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United States Department of Agriculture

Agricultural Research Service

Title: Group I introns in small subunit ribosomal DNA of several Phaeosphaeria species

item Wang, Chih-li
item Chang, Pi-fang Linda
item Lin, Ying-hong
item Malkus, Arkadiusz
item Ueng, Peter

Submitted to: Botanical Review
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/14/2008
Publication Date: 4/30/2009
Citation: Wang, C., Chang, P., Lin, Y., Malkus, A., Ueng, P.P. 2009. Group I introns in small subunit ribosomal DNA of several Phaeosphaeria species. Botanical Review. 50:137-147.

Interpretive Summary: Septoria disease is responsible for significant economic losses in the production of cereal crops. The disease is caused by a complex of several different species of fungus that are difficult to distinguish from one another. From the Septoria disease fungi, we isolated and characterized the ribosomal RNA genes that are involved in protein translation. Results from this study showed that one of these genes has DNA fragments inserted at specific positions in severl Phaeosphaeria species, and provides useful molecular markers to aid detection of the septoria disease fungi. The findings will be of interest to scientists and diagnostics laboratories.

Technical Abstract: In a study of small subunit ribosomal RNA (SSU-rRNA) gene sequences in Phaeosphaeria species, group I introns were found in 9 of 10 P. avenaria f.sp. avenaria (Paa) isolates, 1 of 2 Phaeosphaeria sp. (P-rye) isolates from Polish rye (Sn48-1), 1 Phaeosphaeria sp. from dallis grass (P-dg) (S-93-48) and both heterothallic P. a. f.sp. triticea (Pat2) isolates (ATCC26370 and ATCC26377). There were no group I introns in wheat- and barley-biotype P. nodorum (PN-w and PN-b), homothallic P. a. f.sp. triticea (Pat1) and P. a. f.sp. triticea (Pat3) from the state of Washington. The sizes of introns were 362 bp for Pav.nS943 (from Paa), 363 bp for Pse.nS943 (from P-rye), 460 bp for Pho.nS1533 (from Pat2) and 383 bp for Ppa.nS1199 (P-dg). Based on the reference 16S rDNA nucleotide sequence of Escherichia coli (accession number J01695), the intron inserted positions of Pav.nS943, Pse.nS943, Ppa.nS1199 and Pho.nS1533 were determined to be at nt943, nt943, nt1199 and nt1533, respectively. The intron inserted position at nt1533 was newly discovered. The phylogenetic relationships based on aligned conserved secondary structure component sequences of group I introns showed that three introns from cereal Phaeosphaeria species (Pav.nS943, Pse.nS943 and Pho.nS1533) were likely affiliated with subgroup IC1 introns while Ppa.nS1199 intron from the dallis grass pathogen belonged to subgroup IE3. There were no genetic insertions in the large subunit rRNA (LSU-rRNA) gene of Phaeosphaeria species. Based on the 3,291 bp nucleotide sequences of LSU-rRNA, Pat1 was phylogenetically more closely related to Paa/P-dg/PN-b/Pat3 clade than PN-w/P-rye/Pat2.

Last Modified: 06/26/2017
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