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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

Chromosomal rearrangement between Fv Mont-1 and Fv Clinton-1B.Each horizontal line represents a contig with its name and orientation (+ denotes forward) given on the right. A unique significant match between contig regions in opposite orientations is indicated by a pair of cross lines; one in the same orientation by a pair of parallel lines. In each case, the percent identity of the match is shown next to the lines. The beginning and end of each contig region in the match are marked with vertical arrows along with their positions in bp. A red box in contig mc28.4 and a black box in contig cc26.1 represent different islands surrounded by the match; the black box is part of the match with contig mc184.2.
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pone.0158183.g003: Chromosomal rearrangement between Fv Mont-1 and Fv Clinton-1B.Each horizontal line represents a contig with its name and orientation (+ denotes forward) given on the right. A unique significant match between contig regions in opposite orientations is indicated by a pair of cross lines; one in the same orientation by a pair of parallel lines. In each case, the percent identity of the match is shown next to the lines. The beginning and end of each contig region in the match are marked with vertical arrows along with their positions in bp. A red box in contig mc28.4 and a black box in contig cc26.1 represent different islands surrounded by the match; the black box is part of the match with contig mc184.2.

Mentions: By contrast, we detected significant variation in mc28.2 and mc28.4 between the reference isolate and Fv Clinton-1B by finding unique significant matches in a comparison of these contigs with the Fv Clinton-1B genome assembly. Some of the matches suggest a chromosomal rearrangement between the reference isolate and Fv Clinton-1B, and the presence of two genomic segments in the reference isolate that were 95% identical over some of their lengths but were quite different over the rest (Fig 3). The sequence integrity of cc26.1 over the breakpoint (marked by a green arrow in Fig 3) was confirmed by a match of 96% identity between a region of cc26.1 from 28,492 to 52,548 bp and a region of a contig of 27,382 bp from a genome assembly of Fv LL0009; the percent identity of the match around the breakpoint was nearly 99%. In addition, by mapping short reads from each isolate onto the Fv Clinton-1B genome assembly, we found that cc26.1 was covered at a depth above 200 over the breakpoint by reads from the five isolates: Fv Clinton-1B (at a depth of 414), Fv LL0009 (319), Fc 31157 (722), Fp 31156 (494), and Fb 31757 (231). However, cc26.1 was not covered at the breakpoint by any reads from Fv 34551, although cc26.1 was deeply covered before and after the breakpoint by these reads. Therefore, the rearrangement type in cc26.1 of Fv Clinton-1B was not present in Fv 34551; the rearrangement type in mc28.2 and mc28.4 of Fv Mont-1 was present only in Fv 34551 based on the deep read coverage of mc28.2 around the breakpoint (at a depth of 240) and of mc28.4 around the breakpoint (231). Furthermore, a type-2 SNP G/A (G, REF allele; A, ALT allele) was found near the breakpoint in cc26.1 in Fv Clinton-1B (G at a coverage depth of 253; A at 153), Fc 31157 (567/179), and Fp 31156 (278/224), a sign that two polymorphic segments were present in each of these three isolates.


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)

Chromosomal rearrangement between Fv Mont-1 and Fv Clinton-1B.Each horizontal line represents a contig with its name and orientation (+ denotes forward) given on the right. A unique significant match between contig regions in opposite orientations is indicated by a pair of cross lines; one in the same orientation by a pair of parallel lines. In each case, the percent identity of the match is shown next to the lines. The beginning and end of each contig region in the match are marked with vertical arrows along with their positions in bp. A red box in contig mc28.4 and a black box in contig cc26.1 represent different islands surrounded by the match; the black box is part of the match with contig mc184.2.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0158183.g003: Chromosomal rearrangement between Fv Mont-1 and Fv Clinton-1B.Each horizontal line represents a contig with its name and orientation (+ denotes forward) given on the right. A unique significant match between contig regions in opposite orientations is indicated by a pair of cross lines; one in the same orientation by a pair of parallel lines. In each case, the percent identity of the match is shown next to the lines. The beginning and end of each contig region in the match are marked with vertical arrows along with their positions in bp. A red box in contig mc28.4 and a black box in contig cc26.1 represent different islands surrounded by the match; the black box is part of the match with contig mc184.2.
Mentions: By contrast, we detected significant variation in mc28.2 and mc28.4 between the reference isolate and Fv Clinton-1B by finding unique significant matches in a comparison of these contigs with the Fv Clinton-1B genome assembly. Some of the matches suggest a chromosomal rearrangement between the reference isolate and Fv Clinton-1B, and the presence of two genomic segments in the reference isolate that were 95% identical over some of their lengths but were quite different over the rest (Fig 3). The sequence integrity of cc26.1 over the breakpoint (marked by a green arrow in Fig 3) was confirmed by a match of 96% identity between a region of cc26.1 from 28,492 to 52,548 bp and a region of a contig of 27,382 bp from a genome assembly of Fv LL0009; the percent identity of the match around the breakpoint was nearly 99%. In addition, by mapping short reads from each isolate onto the Fv Clinton-1B genome assembly, we found that cc26.1 was covered at a depth above 200 over the breakpoint by reads from the five isolates: Fv Clinton-1B (at a depth of 414), Fv LL0009 (319), Fc 31157 (722), Fp 31156 (494), and Fb 31757 (231). However, cc26.1 was not covered at the breakpoint by any reads from Fv 34551, although cc26.1 was deeply covered before and after the breakpoint by these reads. Therefore, the rearrangement type in cc26.1 of Fv Clinton-1B was not present in Fv 34551; the rearrangement type in mc28.2 and mc28.4 of Fv Mont-1 was present only in Fv 34551 based on the deep read coverage of mc28.2 around the breakpoint (at a depth of 240) and of mc28.4 around the breakpoint (231). Furthermore, a type-2 SNP G/A (G, REF allele; A, ALT allele) was found near the breakpoint in cc26.1 in Fv Clinton-1B (G at a coverage depth of 253; A at 153), Fc 31157 (567/179), and Fp 31156 (278/224), a sign that two polymorphic segments were present in each of these three isolates.

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