eu40  (ATCC)


Bioz Verified Symbol ATCC is a verified supplier
Bioz Manufacturer Symbol ATCC manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 86

    Structured Review

    ATCC eu40
    The candidate vic1 locus. Density plots of sequence reads that match by sequence similarity to a corresponding portion of Scaffold 5 of the EP155 reference genome assembly (coordinates indicated at the top) near a vic1 linkage marker (E190825) are shown for three strains that differ from EP155 (2211-22) at the vic1 locus (allele 1), EU55 (1221-22), EU31 (1211-22), and <t>EU40</t> (1122-11) and for strain EU60 (2221-22) that is the same as EP155 at the vic1 locus (allele 2). Strain EU55 was sequenced using Roche 454 GS FLX Titanium protocols, and the other strains were sequenced with Illumina HiSeq protocols. Forward reads are indicated in green, reverse reads are indicated in red, paired reads are indicated in blue. The region containing the highly polymorphic sequences is indicated by the absence of matched reads (gap). The ORFs located within a ∼14-kb region containing the gap are shown below the sequence read-density plots. A polymorphic gene encoding a HET-domain-containing protein (91% amino acid identity between alleles 1 and 2) was designated as vic1a-1 for allele 1 present in EU31, EU40, and EU55 and as vic1a-2 for allele 2 present in reference strain EP155 and strain EU60. The gene encoding the DUF1909-domain-containing protein present in allele 2, but absent in allele 1 (i.e., idiomorphic), was designated vic1b-2. The position of the vic1 linkage marker E190825 relative to the vic1 gene candidates is also indicated. The C. parasitica strain EP155 reference genome assembly is available at http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html. The Joint Genome Institute (JGI) protein identity (ID) numbers for vic1a-2 and vic1b-2 are 330677 and 356517, respectively.
    Eu40, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/eu40/product/ATCC
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    eu40 - by Bioz Stars, 2024-02
    86/100 stars

    Images

    1) Product Images from "Vegetative Incompatibility Loci with Dedicated Roles in Allorecognition Restrict Mycovirus Transmission in Chestnut Blight Fungus"

    Article Title: Vegetative Incompatibility Loci with Dedicated Roles in Allorecognition Restrict Mycovirus Transmission in Chestnut Blight Fungus

    Journal: Genetics

    doi: 10.1534/genetics.114.164574

    The candidate vic1 locus. Density plots of sequence reads that match by sequence similarity to a corresponding portion of Scaffold 5 of the EP155 reference genome assembly (coordinates indicated at the top) near a vic1 linkage marker (E190825) are shown for three strains that differ from EP155 (2211-22) at the vic1 locus (allele 1), EU55 (1221-22), EU31 (1211-22), and EU40 (1122-11) and for strain EU60 (2221-22) that is the same as EP155 at the vic1 locus (allele 2). Strain EU55 was sequenced using Roche 454 GS FLX Titanium protocols, and the other strains were sequenced with Illumina HiSeq protocols. Forward reads are indicated in green, reverse reads are indicated in red, paired reads are indicated in blue. The region containing the highly polymorphic sequences is indicated by the absence of matched reads (gap). The ORFs located within a ∼14-kb region containing the gap are shown below the sequence read-density plots. A polymorphic gene encoding a HET-domain-containing protein (91% amino acid identity between alleles 1 and 2) was designated as vic1a-1 for allele 1 present in EU31, EU40, and EU55 and as vic1a-2 for allele 2 present in reference strain EP155 and strain EU60. The gene encoding the DUF1909-domain-containing protein present in allele 2, but absent in allele 1 (i.e., idiomorphic), was designated vic1b-2. The position of the vic1 linkage marker E190825 relative to the vic1 gene candidates is also indicated. The C. parasitica strain EP155 reference genome assembly is available at http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html. The Joint Genome Institute (JGI) protein identity (ID) numbers for vic1a-2 and vic1b-2 are 330677 and 356517, respectively.
    Figure Legend Snippet: The candidate vic1 locus. Density plots of sequence reads that match by sequence similarity to a corresponding portion of Scaffold 5 of the EP155 reference genome assembly (coordinates indicated at the top) near a vic1 linkage marker (E190825) are shown for three strains that differ from EP155 (2211-22) at the vic1 locus (allele 1), EU55 (1221-22), EU31 (1211-22), and EU40 (1122-11) and for strain EU60 (2221-22) that is the same as EP155 at the vic1 locus (allele 2). Strain EU55 was sequenced using Roche 454 GS FLX Titanium protocols, and the other strains were sequenced with Illumina HiSeq protocols. Forward reads are indicated in green, reverse reads are indicated in red, paired reads are indicated in blue. The region containing the highly polymorphic sequences is indicated by the absence of matched reads (gap). The ORFs located within a ∼14-kb region containing the gap are shown below the sequence read-density plots. A polymorphic gene encoding a HET-domain-containing protein (91% amino acid identity between alleles 1 and 2) was designated as vic1a-1 for allele 1 present in EU31, EU40, and EU55 and as vic1a-2 for allele 2 present in reference strain EP155 and strain EU60. The gene encoding the DUF1909-domain-containing protein present in allele 2, but absent in allele 1 (i.e., idiomorphic), was designated vic1b-2. The position of the vic1 linkage marker E190825 relative to the vic1 gene candidates is also indicated. The C. parasitica strain EP155 reference genome assembly is available at http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html. The Joint Genome Institute (JGI) protein identity (ID) numbers for vic1a-2 and vic1b-2 are 330677 and 356517, respectively.

