Long J et al. (2012), Phylogenetic and molecular evolution of the ADA...

XB-ART-45697

Gene 2012 Oct 01;5071:36-43. doi: 10.1016/j.gene.2012.07.016.

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Phylogenetic and molecular evolution of the ADAM (A Disintegrin And Metalloprotease) gene family from Xenopus tropicalis, to Mus musculus, Rattus norvegicus, and Homo sapiens.

Long J , Li M , Ren Q , Zhang C , Fan J , Duan Y , Chen J , Li B , Deng L .

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ADAM (a disintegrin and metalloprotease) genes have been identified in various tissues and species, and recently associated with several important human diseases such as tumor and asthma. Although various biological processes have been known for the ADAM family in different species including fertilization, neurogenesis, infection and inflammation, little is known about its detailed phylogenetic and molecular evolutionary history. In this study, the ADAMs of Xenopus (Silurana) tropicalis, Mus musculus, Rattus norvegicus, and Homo sapiens were collected and analyzed by using the Bayesian analysis and gene synteny analysis to establish a comprehensive phylogenetic relationship and evolutionary drive of this gene family. It was found that there were more ADAMs in the two rodents than in the amphibian, suggesting an expansion of the ADAM gene family during the early evolution of mammals. All ADAMs from this expansion were retained in both the rodents, but other duplication events occurred subsequently in the two rodents, respectively, leading to the classification of rodent ADAMs as classes I, II and III. Moreover, these duplicated ADAM genes in the rodents were found to be driven by positive selection, which might be the major force to retain them in the genome. Importantly, it was also found that orthologs of ADAM3 and 5 have been lost in humans. These results not only provide valuable information of the evolution of ADAM genes, but may also help in understanding the role of ADAM genes in the pathobiology of relevant diseases.

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Species referenced: Xenopus tropicalis
Genes referenced: adam10 adam11 adam12 adam13 adam15 adam17 adam19 adam22 adam23 adam28.1 adam28.1l adam28.2 adam9

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	Fig. 1. Bayesian phylogenetic tree of the ADAM protein sequences from Xenopus (Silurana) tropicalis, Mus musculus, Rattus norvegicus, and Homo sapiens. The red stars indicate 2 earlier progenitors of the ADAM family. The tree is unrooted and Bayesian posterior probability values (> 70%) are shown at interior nodes. The scale bar corresponds to 0.1 substitutions per site. The duplicated ADAMs in the five classes are marked in red. The species and accession numbers are listed in Table 1. The corresponding amino acid sequence alignment is provided in Fig. S1. The abbreviations used are as follows: Hsa, Homo sapiens: Mumu, M. musculus; Rno, Rattus norvegicus; Xtr, Xenopus (Silurana) tropicalis.
	Fig. 2. Order and orientation of genes syntenic to (A) ADAM1a and ADAM1b; (B) ADAM4, ADAM4b and ADAM21; (C) ADAM6a and ADAM6b; (D) ADAM7, ADAMDEC and ADAM28; (E) ADAMs in clade B; (F) ADAMs in class I; (G) ADAM in class II. Genes are intentionally aligned in columns to facilitate visualization of synteny. For other details, please see the text.
	Fig. S2. The phylogenetic trees with the class V marked as foreground branches in the branch-site model analyses (Table 6).
	Fig. S3. The phylogenetic trees with classes I, II, III and IV marked as foreground branches in the branch-site model analyses (Table 6), respectively.