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Identification of Highly Variable Supernumerary Chromosome Segments in an Asexual Pathogen.

Huang X, Das A, Sahu BB, Srivastava SK, Leandro LF, O'Donnell K, Bhattacharyya MK - PLoS ONE (2016)

Bottom Line: 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).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.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Iowa State University, Ames, Iowa, United States of America.

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 Fusarium virguliforme. 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 Tolypocladium inflatum. 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.

No MeSH data available.


Related in: MedlinePlus

Maximum-likelihood midpoint rooted tree of 11 SDS/BRR Fusarium isolates, inferred from genome-wide SNP data with 200 bootstrap samples.
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pone.0158183.g002: Maximum-likelihood midpoint rooted tree of 11 SDS/BRR Fusarium isolates, inferred from genome-wide SNP data with 200 bootstrap samples.

Mentions: We inferred evolutionary relationships among the 11 isolates by constructing a phylogenetic tree (Fig 2) based on concatenation of 297,076 SNPs from the common reference assembly section sufficiently covered by reads from each isolate. The tree showed three clearly separate clusters: a first one formed by the four F. virguliforme isolates; a second one by Fb 31757, Fc 31157, and Fp 31156; a third one by the three F. tucumaniae isolates. The four F. virguliforme isolates formed a close cluster with extremely low levels of genome-wide variation among them. On the other hand, high levels of genome-wide variation were observed within the sexually reproducing species F. tucumaniae.


Identification of Highly Variable Supernumerary Chromosome Segments in an Asexual Pathogen.

Huang X, Das A, Sahu BB, Srivastava SK, Leandro LF, O'Donnell K, Bhattacharyya MK - PLoS ONE (2016)

Maximum-likelihood midpoint rooted tree of 11 SDS/BRR Fusarium isolates, inferred from genome-wide SNP data with 200 bootstrap samples.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920403&req=5

pone.0158183.g002: Maximum-likelihood midpoint rooted tree of 11 SDS/BRR Fusarium isolates, inferred from genome-wide SNP data with 200 bootstrap samples.
Mentions: We inferred evolutionary relationships among the 11 isolates by constructing a phylogenetic tree (Fig 2) based on concatenation of 297,076 SNPs from the common reference assembly section sufficiently covered by reads from each isolate. The tree showed three clearly separate clusters: a first one formed by the four F. virguliforme isolates; a second one by Fb 31757, Fc 31157, and Fp 31156; a third one by the three F. tucumaniae isolates. The four F. virguliforme isolates formed a close cluster with extremely low levels of genome-wide variation among them. On the other hand, high levels of genome-wide variation were observed within the sexually reproducing species F. tucumaniae.

Bottom Line: 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).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.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Iowa State University, Ames, Iowa, United States of America.

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 Fusarium virguliforme. 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 Tolypocladium inflatum. 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.

No MeSH data available.


Related in: MedlinePlus