    Techniques Used: Sequencing, Marker

    The candidate vic3 locus. Read-density plots of sequence reads mapped by homology to a ∼7.5-kb portion of Scaffold 5 of the EP155 reference genome assembly identified by manual inspection to contain a region of sequence polymorphism (gaps) with a pattern consistent with that for allele distributions at the vic3 locus. Density plots are shown for strains EU55 (1221-22), EU40 (1122-11), and EU60 (2221-22) that differ at the vic3 genetic locus (i.e., contain allele 2) from reference strain EP155 (2211-22) and strain EU31 (1211-22) that, like strain EP155, contains allele 1 at the vic3 locus (Cortesi and Milgroom 1998). The ORFs located within this region are shown for the two alleles below the sequence read-density plots. Polymorphic (46% amino acid identity) ORFs encoding a hypothetical protein were designated vic3a-1 (599 aa) for allele 1 in strains EP155 and EU31 and vic3a-2 (614 aa) for allele 2 present in strains EU55, EU40, and EU60, while two small polymorphic (85% amino acid identity) ORFs encoding a Life-guard-1-like protein were designated vic3b-1 (102 aa) and vic3b-2 (108 aa). These two polymorphic genes were separated by a highly conserved ORF encoding an actin-binding-like protein. Sequencing protocols and color coding of reads are described in Figure 1. The JGI protein ID numbers for vic3a-1 and vic3b-1 are 331201 and 340400, respectively. The protein ID number for the predicted actin-binding-like protein is 331200.
    Figure Legend Snippet: The candidate vic3 locus. Read-density plots of sequence reads mapped by homology to a ∼7.5-kb portion of Scaffold 5 of the EP155 reference genome assembly identified by manual inspection to contain a region of sequence polymorphism (gaps) with a pattern consistent with that for allele distributions at the vic3 locus. Density plots are shown for strains EU55 (1221-22), EU40 (1122-11), and EU60 (2221-22) that differ at the vic3 genetic locus (i.e., contain allele 2) from reference strain EP155 (2211-22) and strain EU31 (1211-22) that, like strain EP155, contains allele 1 at the vic3 locus (Cortesi and Milgroom 1998). The ORFs located within this region are shown for the two alleles below the sequence read-density plots. Polymorphic (46% amino acid identity) ORFs encoding a hypothetical protein were designated vic3a-1 (599 aa) for allele 1 in strains EP155 and EU31 and vic3a-2 (614 aa) for allele 2 present in strains EU55, EU40, and EU60, while two small polymorphic (85% amino acid identity) ORFs encoding a Life-guard-1-like protein were designated vic3b-1 (102 aa) and vic3b-2 (108 aa). These two polymorphic genes were separated by a highly conserved ORF encoding an actin-binding-like protein. Sequencing protocols and color coding of reads are described in Figure 1. The JGI protein ID numbers for vic3a-1 and vic3b-1 are 331201 and 340400, respectively. The protein ID number for the predicted actin-binding-like protein is 331200.

    Techniques Used: Sequencing, Binding Assay

    Polymorphic nonfunctional pseudo vic locus. Density plots of sequence reads mapped by homology to a portion of EP155 (2211-22) sequence assembly Scaffold 6 extending from map coordinates ∼588,000 to 624,000 are shown for strains EU55 (1221-22), EU31 (1211-22), EU40 (1122-11), and EU60 (2221-22). The defined gap observed at 599,514–606,808 for strains EU55, EU31, and EU60 relative to EP155 and EU40 corresponds to allelic differences in genome organization at this locus as shown in Figure 8 for allele 1 (in strains EP155 and EU40) and allele 2 (in strains EU55, EU31, and EU60). There is no concordance between the polymorphic pattern and allele specificity at any of the genetically defined vic loci; e.g., EP155 (2211-22) and EU40 (1122-11) are heteroallelic at all six genetically defined vic loci, but are homoallelic at this locus.
    Figure Legend Snippet: Polymorphic nonfunctional pseudo vic locus. Density plots of sequence reads mapped by homology to a portion of EP155 (2211-22) sequence assembly Scaffold 6 extending from map coordinates ∼588,000 to 624,000 are shown for strains EU55 (1221-22), EU31 (1211-22), EU40 (1122-11), and EU60 (2221-22). The defined gap observed at 599,514–606,808 for strains EU55, EU31, and EU60 relative to EP155 and EU40 corresponds to allelic differences in genome organization at this locus as shown in Figure 8 for allele 1 (in strains EP155 and EU40) and allele 2 (in strains EU55, EU31, and EU60). There is no concordance between the polymorphic pattern and allele specificity at any of the genetically defined vic loci; e.g., EP155 (2211-22) and EU40 (1122-11) are heteroallelic at all six genetically defined vic loci, but are homoallelic at this locus.

    Techniques Used: Sequencing

    Organization of polymorphic nonfunctional pseudo vic locus alleles. Inspection of the sequence contigs for the two alleles corresponding to the polymorphic region identified on Scaffold 6 spanning positions 599514–606808 in the EP155 reference genome assembly revealed that an ∼7.7-kb portion of the sequence present in EP155 and EU40 (allele 1) was deleted in strains EU55, EU31, and EU60 (allele 2). The allele 1 sequence contained two ORFs not present in allele 2. These encoded a 407-aa protein containing a GTPase domain and a 1211-aa-long HET-domain-containing protein. The two ORFs were flanked by ∼900-bp imperfect (88% identity) direct repeats. The allele 2 sequence lacked the ∼7.7-kb region harboring the GTPase and HET-domain ORFs and contained only one copy of the flanking repeats that consisted of the 5′-proximal two-thirds of the left repeat and the 3′-proximal one-third of the right repeat and a G-C base pair replacing a T-A base pair at the breakpoint as indicated by the red letters. (Figure S9).
    Figure Legend Snippet: Organization of polymorphic nonfunctional pseudo vic locus alleles. Inspection of the sequence contigs for the two alleles corresponding to the polymorphic region identified on Scaffold 6 spanning positions 599514–606808 in the EP155 reference genome assembly revealed that an ∼7.7-kb portion of the sequence present in EP155 and EU40 (allele 1) was deleted in strains EU55, EU31, and EU60 (allele 2). The allele 1 sequence contained two ORFs not present in allele 2. These encoded a 407-aa protein containing a GTPase domain and a 1211-aa-long HET-domain-containing protein. The two ORFs were flanked by ∼900-bp imperfect (88% identity) direct repeats. The allele 2 sequence lacked the ∼7.7-kb region harboring the GTPase and HET-domain ORFs and contained only one copy of the flanking repeats that consisted of the 5′-proximal two-thirds of the left repeat and the 3′-proximal one-third of the right repeat and a G-C base pair replacing a T-A base pair at the breakpoint as indicated by the red letters. (Figure S9).

