaeon (Halogeometricum borinquense) and a giant virus (Acanthamoeba polyphaga mimivirus). As previously, inspection of genomic databases and expressed sequence tags did not support the presence of NATs in plants. Annotation of retrieved sequences was carried out both computationally and manually, based on consensus criteria. New NAT sequences were named according to the current nomenclature for non-human NATs (http://www.mbg.duth.gr/non-humannatnomenclature/) and were submitted to the EMBL third-party annotation database. Of the reconstructed NAT open reading frames (ORFs) of lower eukaryotes, a substantial number (28% in protists, 78% in fungi) were predicted to contain at least one intron. Segmented ORFs were also found in lower chordates, suggesting the loss and re-appearance of introns more than once during eukaryotic NAT evolution. Upstream non-coding exons were also evident in several eukaryotic taxa. We have employed our exhaustive dataset of annotated NAT-homologous sequences to perform a comprehensive phylogenetic analysis. Neighbor-Joining, Maximum Parsimony and Bayesian-Inference methods were used to thoroughly evaluate NAT phylogenetic history. The NATs of higher animals and possibly fungi appear to be monophyletic, but evidence supports a mixed phylogeny of NATs among bacteria, protists and possibly some invertebrates, as summarized below: Prokaryotes: The phylogenetic clustering of bacterial NATs did not deviate substantially from the consensus taxonomy, while in organisms with more than one NAT genes there were examples of both paralogous and independent origin of the sister loci. The archaeal NAT protein exhibited 30-40% match with the NATs of taxonomically diverse bacteria and certain fishes. Protists: The presence of more than one NAT genes per genome was evident in most surveyed species and these almost always represented recently diverged paralogues. Of exception were some NAT paralogues of cellular slime molds which clustered with the NAT paralogues of the Bacillus bacteria, supporting the occurrence of horizontal gene transfer between the two taxonomic groups. Overall, our findings indicated a mixed phylogeny of NATs among bacteria and protists. Fungi: Ascomycetes described as typically pathogenic to animals or humans possess one NAT, while those infecting plants generally possess multiple NATs. The phylogenetic analysis clustered the NAT1 sequences of animal pathogens as a monophyletic sister clade to the monophyletic Eurotiales orthologues. Paralogy between the fungal NAT genes was limited and the overall pattern of phylogeny supported distinct NAT lineages of orthologues, many of which are within plant pathogens. The fungal NATs are distinctly monophyletic with the possible exception of one basidiomycete homologue. Animals: We report homologues in the lower phyla of cnidarians and potentially rotifers, while the presence of NATs in the protostomes is uncertain. The phylogenetic relationships of chordate NATs follows the consensus taxonomy and paralogous NAT genes have derived from recent genomic duplications, with few exceptions. The analysis indicates a monophyletic and fully supported clade of animal NATs, with the possible exception of the homologues of echinoderms and hemichordates.

Last Modified: 9/2/2014
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