Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome

Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4× coverage) and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element–like and long interspersed element–like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes.     

Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome

Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4× coverage) and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element–like and long interspersed element–like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes.     

Embryonic staging and external features of development of the Chimaeroid fish,Callorhinchus milii (Holocephali,Callorhinchidae)

The development of Callorhinchus milii, a primitive chondrichthyan fish (Subclass Holocephali) is described in detail based on a complete series of embryos from stage 17 to hatching. The external features of these specimens, in comparison with other chondrichthyan embryos, are used to establish the first staging table for any chimaeroid species. Each stage of C. milii is defined by a suite of morphological characters in addition to total length, including the number of somites, extent of external pigmentation, eye size and shape, head flexure, heart morphology, and size and shape of paired and unpaired fins. Particular attention is given to features of the gill arches and associated structures, including external gill filaments and the opercular flap. Embryos of this species also possess a transient rostral bulb, a feature unique to chimaeroids. Embryological development of Callorhinchus milii is similar to that previously described for sharks and batoids (Subclass Elasmobranchii), including the spiny dogfish, Squalus acanthias, the Japanese bullshark, Heterodontus japonicus, the lesser spotted dogfish, Scyliorhinus canicula, the frill shark, Chlamydoselachus anguineus, the guitarfish, Rhinobatus halavi, and the skate, Raja brachyura. Callorhinchus milii is also similar in overall development to another holocephalan, Hydrolagus colliei. A review of previous staging schemes confirms that early morphological development in all three major chondrichthyan lineages (sharks, batoids, and chimaeras) can be correlated using a common set of stages. A uniform staging system is provided that should prove useful in continuing ontogenetic and phylogenetic studies of this entire clade of fishes. J. Morphol. 236:25–47, 1998. © 1998 Wiley-Liss, Inc.     

Glial architecture of the ghost shark (Callorhinchus milii, Holocephali, Chondrichthyes) as revealed by different immunohistochemical markers

This article presents the first study on the glial architecture of a representative species of Holocephali, Callorhinchus milii (ghost shark). Holocephali are a small subclass of Chondrichthyes, with only a few extant genera, and those are considered to have a brain organization more similar to squalomorph sharks than to galeomorph sharks, skates, and rays. Three different astroglial markers--glial fibrillary acidic protein, S-100 protein, and glutamine synthetase (GS)--were investigated by immunohistochemical methods, applying both diaminobenzidine (DAB) and fluorescent techniques. They revealed similar glial structures, although most of them were detected by immunohistochemical reaction against GS and visualized by DAB. The predominant elements were radial ependymoglia spanning the area between the ventricular and meningeal surfaces, as in squalomorph sharks. Other similar features were the light appearance of myelinated neural tracts devoid of immunoreactivity, and the glial architecture of the reticular formation of the brain stem, cerebellum, and tectum, the latter with recognizable layers. The immunoreactivity of the vascular walls was similar; however, it is believed that different cell types form the blood-brain barrier in chimeras and in elasmobranchs. Some glial structures, however, resembled those of skates, rays, and galeomorph sharks. In C. milii astrocyte-like elements were observed in the telencephalon, using GS and S-100, although typical astrocyte-rich regions were not found. In some areas, especially the telencephalon, not only endfeet but also cell bodies were observed to be attached to the meningeal surface, with processes extending into the brain substance.     

Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)

Recent development of deep sequencing technologies has facilitated de novo genome sequencing projects, now conducted even by individual laboratories. However, this will yield more and more genome sequences that are not well assembled, and will hinder thorough annotation when no closely related reference genome is available. One of the challenging issues is the identification of protein-coding sequences split into multiple unassembled genomic segments, which can confound orthology assignment and various laboratory experiments requiring the identification of individual genes. In this study, using the genome of a cartilaginous fish, Callorhinchus milii, as test case, we performed gene prediction using a model specifically trained for this genome. We implemented an algorithm, designated ESPRIT, to identify possible linkages between multiple protein-coding portions derived from a single genomic locus split into multiple unassembled genomic segments. We developed a validation framework based on an artificially fragmented human genome, improvements between early and recent mouse genome assemblies, comparison with experimentally validated sequences from GenBank, and phylogenetic analyses. Our strategy provided insights into practical solutions for efficient annotation of only partially sequenced (low-coverage) genomes. To our knowledge, our study is the first formulation of a method to link unassembled genomic segments based on proteomes of relatively distantly related species as references.     

