Fungal Genomics & Biology
Open Access

Abstract

Fungal rDNA Analysis in the NGS Era: Progress, Insights and Challenges

Oliver Blechert and Ping Zhan*

Background: Ribosomal DNA (rDNA), consisting of the 18S, 5.8S, 25S and 5S rRNA genes and noncoding functional elements in eukaryotes, is a region in the genome with very high activity with respect to transcription and genomic rearrangement. Due to its highly repetitive and complex structure, detailed sequence analyses are challenging and often neglected. In this study, a systematic survey of rDNA organization across the fungal kingdom was performed.

Methods: We analysed all fungal genome assemblies available at NCBI, in total 6779, by bioinformatic methods. For this, we developed a batch of Python scripts to process the data. For de-novo assembling of NGS data, we wrote the Ansi C program ‘YNGS’.

Results: Only 15% of the fungal genome assemblies at NCBI possessed the sequence of an entire rDNA unit. Most assemblies of the rDNA were incomplete and were interrupted in the internal spacer regions. Next, we analysed the rDNA organisation. Basidiomycota, with the exception of the Ustilaginomycetes, had 5S gene inserted in the rDNA units as well Blastocladiomycota, Chytridiomycota and Mucoromycota. Ascomycota, with the exception of Saccharomycetes, lacked 5S insertions in the rDNA units. Here, the 5S genes were scattered in the genome and tandem arrays of 5S genes were very uncommon. With the YNGS software, we assembeled 17 entier rDNA unities and calculated an amount of 25 to 161 rDNA repeated units per genome.

Conclusion: In contrast to the rDNA gene region, the internal spacer regions are still challenging to analyse, even in the NGS era. Transcriptional regulation, replication machinary and genome rearrengment elements are meeting together. Sophisticate regulations are necessary for a smooth flow.

Published Date: 2022-12-05; Received Date: 2022-11-02