Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina)

Abstract

Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae, the most common cause of mucormycosis worldwide. The genome assembly encompasses 33.6 MB and 12,379 protein-coding genes. This study reveals four major differences of the L. corymbifera genome to R. oryzae: (i) the presence of an highly elevated number of gene duplications which are unlike R. oryzae not due to whole genome duplication (WGD), (ii) despite the relatively high incidence of introns, alternative splicing (AS) is not frequently observed for the generation of paralogs and in response to stress, (iii) the content of repetitive elements is strikingly low (<5%), (iv) L. corymbifera is typically haploid. Novel virulence factors were identified which may be involved in the regulation of the adaptation to iron-limitation, e.g. LCor01340.1 encoding a putative siderophore transporter and LCor00410.1 involved in the siderophore metabolism. Genes encoding the transcription factors LCor08192.1 and LCor01236.1, which are similar to GATA type regulators and to calcineurin regulated CRZ1, respectively, indicating an involvement of the calcineurin pathway in the adaption to iron limitation. Genes encoding MADS-box transcription factors are elevated up to 11 copies compared to the 1–4 copies usually found in other fungi. More findings are: (i) lower content of tRNAs, but unique codons in L. corymbifera, (ii) Over 25% of the proteins are apparently specific for L. corymbifera. (iii) L. corymbifera contains only 2/3 of the proteases (known to be essential virulence factors) in comparision to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.

Author Summary

Lichtheimia species are ubiquitous saprophytic fungi, which cause life-threating infections in humans. In contrast to the mucoralean pathogen R. oryzae, Lichtheimia species belong to the ancient mucoralean lineages. We determined the genome of L. corymbifera (formerly Mycocladus corymbifer ex Absidia corymbifera) and found high dissimilarities between L. corymbifera and other sequenced mucoralean fungi in terms of gene families and syntenies. A highly elevated number of gene duplications and expansions was observed, which comprises virulence-associated genes like proteases, transporters and iron uptake genes but also transcription factors and genes involved in signal transduction. In contrast to R. oryzae, we did not find evidence for a recent whole genome duplication in Lichtheimia. However, gene duplications create functionally diverse paralogs in L. corymbifera, which are differentially expressed in virulence-related compared to standard conditions. In addition, new potential virulence factors could be identified which may play a role in the regulation of the adaptation to iron-limitation. The L. corymbifera genome and the phylome will advance further research and better understanding of virulence mechanisms of these medically important pathogens at the level of genome architecture and evolution.