    Techniques Used: Sequencing

    PCR-based differentiation of alleles for pseudo vic locus at C. parasitica genome Scaffold 6: 599,514–606,808
    Figure Legend Snippet: PCR-based differentiation of alleles for pseudo vic locus at C. parasitica genome Scaffold 6: 599,514–606,808

    Techniques Used:

    eu40  (ATCC)


    Bioz Verified Symbol ATCC is a verified supplier
    Bioz Manufacturer Symbol ATCC manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 86

    Structured Review

    ATCC eu40
    The candidate vic1 locus. Density plots of sequence reads that match by sequence similarity to a corresponding portion of Scaffold 5 of the EP155 reference genome assembly (coordinates indicated at the top) near a vic1 linkage marker (E190825) are shown for three strains that differ from EP155 (2211-22) at the vic1 locus (allele 1), EU55 (1221-22), EU31 (1211-22), and <t>EU40</t> (1122-11) and for strain EU60 (2221-22) that is the same as EP155 at the vic1 locus (allele 2). Strain EU55 was sequenced using Roche 454 GS FLX Titanium protocols, and the other strains were sequenced with Illumina HiSeq protocols. Forward reads are indicated in green, reverse reads are indicated in red, paired reads are indicated in blue. The region containing the highly polymorphic sequences is indicated by the absence of matched reads (gap). The ORFs located within a ∼14-kb region containing the gap are shown below the sequence read-density plots. A polymorphic gene encoding a HET-domain-containing protein (91% amino acid identity between alleles 1 and 2) was designated as vic1a-1 for allele 1 present in EU31, EU40, and EU55 and as vic1a-2 for allele 2 present in reference strain EP155 and strain EU60. The gene encoding the DUF1909-domain-containing protein present in allele 2, but absent in allele 1 (i.e., idiomorphic), was designated vic1b-2. The position of the vic1 linkage marker E190825 relative to the vic1 gene candidates is also indicated. The C. parasitica strain EP155 reference genome assembly is available at http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html. The Joint Genome Institute (JGI) protein identity (ID) numbers for vic1a-2 and vic1b-2 are 330677 and 356517, respectively.
    Eu40, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/eu40/product/ATCC
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    eu40 - by Bioz Stars, 2024-02
    86/100 stars

    Images

    1) Product Images from "Vegetative Incompatibility Loci with Dedicated Roles in Allorecognition Restrict Mycovirus Transmission in Chestnut Blight Fungus"

    Article Title: Vegetative Incompatibility Loci with Dedicated Roles in Allorecognition Restrict Mycovirus Transmission in Chestnut Blight Fungus

    Journal: Genetics

    doi: 10.1534/genetics.114.164574

    The candidate vic1 locus. Density plots of sequence reads that match by sequence similarity to a corresponding portion of Scaffold 5 of the EP155 reference genome assembly (coordinates indicated at the top) near a vic1 linkage marker (E190825) are shown for three strains that differ from EP155 (2211-22) at the vic1 locus (allele 1), EU55 (1221-22), EU31 (1211-22), and EU40 (1122-11) and for strain EU60 (2221-22) that is the same as EP155 at the vic1 locus (allele 2). Strain EU55 was sequenced using Roche 454 GS FLX Titanium protocols, and the other strains were sequenced with Illumina HiSeq protocols. Forward reads are indicated in green, reverse reads are indicated in red, paired reads are indicated in blue. The region containing the highly polymorphic sequences is indicated by the absence of matched reads (gap). The ORFs located within a ∼14-kb region containing the gap are shown below the sequence read-density plots. A polymorphic gene encoding a HET-domain-containing protein (91% amino acid identity between alleles 1 and 2) was designated as vic1a-1 for allele 1 present in EU31, EU40, and EU55 and as vic1a-2 for allele 2 present in reference strain EP155 and strain EU60. The gene encoding the DUF1909-domain-containing protein present in allele 2, but absent in allele 1 (i.e., idiomorphic), was designated vic1b-2. The position of the vic1 linkage marker E190825 relative to the vic1 gene candidates is also indicated. The C. parasitica strain EP155 reference genome assembly is available at http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html. The Joint Genome Institute (JGI) protein identity (ID) numbers for vic1a-2 and vic1b-2 are 330677 and 356517, respectively.
    Figure Legend Snippet: The candidate vic1 locus. Density plots of sequence reads that match by sequence similarity to a corresponding portion of Scaffold 5 of the EP155 reference genome assembly (coordinates indicated at the top) near a vic1 linkage marker (E190825) are shown for three strains that differ from EP155 (2211-22) at the vic1 locus (allele 1), EU55 (1221-22), EU31 (1211-22), and EU40 (1122-11) and for strain EU60 (2221-22) that is the same as EP155 at the vic1 locus (allele 2). Strain EU55 was sequenced using Roche 454 GS FLX Titanium protocols, and the other strains were sequenced with Illumina HiSeq protocols. Forward reads are indicated in green, reverse reads are indicated in red, paired reads are indicated in blue. The region containing the highly polymorphic sequences is indicated by the absence of matched reads (gap). The ORFs located within a ∼14-kb region containing the gap are shown below the sequence read-density plots. A polymorphic gene encoding a HET-domain-containing protein (91% amino acid identity between alleles 1 and 2) was designated as vic1a-1 for allele 1 present in EU31, EU40, and EU55 and as vic1a-2 for allele 2 present in reference strain EP155 and strain EU60. The gene encoding the DUF1909-domain-containing protein present in allele 2, but absent in allele 1 (i.e., idiomorphic), was designated vic1b-2. The position of the vic1 linkage marker E190825 relative to the vic1 gene candidates is also indicated. The C. parasitica strain EP155 reference genome assembly is available at http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html. The Joint Genome Institute (JGI) protein identity (ID) numbers for vic1a-2 and vic1b-2 are 330677 and 356517, respectively.

    Techniques Used: Sequencing, Marker

    The candidate vic3 locus. Read-density plots of sequence reads mapped by homology to a ∼7.5-kb portion of Scaffold 5 of the EP155 reference genome assembly identified by manual inspection to contain a region of sequence polymorphism (gaps) with a pattern consistent with that for allele distributions at the vic3 locus. Density plots are shown for strains EU55 (1221-22), EU40 (1122-11), and EU60 (2221-22) that differ at the vic3 genetic locus (i.e., contain allele 2) from reference strain EP155 (2211-22) and strain EU31 (1211-22) that, like strain EP155, contains allele 1 at the vic3 locus (Cortesi and Milgroom 1998). The ORFs located within this region are shown for the two alleles below the sequence read-density plots. Polymorphic (46% amino acid identity) ORFs encoding a hypothetical protein were designated vic3a-1 (599 aa) for allele 1 in strains EP155 and EU31 and vic3a-2 (614 aa) for allele 2 present in strains EU55, EU40, and EU60, while two small polymorphic (85% amino acid identity) ORFs encoding a Life-guard-1-like protein were designated vic3b-1 (102 aa) and vic3b-2 (108 aa). These two polymorphic genes were separated by a highly conserved ORF encoding an actin-binding-like protein. Sequencing protocols and color coding of reads are described in Figure 1. The JGI protein ID numbers for vic3a-1 and vic3b-1 are 331201 and 340400, respectively. The protein ID number for the predicted actin-binding-like protein is 331200.
    Figure Legend Snippet: The candidate vic3 locus. Read-density plots of sequence reads mapped by homology to a ∼7.5-kb portion of Scaffold 5 of the EP155 reference genome assembly identified by manual inspection to contain a region of sequence polymorphism (gaps) with a pattern consistent with that for allele distributions at the vic3 locus. Density plots are shown for strains EU55 (1221-22), EU40 (1122-11), and EU60 (2221-22) that differ at the vic3 genetic locus (i.e., contain allele 2) from reference strain EP155 (2211-22) and strain EU31 (1211-22) that, like strain EP155, contains allele 1 at the vic3 locus (Cortesi and Milgroom 1998). The ORFs located within this region are shown for the two alleles below the sequence read-density plots. Polymorphic (46% amino acid identity) ORFs encoding a hypothetical protein were designated vic3a-1 (599 aa) for allele 1 in strains EP155 and EU31 and vic3a-2 (614 aa) for allele 2 present in strains EU55, EU40, and EU60, while two small polymorphic (85% amino acid identity) ORFs encoding a Life-guard-1-like protein were designated vic3b-1 (102 aa) and vic3b-2 (108 aa). These two polymorphic genes were separated by a highly conserved ORF encoding an actin-binding-like protein. Sequencing protocols and color coding of reads are described in Figure 1. The JGI protein ID numbers for vic3a-1 and vic3b-1 are 331201 and 340400, respectively. The protein ID number for the predicted actin-binding-like protein is 331200.

