Insights into metazoan evolution from Alvinella pompejana cDNAs

Abstract

Background: Alvinella pompejana is a representative of Annelids, a key phylum for evo-devo studies that is still poorly studied at the sequence level. A. pompejana inhabits deep-sea hydrothermal vents and is currently known as one of the most thermotolerant Eukaryotes in marine environments, withstanding the largest known chemical and thermal ranges (from 5 to 105°C). This tube-dwelling worm forms dense colonies on the surface of hydrothermal chimneys and can withstand long periods of hypo/anoxia and long phases of exposure to hydrogen sulphides. A. pompejana specifically inhabits chimney walls of hydrothermal vents on the East Pacific Rise. To survive, Alvinella has developed numerous adaptations at the physiological and molecular levels, such as an increase in the thermostability of proteins and protein complexes. It represents an outstanding model organism for studying adaptation to harsh physicochemical conditions and for isolating stable macromolecules resistant to high temperatures.

Results: We have constructed four full length enriched cDNA libraries to investigate the biology and evolution of this intriguing animal. Analysis of more than 75,000 high quality reads led to the identification of 15,858 transcripts and 9,221 putative protein sequences. Our annotation reveals a good coverage of most animal pathways and networks with a prevalence of transcripts involved in oxidative stress resistance, detoxification, anti-bacterial defence, and heat shock protection. Alvinella proteins seem to show a slow evolutionary rate and a higher similarity with proteins from Vertebrates compared to proteins from Arthropods or Nematodes. Their composition shows enrichment in positively charged amino acids that might contribute to their thermostability. The gene content of Alvinella reveals that an important pool of genes previously considered to be specific to Deuterostomes were in fact already present in the last common ancestor of the Bilaterian animals, but have been secondarily lost in model invertebrates. This pool is enriched in glycoproteins that play a key role in intercellular communication, hormonal regulation and immunity.

Conclusions: Our study starts to unravel the gene content and sequence evolution of a deep-sea annelid, revealing key features in eukaryote adaptation to extreme environmental conditions and highlighting the proximity of Annelids and Vertebrates.

Figure 1

Screenshots of the Alvinella website illustrating some of the visualisation tools.

Figure 2

The 30 most frequent PFAM-A domains identified in A. pompejana protein sequences. The Y-axis indicates the total number of reads encoding proteins with this domain. We used a logarithmic scale for representation constraints. Bars are coloured according to functional role categories: respiration, oxidative stress and/or detoxification in blue, protein-protein or protein-DNA/RNA interactions in green, structural proteins in red, anti-bacterial defence in orange and others in grey.

Figure 3

Bayesian phylogeny of Metazoa. The analysis was performed on a concatenation of 76 ribosomal protein family alignments, with Saccharomyces cerevisiae as the outgroup. The scale bar indicates the expected number of amino acid substitutions per aligned position. All nodes were resolved in 100% of the sampled topologies from the Bayesian analysis, except the node indicated by a square (support value of 96%).