The African coelacanth genome provides insights into tetrapod evolution.

The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.

Discovery of evocalcet, a next-generation calcium-sensing receptor agonist for the treatment of hyperparathyroidism.

The calcium-sensing receptor (CaSR) plays an important role in sensing extracellular calcium ions and regulating parathyroid hormone secretion by parathyroid gland cells, and the receptor is a suitable target for the treatment of hyperparathyroidism. Cinacalcet hydrochloride is a representative CaSR agonist which widely used for the hyperparathyroidism. However, it has several issues to clinical use, such as nausea/vomiting and strong inhibition of CYP2D6. We tried to improve these issues of cinacalcet for a new pharmaceutical agent as a preferable CaSR agonist. Optimization from cinacalcet resulted in the identification of pyrrolidine compounds and successfully led to the discovery of evocalcet as an oral allosteric CaSR agonist. Evocalcet, which exhibited highly favorable profiles such as CaSR agonistic activity and good DMPK profiles, will provide a novel therapeutic option for secondary hyperparathyroidism.

Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome.

The living coelacanth is a lobe-finned fish that represents an early evolutionary departure from the lineage that led to land vertebrates, and is of extreme interest scientifically. It has changed very little in appearance from fossilized coelacanths of the Cretaceous (150 to 65 million years ago), and is often referred to as a "living fossil." An important general question is whether long-term stasis in morphological evolution is associated with stasis in genome evolution. To this end we have used targeted genome sequencing for acquiring 1,612,752 bp of high quality finished sequence encompassing the four HOX clusters of the Indonesian coelacanth Latimeria menadoensis. Detailed analyses were carried out on genomic structure, gene and repeat contents, conserved noncoding regions, and relative rates of sequence evolution in both coding and noncoding tracts. Our results demonstrate conclusively that the coelacanth HOX clusters are evolving comparatively slowly and that this taxon should serve as a viable outgroup for interpretation of the genomes of tetrapod species.

Theria-specific homeodomain and cis-regulatory element evolution of the Dlx3-4 bigene cluster in 12 different mammalian species.

The mammalian Dlx3 and Dlx4 genes are configured as a bigene cluster, and their respective expression patterns are controlled temporally and spatially by cis-elements that largely reside within the intergenic region of the cluster. Previous work revealed that there are conspicuously conserved elements within the intergenic region of the Dlx3-4 bigene clusters of mouse and human. In this paper we have extended these analyses to include 12 additional mammalian taxa (including a marsupial and a monotreme) in order to better define the nature and molecular evolutionary trends of the coding and non-coding functional elements among morphologically divergent mammals. Dlx3-4 regions were fully sequenced from 12 divergent taxa of interest. We identified three theria-specific amino acid replacements in homeodomain of Dlx4 gene that functions in placenta. Sequence analyses of constrained nucleotide sites in the intergenic non-coding region showed that many of the intergenic conserved elements are highly conserved and have evolved slowly within the mammals. In contrast, a branchial arch/craniofacial enhancer I37-2 exhibited accelerated evolution at the branch between the monotreme and therian common ancestor despite being highly conserved among therian species. Functional analysis of I37-2 in transgenic mice has shown that the equivalent region of the platypus fails to drive transcriptional activity in branchial arches. These observations, taken together with our molecular evolutionary data, suggest that theria-specific episodic changes in the I37-2 element may have contributed to craniofacial innovation at the base of the mammalian lineage.

Roles of Mono- and Bi-articular Muscles in Human Limbs: Two-joint Link Model and Applications.