    Techniques Used: Sequencing, Binding Assay

    Polymorphic nonfunctional pseudo vic locus. Density plots of sequence reads mapped by homology to a portion of EP155 (2211-22) sequence assembly Scaffold 6 extending from map coordinates ∼588,000 to 624,000 are shown for strains EU55 (1221-22), EU31 (1211-22), EU40 (1122-11), and EU60 (2221-22). The defined gap observed at 599,514–606,808 for strains EU55, EU31, and EU60 relative to EP155 and EU40 corresponds to allelic differences in genome organization at this locus as shown in Figure 8 for allele 1 (in strains EP155 and EU40) and allele 2 (in strains EU55, EU31, and EU60). There is no concordance between the polymorphic pattern and allele specificity at any of the genetically defined vic loci; e.g., EP155 (2211-22) and EU40 (1122-11) are heteroallelic at all six genetically defined vic loci, but are homoallelic at this locus.
    Figure Legend Snippet: Polymorphic nonfunctional pseudo vic locus. Density plots of sequence reads mapped by homology to a portion of EP155 (2211-22) sequence assembly Scaffold 6 extending from map coordinates ∼588,000 to 624,000 are shown for strains EU55 (1221-22), EU31 (1211-22), EU40 (1122-11), and EU60 (2221-22). The defined gap observed at 599,514–606,808 for strains EU55, EU31, and EU60 relative to EP155 and EU40 corresponds to allelic differences in genome organization at this locus as shown in Figure 8 for allele 1 (in strains EP155 and EU40) and allele 2 (in strains EU55, EU31, and EU60). There is no concordance between the polymorphic pattern and allele specificity at any of the genetically defined vic loci; e.g., EP155 (2211-22) and EU40 (1122-11) are heteroallelic at all six genetically defined vic loci, but are homoallelic at this locus.

    Techniques Used: Sequencing

    Organization of polymorphic nonfunctional pseudo vic locus alleles. Inspection of the sequence contigs for the two alleles corresponding to the polymorphic region identified on Scaffold 6 spanning positions 599514–606808 in the EP155 reference genome assembly revealed that an ∼7.7-kb portion of the sequence present in EP155 and EU40 (allele 1) was deleted in strains EU55, EU31, and EU60 (allele 2). The allele 1 sequence contained two ORFs not present in allele 2. These encoded a 407-aa protein containing a GTPase domain and a 1211-aa-long HET-domain-containing protein. The two ORFs were flanked by ∼900-bp imperfect (88% identity) direct repeats. The allele 2 sequence lacked the ∼7.7-kb region harboring the GTPase and HET-domain ORFs and contained only one copy of the flanking repeats that consisted of the 5′-proximal two-thirds of the left repeat and the 3′-proximal one-third of the right repeat and a G-C base pair replacing a T-A base pair at the breakpoint as indicated by the red letters. (Figure S9).
    Figure Legend Snippet: Organization of polymorphic nonfunctional pseudo vic locus alleles. Inspection of the sequence contigs for the two alleles corresponding to the polymorphic region identified on Scaffold 6 spanning positions 599514–606808 in the EP155 reference genome assembly revealed that an ∼7.7-kb portion of the sequence present in EP155 and EU40 (allele 1) was deleted in strains EU55, EU31, and EU60 (allele 2). The allele 1 sequence contained two ORFs not present in allele 2. These encoded a 407-aa protein containing a GTPase domain and a 1211-aa-long HET-domain-containing protein. The two ORFs were flanked by ∼900-bp imperfect (88% identity) direct repeats. The allele 2 sequence lacked the ∼7.7-kb region harboring the GTPase and HET-domain ORFs and contained only one copy of the flanking repeats that consisted of the 5′-proximal two-thirds of the left repeat and the 3′-proximal one-third of the right repeat and a G-C base pair replacing a T-A base pair at the breakpoint as indicated by the red letters. (Figure S9).

    Techniques Used: Sequencing

    PCR-based differentiation of alleles for pseudo vic locus at C. parasitica genome Scaffold 6: 599,514–606,808
    Figure Legend Snippet: PCR-based differentiation of alleles for pseudo vic locus at C. parasitica genome Scaffold 6: 599,514–606,808

    Techniques Used:

    eu40  (ATCC)


    Bioz Verified Symbol ATCC is a verified supplier
    Bioz Manufacturer Symbol ATCC manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 86

    Structured Review

    ATCC eu40
    The candidate vic1 locus. Density plots of sequence reads that match by sequence similarity to a corresponding portion of Scaffold 5 of the EP155 reference genome assembly (coordinates indicated at the top) near a vic1 linkage marker (E190825) are shown for three strains that differ from EP155 (2211-22) at the vic1 locus (allele 1), EU55 (1221-22), EU31 (1211-22), and <t>EU40</t> (1122-11) and for strain EU60 (2221-22) that is the same as EP155 at the vic1 locus (allele 2). Strain EU55 was sequenced using Roche 454 GS FLX Titanium protocols, and the other strains were sequenced with Illumina HiSeq protocols. Forward reads are indicated in green, reverse reads are indicated in red, paired reads are indicated in blue. The region containing the highly polymorphic sequences is indicated by the absence of matched reads (gap). The ORFs located within a ∼14-kb region containing the gap are shown below the sequence read-density plots. A polymorphic gene encoding a HET-domain-containing protein (91% amino acid identity between alleles 1 and 2) was designated as vic1a-1 for allele 1 present in EU31, EU40, and EU55 and as vic1a-2 for allele 2 present in reference strain EP155 and strain EU60. The gene encoding the DUF1909-domain-containing protein present in allele 2, but absent in allele 1 (i.e., idiomorphic), was designated vic1b-2. The position of the vic1 linkage marker E190825 relative to the vic1 gene candidates is also indicated. The C. parasitica strain EP155 reference genome assembly is available at http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html. The Joint Genome Institute (JGI) protein identity (ID) numbers for vic1a-2 and vic1b-2 are 330677 and 356517, respectively.
    Eu40, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/eu40/product/ATCC
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    eu40 - by Bioz Stars, 2024-02
    86/100 stars

