Families of short interspersed elements in the genome of the oomycete plant pathogen, Phytophthora infestans

Stephen C. Whisson, Anna O. Avrova, Olga Lavrova, Leighton Pritchard

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

The first known families of tRNA-related short interspersed elements (SINEs) in the oomycetes were identified by exploiting the genomic DNA sequence resources for the potato late blight pathogen, Phytophthora infestans. Fifteen families of tRNA-related SINEs, as well as predicted tRNAs, and other possible RNA polymerase III-transcribed sequences were identified. The size of individual elements ranges from 101 to 392 bp, representing sequences present from low (1) to highly abundant (over 2000) copy number in the P. infestans genome, based on quantitative PCR analysis. Putative short direct repeat sequences (6-14 bp) flanking the elements were also identified for eight of the SINEs. Predicted SINEs were named in a series prefixed infSINE (for infestans-SINE). Two SINEs were apparently present as multimers of tRNA-related units; four copies of a related unit for infSINEr, and two unrelated units for infSINEz. Two SINEs, infSINEh and infSINEi, were typically located within 400 bp of each other. These were also the only two elements identified as being actively transcribed in the mycelial stage of P. infestans by RT-PCR. It is possible that infSINEh and infSINEi represent active retrotransposons in P. infestans. Based on the quantitative PCR estimates of copy number for all of the elements identified, tRNA-related SINEs were estimated to comprise 0.3% of the 250 Mb P. infestans genome. InfSINE-related sequences were found to occur in species throughout the genus Phytophthora. However, seven elements were shown to be exclusive to P. infestans.

LanguageEnglish
Pages351-365
Number of pages15
JournalFungal Genetics and Biology
Volume42
Issue number4
DOIs
Publication statusPublished - 30 Apr 2005

Fingerprint

Phytophthora infestans
Oomycetes
Plant Genome
Transfer RNA
Polymerase Chain Reaction
Genome
Phytophthora
RNA Polymerase III
Retroelements
Nucleic Acid Repetitive Sequences
Solanum tuberosum

Keywords

  • late blight
  • oomycete
  • phytophthora infestans
  • retrotransposon
  • SINE

Cite this

Whisson, Stephen C. ; Avrova, Anna O. ; Lavrova, Olga ; Pritchard, Leighton. / Families of short interspersed elements in the genome of the oomycete plant pathogen, Phytophthora infestans. 2005 ; Vol. 42, No. 4. pp. 351-365.
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Families of short interspersed elements in the genome of the oomycete plant pathogen, Phytophthora infestans. / Whisson, Stephen C.; Avrova, Anna O.; Lavrova, Olga; Pritchard, Leighton.

Vol. 42, No. 4, 30.04.2005, p. 351-365.

Research output: Contribution to journalArticle

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T1 - Families of short interspersed elements in the genome of the oomycete plant pathogen, Phytophthora infestans

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AU - Avrova, Anna O.

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AU - Pritchard, Leighton

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AB - The first known families of tRNA-related short interspersed elements (SINEs) in the oomycetes were identified by exploiting the genomic DNA sequence resources for the potato late blight pathogen, Phytophthora infestans. Fifteen families of tRNA-related SINEs, as well as predicted tRNAs, and other possible RNA polymerase III-transcribed sequences were identified. The size of individual elements ranges from 101 to 392 bp, representing sequences present from low (1) to highly abundant (over 2000) copy number in the P. infestans genome, based on quantitative PCR analysis. Putative short direct repeat sequences (6-14 bp) flanking the elements were also identified for eight of the SINEs. Predicted SINEs were named in a series prefixed infSINE (for infestans-SINE). Two SINEs were apparently present as multimers of tRNA-related units; four copies of a related unit for infSINEr, and two unrelated units for infSINEz. Two SINEs, infSINEh and infSINEi, were typically located within 400 bp of each other. These were also the only two elements identified as being actively transcribed in the mycelial stage of P. infestans by RT-PCR. It is possible that infSINEh and infSINEi represent active retrotransposons in P. infestans. Based on the quantitative PCR estimates of copy number for all of the elements identified, tRNA-related SINEs were estimated to comprise 0.3% of the 250 Mb P. infestans genome. InfSINE-related sequences were found to occur in species throughout the genus Phytophthora. However, seven elements were shown to be exclusive to P. infestans.

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