We review the two-joint link model of mono- and bi-articular muscles in the human branchium and thigh for applications related to biomechanical studies of tetrapod locomotion including gait analyses of humans and non-human tetrapods. This model has been proposed to elucidate functional roles of human mono- and bi-articular muscles by analyzing human limb movements biomechanically and testing the results both theoretically and mechanically using robotic arms and legs. However, the model has not yet been applied to biomechanical studies of tetrapod locomotion, in part since it was established based mainly on mechanical engineering analyses and because it has been applied mostly to robotics, fields of mechanical engineering, and to rehabilitation sciences. When we discovered and published the identical pairs of mono- and bi-articular muscles in pectoral fins of the coelacanth fish Latimeria chalumnae to those of humans, we recognized the significant roles of mono- and bi-articular muscles in evolution of tetrapod limbs from paired fins and tetrapod limb locomotion. Therefore, we have been reviewing the theoretical background and mechanical parameters of the model in order to analyze functional roles of mono- and bi-articular muscles in tetrapod limb locomotion. Herein, we present re-defined biological parameters including 3 axes among 3 joints of forelimbs or hindlimbs that the model has formulated and provide biological and analytical tools and examples to facilitate applicable power of the model to our on-going gait analyses of humans and tetrapods.

Evaluation of pyrrolin-2-one derivatives synthesized by a new practical method as inhibitors of plasminogen activator inhibitor-1 (PAI-1).

We describe in this Letter a new synthetic method for pyrrolin-2-ones as potent plasminogen activator inhibitor-1 (PAI-1) inhibitors. Pyrrolin-2-one derivatives synthesized from N-2-oxoethylamides and aldehydes in aqueous NaOH by one-pot were evaluated for their PAI-1 inhibitory activity. Among these derivatives, compounds 16 and 18 were found to possess potent PAI-1 inhibitory activity (compound 16: IC(50): 0.69microM, compound 18: IC(50): 0.65microM).

Development of cranial muscles in the actinopterygian fish Senegal bichir, Polypterus senegalus Cuvier, 1829.

Polypterus senegalus Cuvier, 1829 is one of the most basal living actinopterygian fish and a member of the Actinopterygii. We analyzed the spatial and temporal pattern of cranial muscle development of P. senegalus using whole-mount immunostaining and serial sectioning. We described the detailed structure of the external gill muscles which divided into dorsal and ventral parts after yolk exhaustion. The pattern of the division is similar to that of urodeles. We suggest that, the external gill muscles of P. senegalus are involved in spreading and folding of the external gill stem and the branches. The fibers of the external gill muscles appear postero-lateral to the auditory capsule. In addition, the facial nerve passes through the external gills. Therefore, the external gill muscles are probably derived from the m. constrictor hyoideus dorsalis. In contrast to previous studies, we described the mm. interhyoideus and hyohyoideus fibers as independent components in the yolk-sac larvae. The m. hyohyoideus fibers appear lateral to the edge of the ventral portion of the external gill muscles, which are probably derived from the m. constrictor hyoideus dorsalis. These findings suggest that the m. hyohyoidues is derived from the m. constrictor hyoideus dorsalis in P. senegalus. In other actinopterygians, the m. hyohyoideus is derived from the m. constrictor hyoideus ventralis; therefore, the homology of the m. hyohyoidues of P. senegalus and other actinopterygians remains unclear. J. Morphol. 278:450-463, 2017. © 2017 Wiley Periodicals, Inc.

The pectoral fin muscles of the coelacanth Latimeria chalumnae: Functional and evolutionary implications for the fin-to-limb transition and subsequent evolution of tetrapods.

To investigate the morphology and evolutionary origin of muscles in vertebrate limbs, we conducted anatomical dissections, computed tomography and kinematic analyses on the pectoral fin of the African coelacanth, Latimeria chalumnae. We discovered nine antagonistic pairs of pronators and supinators that are anatomically and functionally distinct from the abductor and adductor superficiales and profundi. In particular, the first pronator and supinator pair represents mono- and biarticular muscles; a portion of the muscle fibers is attached to ridges on the humerus and is separated into two monoarticular muscles, whereas, as a biarticular muscle, the main body is inserted into the radius by crossing two joints from the shoulder girdle. This pair, consisting of a pronator and supinator, constitutes a muscle arrangement equivalent to two human antagonistic pairs of monoarticular muscles and one antagonistic pair of biarticular muscles in the stylopod between the shoulder and elbow joints. Our recent kinesiological and biomechanical engineering studies on human limbs have demonstrated that two antagonistic pairs of monoarticular muscles and one antagonistic pair of biarticular muscles in the stylopod (1) coordinately control output force and force direction at the wrist and ankle and (2) achieve a contact task to carry out weight-bearing motion and maintain stable posture. Therefore, along with dissections of the pectoral fins in two lungfish species, Neoceratodus forsteri and Protopterus aethiopicus, we discuss the functional and evolutionary implications for the fin-to-limb transition and subsequent evolution of tetrapods. Anat Rec, 299:1203-1223, 2016. © 2016 Wiley Periodicals, Inc.

