Figure 1.
Phylogenetic Tree of Vertebrates
The vertical axis represents the abundance of extant species in each of the groups. Names of representative member(s) of each of the lineages are given. The extant Actinopterygii (ray-finned fishes) include Cladistia (e.g., bichir, reedfish), Chondrostei (e.g., sturgeons, paddlefish), Ginglymodi (gars), Amiiformes (bowfin), and Teleostei (e.g., fugu, zebrafish); Sarcopterygii (lobe-finned fishes) include coelacanths, lungfish, and tetrapods (amphibians, birds, reptiles, mammals). Among these, only the teleost and tetrapod branches are shown. The divergence times shown are the minimum divergence times estimated based on fossil records. Agnatha-Gnathostomes, 477 My [69]; Chondrichthyes-Osteichthyes, 450 My [17]; elasmobranchs-chimaeras, 374 My [19]; tetrapods and teleost fishes, 416 My [3,4]. Note that these divergence times are more recent than the molecular sequence–based estimates (e.g., Kumar and Hedges [70]: Agnatha-Gnathostomes, 564 My; Chondrichthyes-Osteichthyes, 528 My; tetrapods and teleost fishes, 450 My).
Figure 2.
Classification of Repetitive Elements from Several Sequenced Vertebrate Genomes Using RepeatMasker
Values (% sequenced genome) for each class of repeats were obtained for Takifugu rubripes (fr1), Tetraodon nigroviridis (tetNig1), Danio rerio (danRer3), Xenopus tropicalis (xenTro1), Gallus gallus (galGal2), and Homo sapiens (hg17) from the University of California at Santa Cruz Genome Bioinformatics Site (http://www.genome.ucsc.edu). Callorhinchus milii repeats were identified in the 1.4× sequence generated in this study.
Table 1.
Human Proteins Known to Be Associated with Male Germ Cells, and Present in the Elephant Shark but Divergent or Absent in Teleost Fishes
Figure 3.
NAR-TcR Genes in the Elephant Shark
(A) Alignment of predicted amino acid sequences of some representative elephant shark NAR-TcRV (esNAR-TcR1 and esNAR-TcR2) with their homologs from the nurse shark (nsNAR-TcR1 to nsNAR-TcR4) and IgNARV sequences from nurse shark (nsNART1 and nsNART2), wobbeygong shark (wgNART2a and wgNART2b) and guitarfish (gfNAR). Alignment of CDR3s, which are highly variable in sequence and length, is not shown.
(B) Alignment of predicted amino acid sequences of putative elephant shark NAR-TcRV–associated TcRδV (esDeltaV1 to esDeltaV4) with nurse shark NAR-TcRV–associated TcRδV sequences (nsDeltaV1 to nsDeltaV4), and typical nurse shark TcRδV sequences (nsDeltaV5 to nsDeltaV8). Leader regions, β-strands, and complementarity-determining regions (CDRs) are indicated above each alignment. Conserved residues are highlighted in blue and gray, and conserved cysteine residues in immunoglobulin superfamily canonical intradomain and putative interdomain disulfide bridges are highlighted in red. Note the conserved cysteine residue in the a-b loop and the absence of the canonical tryptophan of the “WYRK” motif in the NAR-TcRV sequences (alignment A). The NAR-TcRV–associated TcRδV lacks the leader peptide, and encodes a conserved cysteine residue in the CDR1 (alignment B). Sequences of nurse shark, wobbeygong shark, and guitarfish are taken from Criscitiello et al. [43].
Figure 4.
Hox Genes in the Elephant Shark and Horn Shark
Hox genes belonging to putative four Hox clusters (esHoxA to esHoxD) identified in the elephant shark assembly are shown as dark filled boxes. Linkage of genes is inferred from linkage information in horn shark and other vertebrates. For comparison, horn shark HoxA and HoxD cluster (hsHoxA and hsHoxD) genes (light filled boxes) are shown [51,52]. In the horn shark, only a partial HoxD cluster (from HoxD5 to HoxD14) has been sequenced, and HoxB and HoxC clusters are yet to be sequenced.
Figure 5.
The Evolution of Vertebrate Hox Cluster Organization and the History of Whole-Genome Duplications in Vertebrates
The additional Hox genes in the lamprey (shown as white arrows) are the result of a lineage-specific duplication of the “AB” or “CD” Hox cluster. In the horn shark, only a partial HoxD cluster (from HoxD5 to HoxD14) has been sequenced, and HoxB and HoxC clusters are yet to be sequenced. The number of Hox clusters in various lineages is consistent with one round of genome duplication (“1R”) during the evolution of jawless vertebrates from chordate invertebrates, a second round (“2R”) before the emergence of jawed vertebrates but after the divergence of the lamprey lineage, and a third round (“3R”) in the ray-finned fish lineage before the divergence of zebrafish and fugu lineages. See text for the source of Hox cluster information.