Neuropeptide Y-family peptides and receptors in the elephant shark, Callorhinchus milii confirm gene duplications before the gnathostome radiation

We describe here the repertoire of neuropeptide Y (NPY) peptides and receptors in the elephant shark Callorhinchus milii, belonging to the chondrichthyans that diverged from the rest of the gnathostome (jawed vertebrate) lineage about 450 million years ago and the first chondrichthyan with a genome project. We have identified two peptide genes that are orthologous to NPY and PYY (peptide YY) in other vertebrates, and seven receptor genes orthologous to the Y1, Y2, Y4, Y5, Y6, Y7 and Y8 subtypes found in tetrapods and teleost fishes. The repertoire of peptides and receptors seems to reflect the ancestral configuration in the predecessor of all gnathostomes, whereas other lineages such as mammals and teleosts have lost one or more receptor genes or have acquired 1-2 additional peptide genes. Both the peptides and receptors showed broad and overlapping mRNA expression which may explain why some receptor gene losses could take place in some lineages, but leaves open the question why all the known ancestral receptors have been retained in the elephant shark.     

Functional anatomy and sexual dimorphism of the cephalic clasper in the pacific ratfish (Chimaera collei)

The cephalic clasper of the male Chimaera collei is a cartilaginous rod equipped with denticles and presumably used to grasp the female during copulation. It is attached to the skull by ligaments but there is no joint cavity or articular surface. It has no intrinsic muscles, its movements being provided by attachments to muscles of the lower jaw and labial cartilages. The cephalic clasper is apparently elevated by a branch of the preorbitalis muscle, whose main function is to elevate the lower jaw. It appears to be forcefully depressed during copulation by M. levator anguli oris, whose primary function is to move the labial cartilages. When not in use, the cephalic clasper is held passively depressed by an elastic tendon from M. preorbitalis. In the female the cephalic clasper is represented by an apparently functionless rudiment.     

Chimaera compacta,a new species from southern Indian Ocean,and an estimate of phylogenetic relationships within the genus Chimaera (Chondrichthyes: Chimaeridae)

Ichthyological Research - Chimaera compacta sp. nov., a new species of shortnose chimaera (Holocephali: Chimaeriformes: Chimaeridae), is described from a single specimen collected at 595–655...     

Elephant (Loxodonta africana) Disturbance to Riparian Woodland: Effects on Tree-Species Richness,Diversity and Functional Redundancy

The substantial increase in elephant populations across many areas in southern Africa over past decades is prompting concerns about the effects on biodiversity. We investigated the outcomes of elephant disturbance on tree-species presence, density, and richness, and on alpha and beta diversity within riparian woodland in Chobe National Park, Botswana. We enumerated all tree species occurring in 32 plots (0.06 ha) along the Chobe riverfront. Plots were stratified by soil type (nutrient-rich alluvium vs. nutrient-poor Kalahari sand covering alluvium) and elephant impact (high vs. low impact on both soil types). We tested four predictions: elephants reduce tree density, richness, and alpha diversity; beta diversity is greater in vegetation subjected to high elephant impact; elephant impact on tree-species composition is greater on nutrient-poor than on nutrient-rich soil; and the loss or decline of abundant tree species on heavily disturbed sites is offset by an increase in abundance of functionally similar species, ones that are minor on lightly disturbed sites. Elephant browsing substantially affected tree-species composition, reducing density, species richness, evenness, and alpha diversity but had no effect on beta diversity. The dominant species on relatively undisturbed areas were partly replaced by functionally similar species on heavily disturbed sites. Soil type influenced species composition on lightly disturbed sites but was less important at higher elephant densities. Our findings are important for areas with extreme dry-season densities of elephants but should not be extrapolated to infer purported effects of elephants on tree diversity at lower densities.     

Histology and Ultrastructure of the Cranial Lymphohaemopoietic Tissue in Chimaera monstrosa (Pisces,Holocephali)

In the present ultrastructural study we have extended previous reports on the histological organization and cell components of the lymphohaemopoietic masses occurring in the cranium, mainly in the orbit, the preorbital canal, and the suprapalatal and coiacoid areas of the holocephalan Chimaera monstrosa. Mature and developing granulocytes, monocytes, macrophages, lymphocytes and plasma cells occur in a reticular and/or fibroblastic supporting stroma inside the cartilaginous skeleton. Heterophils, which are the most abundant granulocytes in the cranial tissue, contain two distinct cytoplasmic granular populations, whereas eosinophils show one uniformly electron dense granule type. Heterophils and eosinophils may differentiate from a common precursor producing granules of each cell type in relation to the activity of rough endoplasmic reticulum and Golgi complex. The presence of macrophages, lymphocytes and developing and mature plasma cells suggests an important role of the cranial lymphohaemopoietic tissue in eliciting the immune responses. A phylogenetical relationship between this tissue and the higher vertebrate bone marrow is proposed on the basis of histological similarities between the cell microenvironments governing haemopoietic differentiation in these organs.     

