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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

Eight sequence alignments with SNPs and small indels (4 to 166 bp).Each alignment is composed of two or three sequence types (denoted by Types a, b and c): a reference contig, a contig in the Fv Clinton-1B assembly, and sometimes short reads from one of the ten isolates, which were mapped to one of the two contigs. The name of each contig along with its orientation (+ denotes forward and—denotes reverse), or the name of the isolate if present, is shown to the right of its sequence type. Every allele in the contig is marked with an arrow and a number in bp showing its position. Notation: mc184.2, Fv Mont-1 contig 184.2; cc26.1, Fv Clinton-1B contig 26.1.
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pone.0158183.g004: Eight sequence alignments with SNPs and small indels (4 to 166 bp).Each alignment is composed of two or three sequence types (denoted by Types a, b and c): a reference contig, a contig in the Fv Clinton-1B assembly, and sometimes short reads from one of the ten isolates, which were mapped to one of the two contigs. The name of each contig along with its orientation (+ denotes forward and—denotes reverse), or the name of the isolate if present, is shown to the right of its sequence type. Every allele in the contig is marked with an arrow and a number in bp showing its position. Notation: mc184.2, Fv Mont-1 contig 184.2; cc26.1, Fv Clinton-1B contig 26.1.

Mentions: A total of eight contig sequence alignments showing SNPs and small indels between the reference isolate and Fv Clinton-1B are shown in Fig 4. Each alignment contained two or more instances of polymorphism, all of which were close enough to be linked by 102-bp reads. We checked for the presence/absence of these polymorphic sequences in each of the top six isolates in Table 2. This was done by mapping short reads from each of the six isolates onto the genome assembly of the reference isolate and again onto that of Fv Clinton-1B. We found additional types of polymorphic sequences by examining the read coverage of each contig sequence. Thus, some alignments in Fig 4 contained three polymorphic sequences. For each isolate and for each sequence in each alignment, Table 3 shows the number of reads from the isolate that matched and linked all alleles in the sequence. Note that for some isolates and alignments, the read counts from the isolate for each sequence in the alignment were quite different (e.g. a range of 33-78 reads per sequence for isolate Fv Clinton-1B and Alignment A3). The most likely explanation for the large difference in read count between the three types in isolate Fv Clinton-1B is that at least 4 copies of the supernumerary segment were present in this isolate, with type A3.Tb present in more copies than types A3.Ta and A3.Tc. In light of this observation, a segment with two or more highly polymorphic copies in an isolate is also called supernumerary. Thus, the detection of a significant number of type-2 SNPs in an isolate indicates the presence of a supernumerary segment.


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)

Eight sequence alignments with SNPs and small indels (4 to 166 bp).Each alignment is composed of two or three sequence types (denoted by Types a, b and c): a reference contig, a contig in the Fv Clinton-1B assembly, and sometimes short reads from one of the ten isolates, which were mapped to one of the two contigs. The name of each contig along with its orientation (+ denotes forward and—denotes reverse), or the name of the isolate if present, is shown to the right of its sequence type. Every allele in the contig is marked with an arrow and a number in bp showing its position. Notation: mc184.2, Fv Mont-1 contig 184.2; cc26.1, Fv Clinton-1B contig 26.1.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0158183.g004: Eight sequence alignments with SNPs and small indels (4 to 166 bp).Each alignment is composed of two or three sequence types (denoted by Types a, b and c): a reference contig, a contig in the Fv Clinton-1B assembly, and sometimes short reads from one of the ten isolates, which were mapped to one of the two contigs. The name of each contig along with its orientation (+ denotes forward and—denotes reverse), or the name of the isolate if present, is shown to the right of its sequence type. Every allele in the contig is marked with an arrow and a number in bp showing its position. Notation: mc184.2, Fv Mont-1 contig 184.2; cc26.1, Fv Clinton-1B contig 26.1.
Mentions: A total of eight contig sequence alignments showing SNPs and small indels between the reference isolate and Fv Clinton-1B are shown in Fig 4. Each alignment contained two or more instances of polymorphism, all of which were close enough to be linked by 102-bp reads. We checked for the presence/absence of these polymorphic sequences in each of the top six isolates in Table 2. This was done by mapping short reads from each of the six isolates onto the genome assembly of the reference isolate and again onto that of Fv Clinton-1B. We found additional types of polymorphic sequences by examining the read coverage of each contig sequence. Thus, some alignments in Fig 4 contained three polymorphic sequences. For each isolate and for each sequence in each alignment, Table 3 shows the number of reads from the isolate that matched and linked all alleles in the sequence. Note that for some isolates and alignments, the read counts from the isolate for each sequence in the alignment were quite different (e.g. a range of 33-78 reads per sequence for isolate Fv Clinton-1B and Alignment A3). The most likely explanation for the large difference in read count between the three types in isolate Fv Clinton-1B is that at least 4 copies of the supernumerary segment were present in this isolate, with type A3.Tb present in more copies than types A3.Ta and A3.Tc. In light of this observation, a segment with two or more highly polymorphic copies in an isolate is also called supernumerary. Thus, the detection of a significant number of type-2 SNPs in an isolate indicates the presence of a supernumerary segment.

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