Evolution and diversity of 5S rRNA gene family organization in Pythium and other stramenopiles

The 5S ribosomal RNA (rRNA) gene family organization among 90 species of Pythium was investigated to see whether a pattern could be discerned that might be related to evolutionary or ecological factors. The genus has at least three main lines of evolution, and a dominant pattern of 5S gene organization was found in each group, with a few notable exceptions. Species with filamentous sporangia and their relatives (Group 1A) had 5S genes 1 linked to the ribosomal DNA (rDNA) repeat that were predominately coded for on the opposite DNA strand ('inverted' orientation). A small group of species with a variety of sporangial forms (Group 1B) was related to Group 1A but had unlinked 5S genes. The main group of species with spherical zoosporangia (Group 2) generally had unlinked 5S genes in tandem arrays. The six species in Group 3, although they have spherical sporangia, had linked genes on the same strand as the other rRNA genes ('non-inverted') and 4 of the 6 species each had pairs of tandem 5S genes. In Group 2, although most species had unlinked 5S genes, one major group, believed to be a clade on the basis of ITS sequences, and two other unrelated species, had linked 5S genes. In three species, (P. anandrum, P. tracheiphilum and P. ostracodes) both linked and unlinked genes have been detected. 5S rRNA genes undergo translocation in the course of evolution and so they alternate between the linked and the unlinked states, and the inverted and non-inverted orientations, but a nonrandom pattern could be discerned.; Over 50 species of Phytophthora and Halophytophthora were surveyed for their 5S rRNA gene organization. The predominant pattern found was that the 5S gene is linked and non-inverted in orientation with respect to the other rRNA genes of the rDNA repeat. A few species of Phytophthora and Halophytophthora have their 5S genes unlinked to the rDNA repeat and located in 5S tandem arrays. This confirms earlier findings with the genus Pythium which indicated that 5S genes are readily rearranged but that 5S family organization is stable in large groups of related species.; The organization of the 5S rRNA gene family in Rhizidiomyces apophysatus and Hyphochytrium catenoides was investigated to determine whether 5S genes are linked or unlinked with respect to other rRNA genes, and to see whether the resulting pattern was consistent with the evolution of 5S gene organization of other stramenopilous fungi. Both organisms were found to have 5S genes linked to the rDNA repeat and to be coded on the same DNA strand as the other rRNA genes. H. catenoides also had arrays of tandem repeats of 5S sequences unlinked to the rDNA repeat. (Abstract shortened by UMI.); 1Note: The expression "5S genes" will be used throughout as a short form for "5S rRNA genes".