On the South Atlantic distribution of Callorhinchus callorhynchus (Holocephali: Callorhynchidae)

The four species of the family Callorhynchidae are restricted to the southern hemisphere ( Didier 1995 ) and have the most littoral-related distribution among holocephalans.     

鲨鱼软骨血管生成抑制因子的纯化和功能

以中国东海鲸鲨软骨为原料,通过盐抽提、丙酮分级沉淀、离子交换层折、分子筛层析、高效液相色谱等步骤,获得鲨鱼软骨血管生成抑制因子－Ｉ（ｓｈａｒｋ ｃａｒｔｉｌｇａｅ ａｎｇｉｏｇｅｎｅｓｉｓ ｉｎｈｉｂｉｔｏｒｙ ｆａｃｔｏｒ－Ｉ,ＳＣＡＩＦ－Ｉ）,对其分子量、抑制血管生成及抑制肿瘤生长活性进行了研究。结果显示ＳＣＡＩＦ－Ｉ分子量１８ｋＤ,在细胞和整体水平上显著抑制新血管生成,显著抑制小鼠肿瘤的生长     

Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes)

Sharks are a diverse and ecologically important group, including some of the ocean's largest predatory animals. Sharks are also commercially important, with many species suffering overexploitation and facing extinction. However, despite a long evolutionary history, commercial, and conservation importance, phylogenetic relationships within the sharks are poorly understood. To date, most studies have either focused on smaller clades within sharks, or sampled taxa sparsely across the group. A more detailed species-level phylogeny will offer further insights into shark taxonomy, provide a tool for comparative analyses, as well as facilitating phylogenetic estimates of conservation priorities. We used four mitochondrial and one nuclear gene to investigate the phylogenetic relationships of 229 species (all eight Orders and 31 families) of sharks, more than quadrupling the number of taxon sampled in any prior study. The resulting Bayesian phylogenetic hypothesis agrees with prior studies on the major relationships of the sharks phylogeny; however, on those relationships that have proven more controversial, it differs in several aspects from the most recent molecular studies. The phylogeny supports the division of sharks into two major groups, the Galeomorphii and Squalimorphii, rejecting the hypnosqualean hypothesis that places batoids within sharks. Within the squalimorphs the orders Hexanchiformes, Squatiniformes, Squaliformes, and Pristiophoriformes are broadly monophyletic, with minor exceptions apparently due to missing data. Similarly, within Galeomorphs, the orders Heterodontiformes, Lamniformes, Carcharhiniformes, and Orectolobiformes are broadly monophyletic, with a couple of species 'misplaced'. In contrast, many of the currently recognized shark families are not monophyletic according to our results. Our phylogeny offers some of the first clarification of the relationships among families of the order Squaliformes, a group that has thus far received relatively little phylogenetic attention. Our results suggest that the genus Echinorhinus is not a squaliform, but rather related to the saw sharks, a hypothesis that might be supported by both groups sharing 'spiny' snouts. In sum, our results offer the most detailed species-level phylogeny of sharks to date and a tool for comparative analyses.     

First record of the opal chimaera,Chimaera opalescens (Holocephali: Chimaeridae) and revision of the occurrence of the rabbitfish Chimaera monstrosa in the Azores waters

The presence of the opal chimaera, Chimaera opalescens, is reported for the first time in the deep waters of the Azores, with the capture of four specimens by fishermen and the video recording of an additional five individuals. Species identification was supported by the 646 bp sequenced fragment of the mitochondrial gene cytochrome oxidase subunit I. Because C. opalescens is a recently recognised species that had been recurrently misidentified as rabbitfish, Chimaera monstrosa, the historical data of C. monstrosa in the Azores were reviewed to assess the possible presence of both Chimaera species in the region. Although several authors have reported the occurrence of C. monstrosa in the Azorean waters since the 1800s, the majority of these are based on only three specimens caught during the late 1800s. The investigation performed using literature and examination of the museum specimens still available concluded that the most likely scenario is that C. monstrosa is absent from the Azores and past records of that species in the region are most likely misidentifications of C. opalescens.