    Images

    1) Product Images from "Vegetative Incompatibility Loci with Dedicated Roles in Allorecognition Restrict Mycovirus Transmission in Chestnut Blight Fungus"

    Article Title: Vegetative Incompatibility Loci with Dedicated Roles in Allorecognition Restrict Mycovirus Transmission in Chestnut Blight Fungus

    Journal: Genetics

    doi: 10.1534/genetics.114.164574

    The candidate vic1 locus. Density plots of sequence reads that match by sequence similarity to a corresponding portion of Scaffold 5 of the EP155 reference genome assembly (coordinates indicated at the top) near a vic1 linkage marker (E190825) are shown for three strains that differ from EP155 (2211-22) at the vic1 locus (allele 1), EU55 (1221-22), EU31 (1211-22), and EU40 (1122-11) and for strain EU60 (2221-22) that is the same as EP155 at the vic1 locus (allele 2). Strain EU55 was sequenced using Roche 454 GS FLX Titanium protocols, and the other strains were sequenced with Illumina HiSeq protocols. Forward reads are indicated in green, reverse reads are indicated in red, paired reads are indicated in blue. The region containing the highly polymorphic sequences is indicated by the absence of matched reads (gap). The ORFs located within a ∼14-kb region containing the gap are shown below the sequence read-density plots. A polymorphic gene encoding a HET-domain-containing protein (91% amino acid identity between alleles 1 and 2) was designated as vic1a-1 for allele 1 present in EU31, EU40, and EU55 and as vic1a-2 for allele 2 present in reference strain EP155 and strain EU60. The gene encoding the DUF1909-domain-containing protein present in allele 2, but absent in allele 1 (i.e., idiomorphic), was designated vic1b-2. The position of the vic1 linkage marker E190825 relative to the vic1 gene candidates is also indicated. The C. parasitica strain EP155 reference genome assembly is available at http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html. The Joint Genome Institute (JGI) protein identity (ID) numbers for vic1a-2 and vic1b-2 are 330677 and 356517, respectively.
    Figure Legend Snippet: The candidate vic1 locus. Density plots of sequence reads that match by sequence similarity to a corresponding portion of Scaffold 5 of the EP155 reference genome assembly (coordinates indicated at the top) near a vic1 linkage marker (E190825) are shown for three strains that differ from EP155 (2211-22) at the vic1 locus (allele 1), EU55 (1221-22), EU31 (1211-22), and EU40 (1122-11) and for strain EU60 (2221-22) that is the same as EP155 at the vic1 locus (allele 2). Strain EU55 was sequenced using Roche 454 GS FLX Titanium protocols, and the other strains were sequenced with Illumina HiSeq protocols. Forward reads are indicated in green, reverse reads are indicated in red, paired reads are indicated in blue. The region containing the highly polymorphic sequences is indicated by the absence of matched reads (gap). The ORFs located within a ∼14-kb region containing the gap are shown below the sequence read-density plots. A polymorphic gene encoding a HET-domain-containing protein (91% amino acid identity between alleles 1 and 2) was designated as vic1a-1 for allele 1 present in EU31, EU40, and EU55 and as vic1a-2 for allele 2 present in reference strain EP155 and strain EU60. The gene encoding the DUF1909-domain-containing protein present in allele 2, but absent in allele 1 (i.e., idiomorphic), was designated vic1b-2. The position of the vic1 linkage marker E190825 relative to the vic1 gene candidates is also indicated. The C. parasitica strain EP155 reference genome assembly is available at http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html. The Joint Genome Institute (JGI) protein identity (ID) numbers for vic1a-2 and vic1b-2 are 330677 and 356517, respectively.

    Techniques Used: Sequencing, Marker

    The candidate vic3 locus. Read-density plots of sequence reads mapped by homology to a ∼7.5-kb portion of Scaffold 5 of the EP155 reference genome assembly identified by manual inspection to contain a region of sequence polymorphism (gaps) with a pattern consistent with that for allele distributions at the vic3 locus. Density plots are shown for strains EU55 (1221-22), EU40 (1122-11), and EU60 (2221-22) that differ at the vic3 genetic locus (i.e., contain allele 2) from reference strain EP155 (2211-22) and strain EU31 (1211-22) that, like strain EP155, contains allele 1 at the vic3 locus (Cortesi and Milgroom 1998). The ORFs located within this region are shown for the two alleles below the sequence read-density plots. Polymorphic (46% amino acid identity) ORFs encoding a hypothetical protein were designated vic3a-1 (599 aa) for allele 1 in strains EP155 and EU31 and vic3a-2 (614 aa) for allele 2 present in strains EU55, EU40, and EU60, while two small polymorphic (85% amino acid identity) ORFs encoding a Life-guard-1-like protein were designated vic3b-1 (102 aa) and vic3b-2 (108 aa). These two polymorphic genes were separated by a highly conserved ORF encoding an actin-binding-like protein. Sequencing protocols and color coding of reads are described in Figure 1. The JGI protein ID numbers for vic3a-1 and vic3b-1 are 331201 and 340400, respectively. The protein ID number for the predicted actin-binding-like protein is 331200.
    Figure Legend Snippet: The candidate vic3 locus. Read-density plots of sequence reads mapped by homology to a ∼7.5-kb portion of Scaffold 5 of the EP155 reference genome assembly identified by manual inspection to contain a region of sequence polymorphism (gaps) with a pattern consistent with that for allele distributions at the vic3 locus. Density plots are shown for strains EU55 (1221-22), EU40 (1122-11), and EU60 (2221-22) that differ at the vic3 genetic locus (i.e., contain allele 2) from reference strain EP155 (2211-22) and strain EU31 (1211-22) that, like strain EP155, contains allele 1 at the vic3 locus (Cortesi and Milgroom 1998). The ORFs located within this region are shown for the two alleles below the sequence read-density plots. Polymorphic (46% amino acid identity) ORFs encoding a hypothetical protein were designated vic3a-1 (599 aa) for allele 1 in strains EP155 and EU31 and vic3a-2 (614 aa) for allele 2 present in strains EU55, EU40, and EU60, while two small polymorphic (85% amino acid identity) ORFs encoding a Life-guard-1-like protein were designated vic3b-1 (102 aa) and vic3b-2 (108 aa). These two polymorphic genes were separated by a highly conserved ORF encoding an actin-binding-like protein. Sequencing protocols and color coding of reads are described in Figure 1. The JGI protein ID numbers for vic3a-1 and vic3b-1 are 331201 and 340400, respectively. The protein ID number for the predicted actin-binding-like protein is 331200.