Acquisition of glial cells missing 2 enhancers contributes to a diversity of ionocytes in zebrafish.

Glial cells missing 2 (gcm2) encoding a GCM-motif transcription factor is expressed in the parathyroid in amniotes. In contrast, gcm2 is expressed in pharyngeal pouches (a homologous site of the parathyroid), gills, and H(+)-ATPase-rich cells (HRCs), a subset of ionocytes on the skin surface of the teleost fish zebrafish. Ionocytes are specialized cells that are involved in osmotic homeostasis in aquatic vertebrates. Here, we showed that gcm2 is essential for the development of HRCs and Na(+)-Cl(-) co-transporter-rich cells (NCCCs), another subset of ionocytes in zebrafish. We also identified gcm2 enhancer regions that control gcm2 expression in ionocytes of zebrafish. Comparisons of the gcm2 locus with its neighboring regions revealed no conserved elements between zebrafish and tetrapods. Furthermore, We observed gcm2 expression patterns in embryos of the teleost fishes Medaka (Oryzias latipes) and fugu (Fugu niphobles), the extant primitive ray-finned fishes Polypterus (Polypterus senegalus) and sturgeon (a hybrid of Huso huso × Acipenser ruhenus), and the amphibian Xenopus (Xenopus laevis). Although gcm2-expressing cells were observed on the skin surface of Medaka and fugu, they were not found in Polypterus, sturgeon, or Xenopus. Our results suggest that an acquisition of enhancers for the expression of gcm2 contributes to a diversity of ionocytes in zebrafish during evolution.

Tuatara (Sphenodon) genomics: BAC library construction, sequence survey, and application to the DMRT gene family.

The tuatara (Sphenodon punctatus) is of "extraordinary biological interest" as the most distinctive surviving reptilian lineage (Rhyncocephalia) in the world. To provide a genomic resource for an understanding of genome evolution in reptiles, and as part of a larger project to produce genomic resources for various reptiles (evogen.jgi.doe.gov/second_levels/BACs/our_libraries.html), a large-insert bacterial artificial chromosome (BAC) library from a male tuatara was constructed. The library consists of 215 424 individual clones whose average insert size was empirically determined to be 145 kb, yielding a genomic coverage of approximately 6.3x. A BAC-end sequencing analysis of 121 420 bp of sequence revealed a genomic GC content of 46.8%, among the highest observed thus far for vertebrates, and identified several short interspersed repetitive elements (mammalian interspersed repeat-type repeats) and long interspersed repetitive elements, including chicken repeat 1 element. Finally, as a quality control measure the arrayed library was screened with probes corresponding to 2 conserved noncoding regions of the candidate sex-determining gene DMRT1 and the DM domain of the related DMRT2 gene. A deep coverage contig spanning nearly 300 kb was generated, supporting the deep coverage and utility of the library for exploring tuatara genomics.

A BAC library of the East African haplochromine cichlid fish Astatotilapia burtoni.

