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The ancient Sox gene family is a group of related transcription factors that perform a number of essential functions during embryonic development. During evolution, this family has undergone considerable expansion, particularly within the vertebrate lineage. In vertebrates SOX proteins are required for the specification, development and/or morphogenesis of most vertebrate innovations. Tunicates and lancelets are evolutionarily positioned as the closest invertebrate relatives to the vertebrate group. By identifying their Sox gene complement we can begin to reconstruct the gene set of the last common chordate ancestor before the split into invertebrates and vertebrate groups. We have identified core SOX family members from the genomes of six invertebrate chordates. Using phylogenetic analysis we determined their evolutionary relationships. We propose that the last common ancestor of chordates had at least seven Sox genes, including the core suite of SoxB, C, D, E and F as well as SoxH., (Copyright © 2015 Elsevier B.V. All rights reserved.)

MicroRNAs (miRNAs) participate in various biological processes via controlling gene activity. Amphioxus is the best available stand-in as the proximate invertebrate ancestor of the vertebrates. Here, we systematically investigated the miRNAs in amphioxus. First, we identified 245 candidate amphioxus miRNAs, in which 183 miRNAs were firstly reported. Second, we gave evidences to support a birth-and-death process of miRNA genes in some families and gave implications for the functional diversification of miRNA during evolution. Third, we identified 47 development-specific expression miRNAs. We found that only 19 miRNAs were expressed in all developmental stages, 16 miRNAs were neurula-specific and 13 miRNAs were larva-specific. In addition, these potential miRNA-targeting genes were mainly classified into development, muscle formation, cell adhesion, and gene regulation categories. Finally, we found 79 immune related genes targeted by 136 miRNAs in amphioxus. In conclusion, our results take an insight into both the function and evolution of the amphioxus miRNAs., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Two dimethylarginine dimethylaminohydrolase (DDAH) homologous genes in amphioxus are identified and cloned. The phylogenetic analysis indicates two DDAHs in amphioxus originated by independent duplication specific in cephalochordate lineage. Analysis of AmphiDDAHa and AmphiDDAHb genomic structure shows their comparability with the DDAH in vertebrate and aboriginality which is consistent with animal classification. To explore the function relationship of AmphiDDAHa and AmphiDDAHb with AmphiNOS, the nitric oxide synthase homologue in amphioxus, we investigate the three genes expression patterns in embryos and adult tissues. The results indicate that these three genes possess different spatial and temporal expression patterns during embryogenesis. AmphiDDAHa transcripts are detected extensively in the differentiating ectoderm, mesendoderm in gastrula/early neurula, the developing and newly formed neural tube, somites, notochord, alimentary canal and epidermis at neurula stage, as well as in the differentiating pharynx and tailbud at early larval stage. While AmphiDDAHb is expressed in the differentiating non-neural ectoderm at the gastrla/early neurula stage, then locates abroad in the developing and formed neural tube, notochord, somites and alimentary canal. AmphiNOS is expressed weakly but widely from early neurula stage to at least 72-h larva stage. In adult, AmphiDDAHa and AmphiNOS share similar expression patterns in diverse adult tissues and cells such as the neural cord, gut, midgut diverticulum, wheel organ, gill, blood vessels, endostyle, oocytes and macrophages. But no expression of AmphiDDAHb is detected in tissues mentioned above. The results suggest that AmphiDDAHa and AmphiDDAHb should be two homologous genes with different functions in amphioxus. AmphiDDAHa may play a conserved role in the regulation of NO synthesis and immune defense, whereas AmphiDDAHb may mainly play the roles in the cell movement or differentiation of embryonic non-neural ectoderm cells during gastrulation and early neurulation.