Genome duplications of early vertebrates as a possible chronicle of the evolutionary history of the neural crest

Abstract

It is now accepted that ancestral vertebrates underwent two rounds of genome duplication. Here we test the possible utility of these genome duplication events as a reference time for the evolutionary history of vertebrates, by tracing the molecular evolutionary history of the genes involved in vertebrate neural crest development. For most transcription factors that are involved in neural crest specification, more than two paralogs are involved in that process. These were likely involved in the specification of the neural crest before the genome duplications occurred in ancestral vertebrates, although FoxD3 may have acquired that role after the genome duplications. By contrast, the epithelial-mesenchymal transition of neural crest cells is controlled by genes that evolved after the genome duplications, such as cadherin6, cadherin7, cadherin11, and rhoB. This suggests that primitive neural crest cells control their delamination by using a small or distinct set of cell adhesion molecules. Alternatively, these observations suggest that delamination of the neural crest evolved after the genome duplications. In that case, the neural crest might have evolved in sequential steps; the specification of the neural crest occurred before the genome duplications, and the neural crest acquired a new cell migration property after the genome duplications.

Figure 1

Molecular phylogenetic tree of Dlx genes. Molecular phylogenetic tree of Dlx genes. The tree is constructed by the quartet maximum likelihood method using TreePuzzle based on amino acid sequences of the homeodomain. Vertebrate genes can be classified into two groups, and each protochordate gene shows phylogenetic affinity to one of them. This suggests that the tandem duplication of Dlx genes predates the divergence of the chordate groups.

Figure 2

Characterization of the ascidian homologs of AP-2. (A-C) The expression of CiAP-2 (A, B) and HrAP-2 (C) at neurula stage. Embryos in A and C are viewed from dorsal side, while B is the lateral view (anterior to the left). Upregulation in the dorsal midline epidermis of AP-2 is observed in both Ciona and Halocynthia (arrowheads). Note that epidermal cells abutting the anterior edge of the neural plate also show upregulation of the AP-2 (arrow). (D) Molecular phylogenetic tree of AP-2 genes. AP-2 from Halocynthia roretzi (HrAP-2) was isolated from a cDNA library of the gastrula stage (Acc. No.: XXXX). The tree is constructed by quartet maximum likelihood method using Treepuzzle based on the conserved amino acid sequences of the helix-span-helix motif.

Figure 2

Characterization of the ascidian homologs of AP-2. (A-C) The expression of CiAP-2 (A, B) and HrAP-2 (C) at neurula stage. Embryos in A and C are viewed from dorsal side, while B is the lateral view (anterior to the left). Upregulation in the dorsal midline epidermis of AP-2 is observed in both Ciona and Halocynthia (arrowheads). Note that epidermal cells abutting the anterior edge of the neural plate also show upregulation of the AP-2 (arrow). (D) Molecular phylogenetic tree of AP-2 genes. AP-2 from Halocynthia roretzi (HrAP-2) was isolated from a cDNA library of the gastrula stage (Acc. No.: XXXX). The tree is constructed by quartet maximum likelihood method using Treepuzzle based on the conserved amino acid sequences of the helix-span-helix motif.

Figure 3

Molecular evolution of cadherin and Rho genes. (A, B) Molecular phylogenetic trees of cadherin (A) and rho (B) genes, constructed by quartet maximum likelihood method using TreePuzzle 5.0 . The amino acid sequences of the C-terminus cytoplasmic domain were used for the cadherin gene analysis, while entire amino acid sequences were used for the rho genes. Nucleotide sequences of rho genes from Branchiostoma belcheri (BbRho) and Halocynthia roretzi (HrRho) by following Acc. Nos. (YYYY for BbRho and ZZZZ for HrRho). (C, D) The expression of CiCadherinII in the neurula (C: lateral view) and tailbud stage embryo (D). CiCadherinII is expressed uniformly in the neural plate of neurula embryo (C), while in tailbud stage, it shows more restricted expression in the neural tube (D), suggesting its role in neuromere formation of ascidian CNS.

Figure 3

Molecular evolution of cadherin and Rho genes. (A, B) Molecular phylogenetic trees of cadherin (A) and rho (B) genes, constructed by quartet maximum likelihood method using TreePuzzle 5.0 . The amino acid sequences of the C-terminus cytoplasmic domain were used for the cadherin gene analysis, while entire amino acid sequences were used for the rho genes. Nucleotide sequences of rho genes from Branchiostoma belcheri (BbRho) and Halocynthia roretzi (HrRho) by following Acc. Nos. (YYYY for BbRho and ZZZZ for HrRho). (C, D) The expression of CiCadherinII in the neurula (C: lateral view) and tailbud stage embryo (D). CiCadherinII is expressed uniformly in the neural plate of neurula embryo (C), while in tailbud stage, it shows more restricted expression in the neural tube (D), suggesting its role in neuromere formation of ascidian CNS.

Figure 3

Molecular evolution of cadherin and Rho genes. (A, B) Molecular phylogenetic trees of cadherin (A) and rho (B) genes, constructed by quartet maximum likelihood method using TreePuzzle 5.0 . The amino acid sequences of the C-terminus cytoplasmic domain were used for the cadherin gene analysis, while entire amino acid sequences were used for the rho genes. Nucleotide sequences of rho genes from Branchiostoma belcheri (BbRho) and Halocynthia roretzi (HrRho) by following Acc. Nos. (YYYY for BbRho and ZZZZ for HrRho). (C, D) The expression of CiCadherinII in the neurula (C: lateral view) and tailbud stage embryo (D). CiCadherinII is expressed uniformly in the neural plate of neurula embryo (C), while in tailbud stage, it shows more restricted expression in the neural tube (D), suggesting its role in neuromere formation of ascidian CNS.