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Constructing Physical and Genomic Maps for Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen, by Comparing Its EST Sequences to the Genomic Sequence of P. graminis f. sp. tritici, the Wheat Stem Rust Pathogen.

Ma J, Chen X, Wang M, Kang Z - Comp. Funct. Genomics (2010)

Bottom Line: The percentages of homologous genes varied greatly among different Pst libraries with 54.51%, 51.21%, and 13.61% for the urediniospore, germinated urediniospore, and haustorial libraries, respectively, with an average of 33.92%.The 1,432 Pst genes with significant homology with Pgt sequences were grouped into physical groups corresponding to 237 Pgt supercontigs.The physical relationship was demonstrated by 12 pairs (57%), out of 21 selected Pst gene pairs, through PCR screening of a Pst BAC library.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.

ABSTRACT
The wheat stripe rust fungus, Puccinia striiformis f. sp. tritici (Pst), does not have a known alternate host for sexual reproduction, which makes it impossible to study gene linkages through classic genetic and molecular mapping approaches. In this study, we compared 4,219 Pst expression sequence tags (ESTs) to the genomic sequence of P. graminis f. sp. tritici (Pgt), the wheat stem rust fungus, using BLAST searches. The percentages of homologous genes varied greatly among different Pst libraries with 54.51%, 51.21%, and 13.61% for the urediniospore, germinated urediniospore, and haustorial libraries, respectively, with an average of 33.92%. The 1,432 Pst genes with significant homology with Pgt sequences were grouped into physical groups corresponding to 237 Pgt supercontigs. The physical relationship was demonstrated by 12 pairs (57%), out of 21 selected Pst gene pairs, through PCR screening of a Pst BAC library. The results indicate that the Pgt genome sequence is useful in constructing Pst physical maps.

No MeSH data available.


Related in: MedlinePlus

An example of physical maps for Pst ESTs based on corresponding sequence positions of homologous genes of Pgt.  All 242 physical groups are presented in Supplementary file 1.  The distance in mega base (Mb) is shown on the left.  The clones in a group indicated by a vertical line are in the same contig and the start and end positions of the sequence matching the positions in the contig are shown in the “( )” following the clone identification number.  The number after the “( )” indicates the number of the gene with multiple positions in the Pgt genome.  An asterisk indicates that the number of matching base pairs is smaller than 100.  The clones underlined were used in PCR amplification of the Pst BAC library.
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fig1: An example of physical maps for Pst ESTs based on corresponding sequence positions of homologous genes of Pgt. All 242 physical groups are presented in Supplementary file 1. The distance in mega base (Mb) is shown on the left. The clones in a group indicated by a vertical line are in the same contig and the start and end positions of the sequence matching the positions in the contig are shown in the “( )” following the clone identification number. The number after the “( )” indicates the number of the gene with multiple positions in the Pgt genome. An asterisk indicates that the number of matching base pairs is smaller than 100. The clones underlined were used in PCR amplification of the Pst BAC library.

Mentions: The 1,432 Pst genes were aligned to 237 physical groups corresponding to 237 Pgt supercontigs (Supplementary file 1). As an example, Figure 1 shows Pst genes aligned to Pgt supercontig 1. The number of genes for each supercontig from each Pst cDNA library is shown in Table 3. The 237 physical groups ranged from 2,878 to 3,081,398 bp with most of the groups ranging from 5.0 Kb to 2.0 Mb (Figure 2(a)). Overall, the 1,432 genes matched 787,413 bp and spanned over 86.55 Mb of the Pgt genomic sequences. Because the majority of the 1,432 unigenes were aligned to more than one sequence locus, a total of 4,604 gene loci were obtained (Table 3). The fold of multiple loci per unique gene was unbalanced among the three libraries with 1.30 for the GermUred library, 1.53 for the Ured library, and 10.58 for the Haus library.


Constructing Physical and Genomic Maps for Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen, by Comparing Its EST Sequences to the Genomic Sequence of P. graminis f. sp. tritici, the Wheat Stem Rust Pathogen.

Ma J, Chen X, Wang M, Kang Z - Comp. Funct. Genomics (2010)

An example of physical maps for Pst ESTs based on corresponding sequence positions of homologous genes of Pgt.  All 242 physical groups are presented in Supplementary file 1.  The distance in mega base (Mb) is shown on the left.  The clones in a group indicated by a vertical line are in the same contig and the start and end positions of the sequence matching the positions in the contig are shown in the “( )” following the clone identification number.  The number after the “( )” indicates the number of the gene with multiple positions in the Pgt genome.  An asterisk indicates that the number of matching base pairs is smaller than 100.  The clones underlined were used in PCR amplification of the Pst BAC library.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2821759&req=5

fig1: An example of physical maps for Pst ESTs based on corresponding sequence positions of homologous genes of Pgt. All 242 physical groups are presented in Supplementary file 1. The distance in mega base (Mb) is shown on the left. The clones in a group indicated by a vertical line are in the same contig and the start and end positions of the sequence matching the positions in the contig are shown in the “( )” following the clone identification number. The number after the “( )” indicates the number of the gene with multiple positions in the Pgt genome. An asterisk indicates that the number of matching base pairs is smaller than 100. The clones underlined were used in PCR amplification of the Pst BAC library.
Mentions: The 1,432 Pst genes were aligned to 237 physical groups corresponding to 237 Pgt supercontigs (Supplementary file 1). As an example, Figure 1 shows Pst genes aligned to Pgt supercontig 1. The number of genes for each supercontig from each Pst cDNA library is shown in Table 3. The 237 physical groups ranged from 2,878 to 3,081,398 bp with most of the groups ranging from 5.0 Kb to 2.0 Mb (Figure 2(a)). Overall, the 1,432 genes matched 787,413 bp and spanned over 86.55 Mb of the Pgt genomic sequences. Because the majority of the 1,432 unigenes were aligned to more than one sequence locus, a total of 4,604 gene loci were obtained (Table 3). The fold of multiple loci per unique gene was unbalanced among the three libraries with 1.30 for the GermUred library, 1.53 for the Ured library, and 10.58 for the Haus library.

Bottom Line: The percentages of homologous genes varied greatly among different Pst libraries with 54.51%, 51.21%, and 13.61% for the urediniospore, germinated urediniospore, and haustorial libraries, respectively, with an average of 33.92%.The 1,432 Pst genes with significant homology with Pgt sequences were grouped into physical groups corresponding to 237 Pgt supercontigs.The physical relationship was demonstrated by 12 pairs (57%), out of 21 selected Pst gene pairs, through PCR screening of a Pst BAC library.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.

ABSTRACT
The wheat stripe rust fungus, Puccinia striiformis f. sp. tritici (Pst), does not have a known alternate host for sexual reproduction, which makes it impossible to study gene linkages through classic genetic and molecular mapping approaches. In this study, we compared 4,219 Pst expression sequence tags (ESTs) to the genomic sequence of P. graminis f. sp. tritici (Pgt), the wheat stem rust fungus, using BLAST searches. The percentages of homologous genes varied greatly among different Pst libraries with 54.51%, 51.21%, and 13.61% for the urediniospore, germinated urediniospore, and haustorial libraries, respectively, with an average of 33.92%. The 1,432 Pst genes with significant homology with Pgt sequences were grouped into physical groups corresponding to 237 Pgt supercontigs. The physical relationship was demonstrated by 12 pairs (57%), out of 21 selected Pst gene pairs, through PCR screening of a Pst BAC library. The results indicate that the Pgt genome sequence is useful in constructing Pst physical maps.

No MeSH data available.


Related in: MedlinePlus