Genome Variations Associated with Viral Susceptibility and Calcification in Emiliania huxleyi

Jessica U. Kegel,Uwe John,Klaus Valentin,Stephan Frickenhaus,Ahmed Moustafa

doi:10.1371/journal.pone.0080684

Abstract

Emiliania huxleyi, a key player in the global carbon cycle is one of the best studied coccolithophores with respect to biogeochemical cycles, climatology, and host-virus interactions. Strains of E. huxleyi show phenotypic plasticity regarding growth behaviour, light-response, calcification, acidification, and virus susceptibility. This phenomenon is likely a consequence of genomic differences, or transcriptomic responses, to environmental conditions or threats such as viral infections. We used an E. huxleyi genome microarray based on the sequenced strain CCMP1516 (reference strain) to perform comparative genomic hybridizations (CGH) of 16 E. huxleyi strains of different geographic origin. We investigated the genomic diversity and plasticity and focused on the identification of genes related to virus susceptibility and coccolith production (calcification). Among the tested 31940 gene models a core genome of 14628 genes was identified by hybridization among 16 E. huxleyi strains. 224 probes were characterized as specific for the reference strain CCMP1516. Compared to the sequenced E. huxleyi strain CCMP1516 variation in gene content of up to 30 percent among strains was observed. Comparison of core and non-core transcripts sets in terms of annotated functions reveals a broad, almost equal functional coverage over all KOG-categories of both transcript sets within the whole annotated genome. Within the variable (non-core) genome we identified genes associated with virus susceptibility and calcification. Genes associated with virus susceptibility include a Bax inhibitor-1 protein, three LRR receptor-like protein kinases, and mitogen-activated protein kinase. Our list of transcripts associated with coccolith production will stimulate further research, e.g. by genetic manipulation. In particular, the V-type proton ATPase 16 kDa proteolipid subunit is proposed to be a plausible target gene for further calcification studies.

Highlights

The prolific coccolithophore Emiliania huxleyi is distributed from sub-polar to tropical latitudes [1,2] and often forms immense coastal and open ocean blooms that can cover more than 50.000 km2 [3,4,5]
Results indicate the presence of different ecotypes of E. huxleyi with differences in genome organization as a response to environmental conditions or potential threats, such as viral infections
Core Genome and Genetic Diversity of E. huxleyi Genomic DNAs of 16 E. huxleyi strains from different geographic regions (Figure 1) were compared in order to identify genomic differences in terms of plasticity and possible relation to virus-susceptibility and calcification

Summary

Introduction

The prolific coccolithophore Emiliania huxleyi is distributed from sub-polar to tropical latitudes [1,2] and often forms immense coastal and open ocean blooms that can cover more than 50.000 km2 [3,4,5]. We used a whole genome microarray comprising unique probes for predicted gene models of the sequenced strain E. huxleyi CCMP1516 (reference strain). We were able to identify candidate genes possibly involved in virus susceptibility and calcification.

Results

Conclusion