Detection of Prokaryotic Genes in the Amphimedon queenslandica Genome

Abstract

Horizontal gene transfer (HGT) is common between prokaryotes and phagotrophic eukaryotes. In metazoans, the scale and significance of HGT remains largely unexplored but is usually linked to a close association with parasites and endosymbionts. Marine sponges (Porifera), which host many microorganisms in their tissues and lack an isolated germ line, are potential carriers of genes transferred from prokaryotes. In this study, we identified a number of potential horizontally transferred genes within the genome of the sponge, Amphimedon queenslandica. We further identified homologs of some of these genes in other sponges. The transferred genes, most of which possess catalytic activity for carbohydrate or protein metabolism, have assimilated host genome characteristics and are actively expressed. The diversity of functions contributed by the horizontally transferred genes is likely an important factor in the adaptation and evolution of A. queenslandica. These findings highlight the potential importance of HGT on the success of sponges in diverse ecological niches.

Ontogenetic Changes in the Bacterial Symbiont Community of the Tropical Demosponge Amphimedon queenslandica: Metamorphosis Is a New Beginning

“…Among putatively horizontally-transferred genes in the A. queenslandica (Conaco et al, 2016) that show significant upregulation from larvae to postlarvae, we identified several associated with hydrolase activity, oxidoreductase activity, carbohydrate metabolism and glycogenesis activity; some of these have putative functions in breaking down cellulose, which is interesting given their upregulation at the time that non-feeding larvae, and subsequently postlarvae, are settling and reorganizing their body plan on coralline algae substrates. We also note that HGTs significantly upregulated later, from the 48 hpi postlarval to adult stage, included those annotated as metalloproteases (e.g., Aspzincin-like peptidase m35, extracellular protease), glycogenesis, hydrolase and sulfatase activity, while those encoding extracellular proteases and metalloproteases showed a sustained upregulation across all three of the successive stages.…”

“…The Cluster 1 gene list (Table S3) includes 14 genes containing ankyrin repeat domains (ANKs) of various types, and 24 genes containing tetratricopeptide repeats (TPRs); one of the latter (Aqu2.1.21073, a glycosyltransferase/tetratricopeptide repeat domain-containing protein) has been identified with high confidence as a gene horizontally transferred from bacteria into the A. queenslandica genome (Conaco et al, 2016). The next most abundant genes families of interest are 19 Deleted in Malignant Brain Tumor 1 (DMBT1) genes, each of which contain scavenger receptor cysteine-rich (SRCR) domains (Rosenstiel et al, 2007), followed by six each of tnf receptor-associated factor (TRAF) genes with putative roles in activation of the immune response (Wiens and Glenney, 2011), and tripartite motif-containing protein family (TRIM) genes that are hypothetically involved in pathogen recognition and host defense (Ozato et al, 2008).…”

“…We were interested in specifically identifying genes in the A. queenslandica genome that are putatively derived from horizontal gene transfer (HGT; Conaco et al, 2016) and significantly upregulated from the larval to the postlarval stage. Among these, we recovered several associated with hydrolase activity, oxidoreductase activity, carbohydrate metabolism and glycogenesis activity (Table S3).…”

“…Together, these findings lead us to suggest that the ANK-and TPR-containing proteins upregulated in Cluster 1 might well be important in mediating sponge-bacterial crosstalk through larval settlement and metamorphosis because they could directly interact with symbiont proteins containing the same domains. It is further notable that one of the Cluster I genes encoding a TPR has been putatively identified as a gene horizontally transferred from bacteria into the A. queenslandica genome (Conaco et al, 2016).…”

The characterization of larval homology: transcriptomic insights into the origin and evolution of animal life cycles

“…Using this approach, I found that DEGs across metamorphosis are characterized by unique, phylum-specific protein domain enrichments in each species, many of which can be correlated to the known biological functions in these species. For instance, I recovered a unique Amphimedonspecific enrichment of the Aspzincin domain (PF14521), which is the result of an established horizontal gene transfer event unique to the Porifera (Conaco et al 2016). I found an overrepresentation of DEGs containing the Ephrin domain in Acropora, which has been implicated in host-endosymbiotic relationships in corals (Ding et al 2016), and was also found to be upregulated in the Acropora pulmata larvae (Polato et al 2013).…”