AUTHOR=Dereeper Alexis , Allouch Nina , Guerlais Vincent , Garnier Maëlle , Ma Laurence , De Jonckheere Johan F. , Joseph Sandeep J. , Ali Ibne Karim M. , Talarmin Antoine , Marcelino Isabel 

TITLE=Naegleria genus pangenome reveals new structural and functional insights into the versatility of these free-living amoebae

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1056418

DOI=10.3389/fmicb.2022.1056418

ISSN=1664-302X

ABSTRACT=<sec><title>Introduction</title><p>Free-living amoebae of the <italic>Naegleria</italic> genus belong to the major protist clade Heterolobosea and are ubiquitously distributed in soil and freshwater habitats. Of the 47 <italic>Naegleria</italic> species described, <italic>N. fowleri</italic> is the only one being pathogenic to humans, causing a rare but fulminant primary amoebic meningoencephalitis. Some <italic>Naegleria</italic> genome sequences are publicly available, but the genetic basis for <italic>Naegleria</italic> diversity and ability to thrive in diverse environments (including human brain) remains unclear.</p></sec><sec><title>Methods</title><p>Herein, we constructed a high-quality <italic>Naegleria</italic> genus pangenome to obtain a comprehensive catalog of genes encoded by these amoebae. For this, we first sequenced, assembled, and annotated six new <italic>Naegleria</italic> genomes.</p></sec><sec><title>Results and Discussion</title><p>Genome architecture analyses revealed that <italic>Naegleria</italic> may use genome plasticity features such as ploidy/aneuploidy to modulate their behavior in different environments. When comparing 14 near-to-complete genome sequences, our results estimated the theoretical <italic>Naegleria</italic> pangenome as a closed genome, with 13,943 genes, including 3,563 core and 10,380 accessory genes. The functional annotations revealed that a large fraction of <italic>Naegleria</italic> genes show significant sequence similarity with those already described in other kingdoms, namely Animalia and Plantae. Comparative analyses highlighted a remarkable genomic heterogeneity, even for closely related strains and demonstrate that <italic>Naegleria</italic> harbors extensive genome variability, reflected in different metabolic repertoires. If <italic>Naegleria</italic> core genome was enriched in conserved genes essential for metabolic, regulatory and survival processes, the accessory genome revealed the presence of genes involved in stress response, macromolecule modifications, cell signaling and immune response. Commonly reported <italic>N. fowleri</italic> virulence-associated genes were present in both core and accessory genomes, suggesting that <italic>N. fowleri</italic>’s ability to infect human brain could be related to its unique species-specific genes (mostly of unknown function) and/or to differential gene expression. The construction of <italic>Naegleria</italic> first pangenome allowed us to move away from a single reference genome (that does not necessarily represent each species as a whole) and to identify essential and dispensable genes in <italic>Naegleria</italic> evolution, diversity and biology, paving the way for further genomic and post-genomic studies.</p></sec>