A BAC library was constructed from Astatotilapia burtoni, a haplochromine cichlid that is found in Lake Tanganyika, East Africa, and its surrounding rivers. The library was generated from genomic DNA of blood cells and comprises 96,768 individual clones. Its median insert size is 150 kb and the coverage is expected to represent about 14 genome equivalents. The coverage evaluation was based on genome size estimates that were obtained by flow cytometry. In addition, hybridization screens with five probes largely corroborate the above coverage estimate, although the number of clones ranged from 5 to 22 authenticated clones per single copy probe. The BAC library described here is expected to be useful to the scientific community interested in cichlid genomics as an important resource to gain new insights into the rapid evolution of the great species diversity of haplochromine cichlid fishes.

Evolutionary constraint on Otx2 neuroectoderm enhancers-deep conservation from skate to mouse and unique divergence in teleost.

Otx2 is a paired type homeobox gene that plays essential roles in each step and site of head development in vertebrates. In the mouse, Otx2 expression in the anterior neuroectoderm is regulated primarily by two distinct enhancers: anterior neuroectoderm (AN) and forebrain/midbrain (FM) enhancers at 92 kb and 75 kb 5'of the Otx2 locus, respectively. The AN enhancer has activity in the entire anterior neuroectoderm at headfold and early somite stages, whereas the FM enhancer is subsequently active in the future caudal forebrain and midbrain ectoderm. In tetrapods, both AN and FM enhancers are conserved, whereas the AN region is missing in teleosts, despite overt Otx2 expression in the anterior neuroectoderm. Here, we show that zebrafish and fugu FM regions drive expression not only in the forebrain and midbrain but also in the anterior neuroectoderm at headfold stage. The analysis of coelacanth and skate genomic Otx2 orthologues suggests that the utilization of the two enhancers, AN and FM, is an ancestral condition. In contrast, the AN enhancer has been specifically lost in the teleost lineage with a compensatory establishment of AN activity within the FM enhancer. Furthermore, the AN activity in the fish FM enhancer was established by recruiting upstream factors different from those that direct the tetrapod AN enhancer, yet zebrafish FM enhancer is active in both mouse and zebrafish anterior neuroectoderm at the headfold stage.

BAC libraries and comparative genomics of aquatic chordate species.

The bacterial artificial chromosome (BAC) system is useful for creating a representation of the genomes of target species. The system is advantageous in that it can accommodate exogenous inserts that are very large (>100 kilobases, kb), thereby allowing entire eukaryotic genes (including flanking regulatory regions) to be encompassed in a single clone. The interest in BACs has recently been spawned by vast improvements in high throughput genomic sequencing such that comparisons of orthologous regions from different genomes (comparative genomics) are being routinely investigated, and comprise a significant component, of all major sequencing centers. In this review, we discuss the general principles of BAC cloning, the resources that are currently available, and some of the applications of the technology. It is not intended to be an exhaustive treatise; rather our goal is to provide a primer of the BAC technology in order to make readers aware of these resources and how they may utilize them in their own research programs.

Neural ectoderm, neural crest, and placodes: Contribution of the otic placode to the ectodermal lining of the embryonic opercular cavity in Atlantic cod (Teleostei).