    Techniques Used: Sequencing, Binding Assay

    Polymorphic nonfunctional pseudo vic locus. Density plots of sequence reads mapped by homology to a portion of EP155 (2211-22) sequence assembly Scaffold 6 extending from map coordinates ∼588,000 to 624,000 are shown for strains EU55 (1221-22), EU31 (1211-22), EU40 (1122-11), and EU60 (2221-22). The defined gap observed at 599,514–606,808 for strains EU55, EU31, and EU60 relative to EP155 and EU40 corresponds to allelic differences in genome organization at this locus as shown in Figure 8 for allele 1 (in strains EP155 and EU40) and allele 2 (in strains EU55, EU31, and EU60). There is no concordance between the polymorphic pattern and allele specificity at any of the genetically defined vic loci; e.g., EP155 (2211-22) and EU40 (1122-11) are heteroallelic at all six genetically defined vic loci, but are homoallelic at this locus.
    Figure Legend Snippet: Polymorphic nonfunctional pseudo vic locus. Density plots of sequence reads mapped by homology to a portion of EP155 (2211-22) sequence assembly Scaffold 6 extending from map coordinates ∼588,000 to 624,000 are shown for strains EU55 (1221-22), EU31 (1211-22), EU40 (1122-11), and EU60 (2221-22). The defined gap observed at 599,514–606,808 for strains EU55, EU31, and EU60 relative to EP155 and EU40 corresponds to allelic differences in genome organization at this locus as shown in Figure 8 for allele 1 (in strains EP155 and EU40) and allele 2 (in strains EU55, EU31, and EU60). There is no concordance between the polymorphic pattern and allele specificity at any of the genetically defined vic loci; e.g., EP155 (2211-22) and EU40 (1122-11) are heteroallelic at all six genetically defined vic loci, but are homoallelic at this locus.

    Techniques Used: Sequencing

    Organization of polymorphic nonfunctional pseudo vic locus alleles. Inspection of the sequence contigs for the two alleles corresponding to the polymorphic region identified on Scaffold 6 spanning positions 599514–606808 in the EP155 reference genome assembly revealed that an ∼7.7-kb portion of the sequence present in EP155 and EU40 (allele 1) was deleted in strains EU55, EU31, and EU60 (allele 2). The allele 1 sequence contained two ORFs not present in allele 2. These encoded a 407-aa protein containing a GTPase domain and a 1211-aa-long HET-domain-containing protein. The two ORFs were flanked by ∼900-bp imperfect (88% identity) direct repeats. The allele 2 sequence lacked the ∼7.7-kb region harboring the GTPase and HET-domain ORFs and contained only one copy of the flanking repeats that consisted of the 5′-proximal two-thirds of the left repeat and the 3′-proximal one-third of the right repeat and a G-C base pair replacing a T-A base pair at the breakpoint as indicated by the red letters. (Figure S9).
    Figure Legend Snippet: Organization of polymorphic nonfunctional pseudo vic locus alleles. Inspection of the sequence contigs for the two alleles corresponding to the polymorphic region identified on Scaffold 6 spanning positions 599514–606808 in the EP155 reference genome assembly revealed that an ∼7.7-kb portion of the sequence present in EP155 and EU40 (allele 1) was deleted in strains EU55, EU31, and EU60 (allele 2). The allele 1 sequence contained two ORFs not present in allele 2. These encoded a 407-aa protein containing a GTPase domain and a 1211-aa-long HET-domain-containing protein. The two ORFs were flanked by ∼900-bp imperfect (88% identity) direct repeats. The allele 2 sequence lacked the ∼7.7-kb region harboring the GTPase and HET-domain ORFs and contained only one copy of the flanking repeats that consisted of the 5′-proximal two-thirds of the left repeat and the 3′-proximal one-third of the right repeat and a G-C base pair replacing a T-A base pair at the breakpoint as indicated by the red letters. (Figure S9).

    Techniques Used: Sequencing

    PCR-based differentiation of alleles for pseudo vic locus at C. parasitica genome Scaffold 6: 599,514–606,808
    Figure Legend Snippet: PCR-based differentiation of alleles for pseudo vic locus at C. parasitica genome Scaffold 6: 599,514–606,808

    Techniques Used:

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • eu40  (ATCC)
    86
    ATCC eu40
    The candidate vic1 locus. Density plots of sequence reads that match by sequence similarity to a corresponding portion of Scaffold 5 of the EP155 reference genome assembly (coordinates indicated at the top) near a vic1 linkage marker (E190825) are shown for three strains that differ from EP155 (2211-22) at the vic1 locus (allele 1), EU55 (1221-22), EU31 (1211-22), and <t>EU40</t> (1122-11) and for strain EU60 (2221-22) that is the same as EP155 at the vic1 locus (allele 2). Strain EU55 was sequenced using Roche 454 GS FLX Titanium protocols, and the other strains were sequenced with Illumina HiSeq protocols. Forward reads are indicated in green, reverse reads are indicated in red, paired reads are indicated in blue. The region containing the highly polymorphic sequences is indicated by the absence of matched reads (gap). The ORFs located within a ∼14-kb region containing the gap are shown below the sequence read-density plots. A polymorphic gene encoding a HET-domain-containing protein (91% amino acid identity between alleles 1 and 2) was designated as vic1a-1 for allele 1 present in EU31, EU40, and EU55 and as vic1a-2 for allele 2 present in reference strain EP155 and strain EU60. The gene encoding the DUF1909-domain-containing protein present in allele 2, but absent in allele 1 (i.e., idiomorphic), was designated vic1b-2. The position of the vic1 linkage marker E190825 relative to the vic1 gene candidates is also indicated. The C. parasitica strain EP155 reference genome assembly is available at http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html. The Joint Genome Institute (JGI) protein identity (ID) numbers for vic1a-2 and vic1b-2 are 330677 and 356517, respectively.
    Eu40, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/eu40/product/ATCC
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    eu40 - by Bioz Stars, 2024-02
    86/100 stars
      Buy from Supplier

