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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 tree of 13 duplicated sequences (length 3,772 bp) in the Fv Mont-1 assembly.Each sequence was named based on its A+T content followed by its contig name. For example, sequence P61.mc37.31 indicates an A+T content of 61% and mc37.31 as its source contig. The four most recently duplicated sequences were P69.mc53.3, P70.mc175.2, P69.mc29.3 and P70.mc147.3, with the highest A+T content range of 69% to 70%. Support values from 100 bootstrap replicates are provided at internodes.
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pone.0158183.g001: Maximum likelihood tree of 13 duplicated sequences (length 3,772 bp) in the Fv Mont-1 assembly.Each sequence was named based on its A+T content followed by its contig name. For example, sequence P61.mc37.31 indicates an A+T content of 61% and mc37.31 as its source contig. The four most recently duplicated sequences were P69.mc53.3, P70.mc175.2, P69.mc29.3 and P70.mc147.3, with the highest A+T content range of 69% to 70%. Support values from 100 bootstrap replicates are provided at internodes.

Mentions: To shed light on the last observation, we selected all of the contigs that were at least 1 kb in the reference assembly and calculated the total number of contig bases covered by reads from Fc 31157 as well as that not covered by reads from this isolate. The size of the covered portion was 39.5 Mb; that of the uncovered portion was 10.9 Mb. The uncovered portion was A+T rich (68%), whereas the covered portion was A+T poor (45%). The content of duplicated sequences in the uncovered portion was 70%, with 48% containing sequences with copy numbers above 20. In sharp contrast, the content of duplicated sequences in the covered portion was 3.8%, with 0.56% containing 20-plus-copy sequences. These results indicate that F. virguliforme and F. cuneirostrum were more diverged in the uncovered portion rich in duplication and A+T content. For example, we observed C-T/G-A substitutions at a rate of 98% (871/887) in a 10-kb alignment (with 91% identity) of two adjacent contigs in the uncovered portion, where the integrity of both Fv Mont-1 contigs were verified based on their nearly complete and SNP-free coverage at a depth above 100 by reads from each of the other three F. virguliforme isolates. Each contig had a best match (with 90% identity) to the Fc 31157 genome assembly and to the Fp 31156 genome assembly, which were 99.95% identical over the match. Moreover, a maximum likelihood tree of 13 duplicated sequences in the Fv Mont-1 assembly illustrates that the more recently duplicated sequences had a higher A+T content (Fig 1).


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 tree of 13 duplicated sequences (length 3,772 bp) in the Fv Mont-1 assembly.Each sequence was named based on its A+T content followed by its contig name. For example, sequence P61.mc37.31 indicates an A+T content of 61% and mc37.31 as its source contig. The four most recently duplicated sequences were P69.mc53.3, P70.mc175.2, P69.mc29.3 and P70.mc147.3, with the highest A+T content range of 69% to 70%. Support values from 100 bootstrap replicates are provided at internodes.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0158183.g001: Maximum likelihood tree of 13 duplicated sequences (length 3,772 bp) in the Fv Mont-1 assembly.Each sequence was named based on its A+T content followed by its contig name. For example, sequence P61.mc37.31 indicates an A+T content of 61% and mc37.31 as its source contig. The four most recently duplicated sequences were P69.mc53.3, P70.mc175.2, P69.mc29.3 and P70.mc147.3, with the highest A+T content range of 69% to 70%. Support values from 100 bootstrap replicates are provided at internodes.
Mentions: To shed light on the last observation, we selected all of the contigs that were at least 1 kb in the reference assembly and calculated the total number of contig bases covered by reads from Fc 31157 as well as that not covered by reads from this isolate. The size of the covered portion was 39.5 Mb; that of the uncovered portion was 10.9 Mb. The uncovered portion was A+T rich (68%), whereas the covered portion was A+T poor (45%). The content of duplicated sequences in the uncovered portion was 70%, with 48% containing sequences with copy numbers above 20. In sharp contrast, the content of duplicated sequences in the covered portion was 3.8%, with 0.56% containing 20-plus-copy sequences. These results indicate that F. virguliforme and F. cuneirostrum were more diverged in the uncovered portion rich in duplication and A+T content. For example, we observed C-T/G-A substitutions at a rate of 98% (871/887) in a 10-kb alignment (with 91% identity) of two adjacent contigs in the uncovered portion, where the integrity of both Fv Mont-1 contigs were verified based on their nearly complete and SNP-free coverage at a depth above 100 by reads from each of the other three F. virguliforme isolates. Each contig had a best match (with 90% identity) to the Fc 31157 genome assembly and to the Fp 31156 genome assembly, which were 99.95% identical over the match. Moreover, a maximum likelihood tree of 13 duplicated sequences in the Fv Mont-1 assembly illustrates that the more recently duplicated sequences had a higher A+T content (Fig 1).

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