Dataset Information

Birth-and-Death Evolution and Reticulation of ITS Segments of Metschnikowia andauensis and Metschnikowia fructicola rDNA Repeats.

ABSTRACT: The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, and ITS2) separates the genes coding for the SSU 18S and the LSU 26S genes in the rDNA units which are organized into long tandem arrays in the overwhelming majority of fungi. As members of a multigenic family, these units are subject of concerted evolution, which homogenizes their sequences. Exceptions have been observed in certain groups of plants and in a few fungal species. In our previous study we described exceptionally high degree of sequence diversity in the D1/D2 domains of two pulcherrimin-producing Metschnikowia (Saccharomycotina) species which appeared to evolve by reticulation. The major goals of this study were the examination of the diversity of the ITS segments and their evolution. We show that the ITS sequences of these species are not homogenized either, differ from each other by up to 38 substitutions and indels which have dramatic effects on the predicted secondary structures of the transcripts. The high intragenomic diversity makes the D1/D2 domains and the ITS spacers unsuitable for barcoding of these species and therefore the taxonomic position of strains previously assigned to them needs revision. By analyzing the genome sequence of the M. fructicola type strain, we also show that the rDNA of this species is fragmented, contains pseudogenes and thus evolves by the birth-and-death mechanism rather than by homogenisation, which is unusual in yeasts. The results of the network analysis of the sequences further indicate that the ITS regions are also involved in reticulation. M. andauensis and M. fructicola can form interspecies hybrids and their hybrids segregate, providing thus possibilities for reticulation of the rDNA repeats.

SUBMITTER: Sipiczki M

PROVIDER: S-EPMC6005844 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Publications

Birth-and-Death Evolution and Reticulation of ITS Segments of <i>Metschnikowia andauensis</i> and <i>Metschnikowia fructicola</i> rDNA Repeats.

Sipiczki Matthias M Horvath Eniko E Pfliegler Walter P WP

Frontiers in microbiology 20180612

The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, and ITS2) separates the genes coding for the SSU 18S and the LSU 26S genes in the rDNA units which are organized into long tandem arrays in the overwhelming majority of fungi. As members of a multigenic family, these units are subject of concerted evolution, which homogenizes their sequences. Exceptions have been observed in certain groups of plants and in a few fungal species. In our previous study we described exceptionally high de ...[more]

PMID: 29946303

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Project description:BACKGROUND:Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. RESULTS:We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci containing up to twelve copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. CONCLUSIONS:The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.

Dataset Information

Birth-and-Death Evolution and Reticulation of ITS Segments of Metschnikowia andauensis and Metschnikowia fructicola rDNA Repeats.

Publications

Birth-and-Death Evolution and Reticulation of ITS Segments of <i>Metschnikowia andauensis</i> and <i>Metschnikowia fructicola</i> rDNA Repeats.

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