Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina)

PLoS Genet. 2014 Aug 14;10(8):e1004496. doi: 10.1371/journal.pgen.1004496. eCollection 2014 Aug.

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 comparison to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alternative Splicing / genetics
  • Evolution, Molecular*
  • Gene Duplication
  • Genome, Fungal*
  • Genomics
  • Humans
  • Mucorales / genetics*
  • Mucorales / pathogenicity
  • Mucormycosis / genetics*
  • Mucormycosis / microbiology
  • Virulence Factors / genetics
  • Virulence Factors / isolation & purification

Substances

  • Virulence Factors

Grant support

TG group is funded in part by a grant from the Spanish Ministry of Science and Innovation (BFU2009-09168). MM group was in part supported by the German Science Foundation (DFG) MA5082/1-1 (KR). MN would like to thank Ulrich Kück for generous support, and the DFG for funding (project NO407/4-1). SB group was in part supported by DFG BO 1910/8-1 (SWi). KV and AAB acknowledge financial support of the Leibniz Institute of Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.