    Image Search Results


    The candidate vic1 locus. Density plots of sequence reads that match by sequence similarity to a corresponding portion of Scaffold 5 of the EP155 reference genome assembly (coordinates indicated at the top) near a vic1 linkage marker (E190825) are shown for three strains that differ from EP155 (2211-22) at the vic1 locus (allele 1), EU55 (1221-22), EU31 (1211-22), and EU40 (1122-11) and for strain EU60 (2221-22) that is the same as EP155 at the vic1 locus (allele 2). Strain EU55 was sequenced using Roche 454 GS FLX Titanium protocols, and the other strains were sequenced with Illumina HiSeq protocols. Forward reads are indicated in green, reverse reads are indicated in red, paired reads are indicated in blue. The region containing the highly polymorphic sequences is indicated by the absence of matched reads (gap). The ORFs located within a ∼14-kb region containing the gap are shown below the sequence read-density plots. A polymorphic gene encoding a HET-domain-containing protein (91% amino acid identity between alleles 1 and 2) was designated as vic1a-1 for allele 1 present in EU31, EU40, and EU55 and as vic1a-2 for allele 2 present in reference strain EP155 and strain EU60. The gene encoding the DUF1909-domain-containing protein present in allele 2, but absent in allele 1 (i.e., idiomorphic), was designated vic1b-2. The position of the vic1 linkage marker E190825 relative to the vic1 gene candidates is also indicated. The C. parasitica strain EP155 reference genome assembly is available at http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html. The Joint Genome Institute (JGI) protein identity (ID) numbers for vic1a-2 and vic1b-2 are 330677 and 356517, respectively.

    Journal: Genetics

    Article Title: Vegetative Incompatibility Loci with Dedicated Roles in Allorecognition Restrict Mycovirus Transmission in Chestnut Blight Fungus

    doi: 10.1534/genetics.114.164574

    Figure Lengend Snippet: The candidate vic1 locus. Density plots of sequence reads that match by sequence similarity to a corresponding portion of Scaffold 5 of the EP155 reference genome assembly (coordinates indicated at the top) near a vic1 linkage marker (E190825) are shown for three strains that differ from EP155 (2211-22) at the vic1 locus (allele 1), EU55 (1221-22), EU31 (1211-22), and EU40 (1122-11) and for strain EU60 (2221-22) that is the same as EP155 at the vic1 locus (allele 2). Strain EU55 was sequenced using Roche 454 GS FLX Titanium protocols, and the other strains were sequenced with Illumina HiSeq protocols. Forward reads are indicated in green, reverse reads are indicated in red, paired reads are indicated in blue. The region containing the highly polymorphic sequences is indicated by the absence of matched reads (gap). The ORFs located within a ∼14-kb region containing the gap are shown below the sequence read-density plots. A polymorphic gene encoding a HET-domain-containing protein (91% amino acid identity between alleles 1 and 2) was designated as vic1a-1 for allele 1 present in EU31, EU40, and EU55 and as vic1a-2 for allele 2 present in reference strain EP155 and strain EU60. The gene encoding the DUF1909-domain-containing protein present in allele 2, but absent in allele 1 (i.e., idiomorphic), was designated vic1b-2. The position of the vic1 linkage marker E190825 relative to the vic1 gene candidates is also indicated. The C. parasitica strain EP155 reference genome assembly is available at http://genome.jgi.doe.gov/Crypa2/Crypa2.home.html. The Joint Genome Institute (JGI) protein identity (ID) numbers for vic1a-2 and vic1b-2 are 330677 and 356517, respectively.

    Article Snippet: C. parasitica strains used in this study included wild-type and genome reference strain EP155 (ATCC 38755) and vic -genotyped tester strains ( Cortesi and Milgroom 1998 ) EU31 (ATCC MYA-1074), EU40 (ATCC MYA-1083), EU55 (ATCC MYA-1098), and EU60 (ATCC MYA-1103).

    Techniques: Sequencing, Marker

    The candidate vic3 locus. Read-density plots of sequence reads mapped by homology to a ∼7.5-kb portion of Scaffold 5 of the EP155 reference genome assembly identified by manual inspection to contain a region of sequence polymorphism (gaps) with a pattern consistent with that for allele distributions at the vic3 locus. Density plots are shown for strains EU55 (1221-22), EU40 (1122-11), and EU60 (2221-22) that differ at the vic3 genetic locus (i.e., contain allele 2) from reference strain EP155 (2211-22) and strain EU31 (1211-22) that, like strain EP155, contains allele 1 at the vic3 locus (Cortesi and Milgroom 1998). The ORFs located within this region are shown for the two alleles below the sequence read-density plots. Polymorphic (46% amino acid identity) ORFs encoding a hypothetical protein were designated vic3a-1 (599 aa) for allele 1 in strains EP155 and EU31 and vic3a-2 (614 aa) for allele 2 present in strains EU55, EU40, and EU60, while two small polymorphic (85% amino acid identity) ORFs encoding a Life-guard-1-like protein were designated vic3b-1 (102 aa) and vic3b-2 (108 aa). These two polymorphic genes were separated by a highly conserved ORF encoding an actin-binding-like protein. Sequencing protocols and color coding of reads are described in Figure 1. The JGI protein ID numbers for vic3a-1 and vic3b-1 are 331201 and 340400, respectively. The protein ID number for the predicted actin-binding-like protein is 331200.

    Journal: Genetics

    Article Title: Vegetative Incompatibility Loci with Dedicated Roles in Allorecognition Restrict Mycovirus Transmission in Chestnut Blight Fungus

    doi: 10.1534/genetics.114.164574

    Figure Lengend Snippet: The candidate vic3 locus. Read-density plots of sequence reads mapped by homology to a ∼7.5-kb portion of Scaffold 5 of the EP155 reference genome assembly identified by manual inspection to contain a region of sequence polymorphism (gaps) with a pattern consistent with that for allele distributions at the vic3 locus. Density plots are shown for strains EU55 (1221-22), EU40 (1122-11), and EU60 (2221-22) that differ at the vic3 genetic locus (i.e., contain allele 2) from reference strain EP155 (2211-22) and strain EU31 (1211-22) that, like strain EP155, contains allele 1 at the vic3 locus (Cortesi and Milgroom 1998). The ORFs located within this region are shown for the two alleles below the sequence read-density plots. Polymorphic (46% amino acid identity) ORFs encoding a hypothetical protein were designated vic3a-1 (599 aa) for allele 1 in strains EP155 and EU31 and vic3a-2 (614 aa) for allele 2 present in strains EU55, EU40, and EU60, while two small polymorphic (85% amino acid identity) ORFs encoding a Life-guard-1-like protein were designated vic3b-1 (102 aa) and vic3b-2 (108 aa). These two polymorphic genes were separated by a highly conserved ORF encoding an actin-binding-like protein. Sequencing protocols and color coding of reads are described in Figure 1. The JGI protein ID numbers for vic3a-1 and vic3b-1 are 331201 and 340400, respectively. The protein ID number for the predicted actin-binding-like protein is 331200.

