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ARS Home » Midwest Area » Peoria, Illinois » National Center for Agricultural Utilization Research » Mycotoxin Prevention and Applied Microbiology Research » Research » Publications at this Location » Publication #320650
Title: Identification of highly variable supernumerary chromosome segments in an asexual pathogen

Author
item HUANG, XIAOQIU - Iowa State University
item ANINDYA, DAS - Iowa State University
item SAHU, BINOD - Iowa State University
item SRIVASTAVA, SUBODH - University Of Arkansas
item LEANDRO, LEONOR - Iowa State University
item O Donnell, Kerry
item BHATTACHARYYA, MADAN - Iowa State University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/16/2016
Publication Date: 8/17/2016
Publication URL: https://handle.nal.usda.gov/10113/5695400
Citation: Huang, X., Das, A., Sahu, B.B., Srivastava, S.K., Leandro, L.F., O'Donnell, K., Bhattacharyya, M.K. 2016. Identification of highly variable supernumerary chromosome segments in an asexual pathogen. PLoS One. doi:10.1371/journal.pone.0158183.

Interpretive Summary: The present comparative genomic study was conducted to elucidate genetic variation among the soybean sudden death syndrome (SDS) and bean root rot (BRR) pathogens. SDS of soybean and bean BRR have become serious constraints to the production of these crops in North and South America. Four closely related but genetically distinct Fusarium species can induce SDS, whereas two phylogenetically distinct fusaria cause BRR of Phaseolus and mung bean. Next generation whole genome sequence data was generated and compared for 11 isolates representing the six pathogens. Comparative genomic analyses identified a core genome that was shared by all 11 isolates and an accessory genome comprising supernumerary chromosomes that were unique within several of the isolates. The genome of the asexual SDS pathogen F. virguliforme was composed of a large core genome and a small supernumerary portion; there was little variation in the core between isolates, but there were a statistically significant number (21 standard deviations above the mean) of single nucleotide polymorphisms (SNPs) in the supernumerary chromosomes between isolates. Numerous instances of horizontal chromosome transfer were detected in the supernumerary chromosomes. Supernumerary chromosomes carry reverse transcriptase-related genes (RVT) and they were highly variable in length. The results suggest that the F. virguliforme genome evolved by two mechanisms: duplication-induced mutation for the core and replication via an RNA intermediate for the supernumerary. Identification of the reverse transcriptase-related enzymes in the supernumerary chromosomes is expected to have important biotechnological applications where they can be used to move genes from one species to another.

Technical Abstract: Supernumerary chromosome segments are known to harbor different transposons from their essential counterparts. The aim of this study was to investigate the role of transposons in the origin and evolution of supernumerary segments in the asexual fungal pathogen Fusariumvirguliforme. We compared the genomes of 11 isolates comprising six Fusarium species that cause soybean sudden death syndrome (SDS) or bean root rot (BRR), and identified significant levels of genetic variation in A+T-rich repeat blocks of the essential chromosomes and in A+T-neutral regions of the supernumerary segments. The A+T-rich repeat blocks in the essential chromosomes were highly variable between F. virguliforme and non-F. virguliforme isolates, but were scarcely variable between F. virguliforme isolates. The A+T-neutral regions in the supernumerary segments, however, were highly variable between F. virguliforme isolates, with a statistically significant number (21 standard deviations above the mean) of single nucleotide polymorphisms (SNPs). And supernumerary sequence types and rearrangement patterns of some F. virguliforme isolates were present in an isolate of F. cuneirostrum but not in the other F. virguliforme isolates. The most variable and highly expressed region in the supernumerary segments contained an active DNA transposon that was a most conserved match between F. virguliforme and the unrelated fungus Tolypocladiuminflatum. This transposon was absent from two of the F. virguliforme isolates. Furthermore, transposons in the supernumerary segments of some F. virguliforme isolates were present in non-F. virguliforme isolates, but were absent from the other F. virguliforme isolates. Two supernumerary P450 enzymes were 43%and 57%identical to their essential counterparts. This study has raised the possibility that transposons generate genetic variation in supernumerary chromosome segments by frequent horizontal transfer within and between closely related species.