Development of neural ectoderm, neural crest, and otic placode with special reference to a new placodal derivative, the ectodermal lining of the opercular cavity, is described in a teleost fish, the Atlantic cod Gadus morhua, from a stage-by-stage examination of embryonic development. The ectodermal lining of the opercular cavity forms by invagination of the otic placode. The neural plate "infolds" by a wave of cellular rearrangement that transforms the neural plate into a neural rod. This transformation creates a distinct dorsal ectodermal cell layer. When the neural rod is arranged as monostratified columnar cells in the forebrain and midbrain, dorsal ectoderm at the midbrain level thickens lateral to the neural rod to form a cell cluster-the presumptive neural crest and placode. Upon migration of the neural crest from the postoptic midbrain, the dorsolateral area of the dorsal ectoderm thickens and segregates from the neural crest as a placode that is continuous with the presumptive lens placode. As the neural crest migrates from the hindbrain, this placode extends along the hindbrain as a single continuous cluster of cells. At the onset of formation of the lens placode, this continuous placode becomes the placode in the postoptic area of the midbrain and separates into the otic placode at the hindbrain. The otic placode gives rise to the otic neuromast and probably the otic lateral line nerves rostrally and to the ectodermal cell lining of the opercular cavity and otic vesicles caudally. The opercular cavity forms by invagination of the otic placode, creating an internal lumen lined by ectoderm that becomes continuous with evaginated endodermal pharyngeal cells. Free neuromasts are observed along the trailing edge of the external opening of the opercular cavity, which lies horizontally, ventral to the otic vesicles. As embryos develop to hatching, the opening rotates and takes up a vertical position. The adult opercular apparatus, including associated bones and muscles, forms during larval stages. The otic neuromast may be a remnant of neuromasts in the spiracle organ. The spiracle opening lies between the mandibular and hyoid arches, whereas the opercular cavity opens between the hyoid and the first branchial arches. The spiracle opening is, therefore, not homologous with the external opening of the opercular cavity, although the cell lining of the spiracle opening may be of placodal origin. J Morphol 231:231-252, 1997. © 1997 Wiley-Liss, Inc.

Ontogeny of feeding and respiration in larval Atlantic cod Gadus morhua (Teleostei, Gadiformes): II. Function.

Feeding mechanisms were studied in larval cod from first feeding to metamorphosis. Structural and functional changes that govern jaw movement and control the flow of water through the mouth change in concert with requirements for food energy. Early in development, exogenous food resources supplement the endogenous yolk-sac, viscerocranial structures and functions are simple and nonintegrated, and respiration is cutaneous. Hyoid coupling, which governs mandibular depression via the mandibulohyoid ligament, serves as the major musculoskeletal linkage for opening the mouth. With growth and differentiation of new structures such as the opercular bones, gills, and secondary lamellae, a second musculoskeletal linkage, the levator-operculi coupling, develops. This coupling mediates mandibular depression via the opercular apparatus and interoperculomandibular ligament and supplements hyoid coupling. Changes in musculoskeletal elements become more complex, facilitating obligatory exogenous feeding and branchial respiration. Thus, increases in structural and functional complexity result in the replacement of the simple, less efficient feeding mechanism by a complex combination of feeding mechanisms similar to those found in adult Atlantic cod. © 1996 Wiley-Liss, Inc.

Ontogeny of feeding and respiration in larval Atlantic cod Gadus morhua (Teleostei, Gadiformes): I. Morphology.

Cranial development in larval Atlantic cod Gadus morhua was studied throughout ontogeny using specimens treated by staining and clearing, scanning electron microscopy and histology. Newly hatched cod larvae have closed mouths, no operculii, five well-developed branchial arches, and transversii ventralis muscles. During the endogenous feeding (yolk-sac) stage, viscerocranial structures remain simple and nonarticulated. Six days after hatching at 5°C, articulation occurs between the quadrate/Meckel's cartilage and the hyomandibula/cranium. Integration of skeletal elements results in a functional jaw that facilitates the transition from endogenous to exogenous feeding. During later ontogenetic stages, the opercular apparatus and levator-operculi coupling develops, facilitating the transition of cutaneous to branchial respiration. Overall, feeding and respiratory needs are met by changes in form (including composition) and function during larval fish growth and are correlated with demands of energy acquisition essential to survival. © 1996 Wiley-Liss, Inc.

Genome resource for the Indonesian coelacanth, Latimeria menadoensis.

We have generated a BAC library from the Indonesian coelacanth, Latimeria menadoensis. This library was generated using genomic DNA of nuclei isolated from heart tissue, and has an average insert size of 171 kb. There are a total of 288 384-well microtiter dishes in the library (110,592 clones) and its genomic representation is estimated to encompass > or = 7X coverage based on the amount of DNA presumably cloned in the library as well as via hybridization with probes to a small set of single copy genes. This genomic resource has been made available to the public and should prove useful to the scientific community for many applications, including comparative genomics, molecular evolution and conservation genetics.