    Article Snippet: C. parasitica strains used in this study included wild-type and genome reference strain EP155 (ATCC 38755) and vic -genotyped tester strains ( Cortesi and Milgroom 1998 ) EU31 (ATCC MYA-1074), EU40 (ATCC MYA-1083), EU55 (ATCC MYA-1098), and EU60 (ATCC MYA-1103).

    Techniques: Sequencing, Binding Assay

    Polymorphic nonfunctional pseudo vic locus. Density plots of sequence reads mapped by homology to a portion of EP155 (2211-22) sequence assembly Scaffold 6 extending from map coordinates ∼588,000 to 624,000 are shown for strains EU55 (1221-22), EU31 (1211-22), EU40 (1122-11), and EU60 (2221-22). The defined gap observed at 599,514–606,808 for strains EU55, EU31, and EU60 relative to EP155 and EU40 corresponds to allelic differences in genome organization at this locus as shown in Figure 8 for allele 1 (in strains EP155 and EU40) and allele 2 (in strains EU55, EU31, and EU60). There is no concordance between the polymorphic pattern and allele specificity at any of the genetically defined vic loci; e.g., EP155 (2211-22) and EU40 (1122-11) are heteroallelic at all six genetically defined vic loci, but are homoallelic at this locus.

    Journal: Genetics

    Article Title: Vegetative Incompatibility Loci with Dedicated Roles in Allorecognition Restrict Mycovirus Transmission in Chestnut Blight Fungus

    doi: 10.1534/genetics.114.164574

    Figure Lengend Snippet: Polymorphic nonfunctional pseudo vic locus. Density plots of sequence reads mapped by homology to a portion of EP155 (2211-22) sequence assembly Scaffold 6 extending from map coordinates ∼588,000 to 624,000 are shown for strains EU55 (1221-22), EU31 (1211-22), EU40 (1122-11), and EU60 (2221-22). The defined gap observed at 599,514–606,808 for strains EU55, EU31, and EU60 relative to EP155 and EU40 corresponds to allelic differences in genome organization at this locus as shown in Figure 8 for allele 1 (in strains EP155 and EU40) and allele 2 (in strains EU55, EU31, and EU60). There is no concordance between the polymorphic pattern and allele specificity at any of the genetically defined vic loci; e.g., EP155 (2211-22) and EU40 (1122-11) are heteroallelic at all six genetically defined vic loci, but are homoallelic at this locus.

    Article Snippet: C. parasitica strains used in this study included wild-type and genome reference strain EP155 (ATCC 38755) and vic -genotyped tester strains ( Cortesi and Milgroom 1998 ) EU31 (ATCC MYA-1074), EU40 (ATCC MYA-1083), EU55 (ATCC MYA-1098), and EU60 (ATCC MYA-1103).

    Techniques: Sequencing

    Organization of polymorphic nonfunctional pseudo vic locus alleles. Inspection of the sequence contigs for the two alleles corresponding to the polymorphic region identified on Scaffold 6 spanning positions 599514–606808 in the EP155 reference genome assembly revealed that an ∼7.7-kb portion of the sequence present in EP155 and EU40 (allele 1) was deleted in strains EU55, EU31, and EU60 (allele 2). The allele 1 sequence contained two ORFs not present in allele 2. These encoded a 407-aa protein containing a GTPase domain and a 1211-aa-long HET-domain-containing protein. The two ORFs were flanked by ∼900-bp imperfect (88% identity) direct repeats. The allele 2 sequence lacked the ∼7.7-kb region harboring the GTPase and HET-domain ORFs and contained only one copy of the flanking repeats that consisted of the 5′-proximal two-thirds of the left repeat and the 3′-proximal one-third of the right repeat and a G-C base pair replacing a T-A base pair at the breakpoint as indicated by the red letters. (Figure S9).

    Journal: Genetics

    Article Title: Vegetative Incompatibility Loci with Dedicated Roles in Allorecognition Restrict Mycovirus Transmission in Chestnut Blight Fungus

    doi: 10.1534/genetics.114.164574

    Figure Lengend Snippet: Organization of polymorphic nonfunctional pseudo vic locus alleles. Inspection of the sequence contigs for the two alleles corresponding to the polymorphic region identified on Scaffold 6 spanning positions 599514–606808 in the EP155 reference genome assembly revealed that an ∼7.7-kb portion of the sequence present in EP155 and EU40 (allele 1) was deleted in strains EU55, EU31, and EU60 (allele 2). The allele 1 sequence contained two ORFs not present in allele 2. These encoded a 407-aa protein containing a GTPase domain and a 1211-aa-long HET-domain-containing protein. The two ORFs were flanked by ∼900-bp imperfect (88% identity) direct repeats. The allele 2 sequence lacked the ∼7.7-kb region harboring the GTPase and HET-domain ORFs and contained only one copy of the flanking repeats that consisted of the 5′-proximal two-thirds of the left repeat and the 3′-proximal one-third of the right repeat and a G-C base pair replacing a T-A base pair at the breakpoint as indicated by the red letters. (Figure S9).

    Article Snippet: C. parasitica strains used in this study included wild-type and genome reference strain EP155 (ATCC 38755) and vic -genotyped tester strains ( Cortesi and Milgroom 1998 ) EU31 (ATCC MYA-1074), EU40 (ATCC MYA-1083), EU55 (ATCC MYA-1098), and EU60 (ATCC MYA-1103).

    Techniques: Sequencing

    PCR-based differentiation of alleles for pseudo vic locus at C. parasitica genome Scaffold 6: 599,514–606,808

    Journal: Genetics

    Article Title: Vegetative Incompatibility Loci with Dedicated Roles in Allorecognition Restrict Mycovirus Transmission in Chestnut Blight Fungus

    doi: 10.1534/genetics.114.164574

    Figure Lengend Snippet: PCR-based differentiation of alleles for pseudo vic locus at C. parasitica genome Scaffold 6: 599,514–606,808

    Article Snippet: C. parasitica strains used in this study included wild-type and genome reference strain EP155 (ATCC 38755) and vic -genotyped tester strains ( Cortesi and Milgroom 1998 ) EU31 (ATCC MYA-1074), EU40 (ATCC MYA-1083), EU55 (ATCC MYA-1098), and EU60 (ATCC MYA-1103).

    Techniques: