A Likely Ancient Genome Duplication in the Speciose Reef-Building Coral Genus, Acropora

Abstract

Summary Whole-genome duplication (WGD) has been recognized as a significant evolutionary force in the origin and diversification of multiple organisms. Acropora , a speciose reef-building coral genus, is suspected to have originated by polyploidy. Yet, there is no genetic evidence to support this hypothesis. Using comprehensive phylogenomic and comparative genomic approaches, we analyzed six Acroporid genomes and found that a WGD event likely occurred ∼31 million years ago in the most recent common ancestor of Acropora , concurrent with a worldwide coral extinction. We found that duplicated genes were highly enriched in gene regulation functions, including those of stress responses. The functional clusters of duplicated genes are related to the divergence of gene expression patterns during development. Some proteinaceous toxins were generated by WGD in Acropora compared with other cnidarian species. Collectively, this study provides evidence for an ancient WGD event in corals, which helps explain the origin and diversification of Acropora .

Evolutionary Analysis of Cystatins of Early-Emerging Metazoans Reveals a Novel Subtype in Parasitic Cnidarians

“…Each taxonomic group evolved multiple stefin and/or type 2 cystatin homologues, forming individual taxonomy-defined clades in the phylogeny. These paralogues probably arose by gene duplication [ 30 ] rather than by whole genome multiplication, as the only basal metazoans for which genome duplication has been suggested are members of the cnidarian genus Acropora [ 69 ]. Multiple out-paralogues found in cnidarians likely originated before cnidarian radiation while, in-paralogues, probably emerged after the speciation event.…”

Proteases—From Basic Structure to Function to Drug Design as Targeted Therapy

“…Two years later, Si-Tayeb et al reported the detection of nMMP-3 in human hepatocellular carcinoma cell line (HepG2) and the identification of a nuclear localization signal (NLS) within the structure of the protease [66]. Since then, the number of reported nMMPs has grown, with some MMP members being localized to the nuclei in a variety of different cells types, originating from normal tissues, cancers, infected cells, and in cells during disease progression (Table 1) [67][68][69][70][71]. For example, nMMP-2 was found in normal skin cells in the lower one-third of the epidermis, whereas in the tumor and pre-cancerous samples, it was predominantly in the upper layers of the skin suggesting that the protein may be expressed at the early stages of squamous cell carcinogenesis [72].…”

“…Apoptosis ↑ Human hepatocellular carcinoma, hepatocellular carcinoma cell line, peritumoral liver, liver myofibroblasts; Chinese hamster ovary cells [56,66] Cell migration ↑ Human normal, osteoarthritic chondrocytes [58] Immune response ↑ Human embryonic kidney epithelial cell line, macrophages [69] Not defined Human megakaryocytes [78] MMP-7…”

“…The cellular anti-viral response against Dengue virus is augmented by MMP-3 [69]. Zuo et al observed that the presence of nMMP-3 within infected cells was increased.…”

“…The silencing of MMP-3 led to increased titers of the virus, decreased levels of cytokines and chemokines, and the reduced activity of NF-κB. Since nMMP-3 was found to be co-localized with intracellular NF-κB, it was suggested that the protease up-regulated the activity of NF-κB via a direct protein-protein interaction, which could subsequently promote the transcription of anti-viral and pro-inflammatory genes [69]. Collectively, such findings suggest that nMMP-3 plays a significant role in the anti-viral defense of the body against Dengue virus.…”