On the diploid state of the fish order Ostariophysi

Our previous study on the order Ostariophysi was limited to members of the family Cyprinidae, suborder Cyprinidea. It was shown that the carp and the goldfish with 104 chromosomes and a DNA value of 50% that of mammals are tetraploid, as the diploid species of this family has 50–52 chromosomes and a 25% DNA value. In order to obtain some idea as to how many changes in DNA values and chromosome complements have occurred among diploid members of Ostariophysi, the study was expanded to cover members of the families Cobitidae and Characinidae of the suborder Cyprinidea as well as members of the families Ictarulidae and Loricaridae of the suborder Siluroidea. Diploid chromosome numbers varied from 50 to 98 and DNA values from 27–51% that of mammals. Apparently, diploid members of Ostariophysi underwent extensive chromosomal rearrangements as well as steady increases in DNA contents by regional duplication of chromosomal segments.In Duarte, this work was supported by a grant CA-05138 from the Nationa Cancer Institute, U.S. Public Health Service, and in part by a research fund established in honor of General James H. Doolittle. Contribution No. 21-67, Department of Biology. In Northwood, this project was supported by the British Empire Cancer Campaign.Fellow of the Institute for Advanced Learning of the City of Hope Medical Center.     

Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions

One important mechanism for functional innovation during evolution is the duplication of genes and entire genomes. Evidence is accumulating that during the evolution of vertebrates from early deuterostome ancestors entire genomes were duplicated through two rounds of duplications (the 'one-to-two-to-four' rule). The first genome duplication in chordate evolution might predate the Cambrian explosion. The second genome duplication possibly dates back to the early Devonian. Recent data suggest that later in the Devonian, the fish genome was duplicated for a third time to produce up to eight copies of the original deuterostome genome. This last duplication took place after the two major radiations of jawed vertebrate life, the ray-finned fish (Actinopterygia) and the sarcopterygian lineage, diverged. Therefore the sarcopterygian fish, which includes the coelacanth, lungfish and all land vertebrates such as amphibians, reptiles, birds and mammals, tend to have only half the number of genes compared with actinopterygian fish. Although many duplicated genes turned into pseudogenes, or even 'junk' DNA, many others evolved new functions particularly during development. The increased genetic complexity of fish might reflect their evolutionary success and diversity.     

Cloning and characterization of the platypus mitochondrial genome

The vertebrate mitochondrial genome is highly conserved in size and gene content. Among the chordates there appears to be one basic gene arrangement, but rearrangements in the mitochondrial gene order of the avian lineages have indicated that the mitochondrial genome may be more variable than once thought. Different gene orders in marsupials and eutherian mammals leave the ancestral mammalian order in some doubt. We have investigated the mitochondrial gene order in the platypus (Ornithorhynchus anatinus), a representative of the third major group of mammals, to determine which mitochondrial gene arrangement is ancestral in mammals. We have found that the platypus mtDNA conforms to the basic chordate gene arrangement, common to fish, amphibians, and eutherian mammals, indicating that this arrangement was the original mammalian arrangement, and that the unusual rearrangements observed in the avians and marsupials are probably lineage-specific. Correspondence to: N.J. Gemmell     

Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements

With the imminent completion of the whole genome sequence of humans, increasing attention is being focused on the annotation of cis-regulatory elements in the human genome. Comparative genomics approaches based on evolutionary conservation have proved useful in the detection of conserved cis-regulatory elements. The pufferfish, Fugu rubripes, is an attractive vertebrate model for comparative genomics, by virtue of its compact genome and maximal phylogenetic distance from mammals. Fugu has lost a large proportion of nonessential DNA, and retained single orthologs for many duplicate genes that arose in the fish lineage. Non-coding sequences conserved between fugu and mammals have been shown to be functional cis-regulatory elements. Thus, fugu is a model fish genome of choice for discovering evolutionarily conserved regulatory elements in the human genome. Such evolutionarily conserved elements are likely to be shared by all vertebrates, and related to regulatory interactions fundamental to all vertebrates. The functions of these conserved vertebrate elements can be rapidly assayed in mammalian cell lines or in transgenic systems such as zebrafish/medaka and Xenopus, followed by validation of crucial elements in transgenic rodents.     

DNA values of four primitive chordates

DNA values lower than the lowest value of the vertebrates were found for a urochordate and a cephalochordate. On the assumption that the genomes of surviving primitive chordata reflect the status of the genomes possessed by ancient organisms from which vertebrates eventually evolved, it is suggested that vertebrates started from an organism with a very small amount of DNA. Two cyclostomes, on the other hand, showed relatively high DNA values suggesting that the increase in DNA both by regional duplication of chromosomal segments and by polyploidization began to occur before vertebrates developed the jaw. The DNA values relative to the human female leucocyte value were: Ciona intestinalis: 6%; Amphioxus lanceolatus: 17%; Lampetra planeri: 38%; and Eptatretus stoutii: 78%.In Northwood, this work was supported by the British Empire Cancer Campaign for Research, and in Duarte by a grant (CA-05138) from the National Cancer Institute, U.S.Public Health Service, and in part by a research fund established in honor of General James H. Doolittle.     

Pan-Vertebrate Toll-Like Receptors During Evolution

Human toll-like receptors (TLRs) recognize pathogen-associated molecular patterns (PAMPs) to raise innate immune responses. The human TLR family was discovered because of its sequence similarity to fruit fly (Drosophila) Toll, which is involved in an anti-fungal response. In this review, we focus on the origin of the vertebrate TLR family highlighted through functional and phylogenetic analyses of TLRs in non-mammalian vertebrates. Recent extensive genome projects revealed that teleosts contain almost all subsets of TLRs that correspond to human TLRs (TLR1, 2, 3, 4, 5, 7, 8, and 9), whereas the urochordate Ciona intestinalis contains only a few TLR genes. Therefore, mammals likely obtained almost all TLR family members at the beginning of vertebrate evolution. This premise is further supported by several functional analyses of non-mammalian TLRs. We have summarized several teleost TLRs with unique properties distinct from mammalian TLRs to outline their specific roles. According to Takifugu rubripes genome project, the puffer fish possesses fish-specific TLR21 and 22. Surprisingly, phylogenetic analyses indicate that TLR21 and 22 emerged during an early period of vertebrate evolution in parallel with other TLRs and that the mammalian ancestor lost TLR21 and 22 during evolution. Our laboratory recently revealed that TLR22 recognizes double-strand RNA and induces interferon production through the TICAM-1 adaptor, as in TLR3, but unlike TLR3, TLR22 localizes to the cell surface. Therefore, differential expression of TLR3 and TLR22, rather than simple redundancy of RNA sensors, may explain the effective protection of fish from RNA virus infection in the water. In this review, we summarize the similarities and differences of the TLR family in various vertebrates and introduce these unique TLRs for a possible application to the field of clinical practices for cancer or virus infection.     

Microchromosomes in holocephalian,chondrostean and holostean fishes

Chondrostean and holostean fish of today are leftover relics: they share some characteristics with the venturesome crossopterygian fish, which launched the evolution of terrestrial vertebrates about 280 million years ago. The chromosome complements and DNA values of one chondrostean and two holostean species as well as one holocephalian species were studied. Their DNA values varied from 37% to 50% of that of mammals, and three of the species contained dot-like microchromosomes in their diploid complements. Their genome size and karyological characteristics are quite similar to those possessed by one group of reptiles and by avian species.In Duarte, this work was supported by a grant CA-05138 from the National Cancer Institute, U.S. Public Health Service, and in part by a grant FR 00433-01, Animal Care Grant, N.I.H. In Northwood, this project was supported by the British Empire Cancer Campaign.Fellow of the Institute for Advanced Learning of the City of Hope Medical Center.     

Genome size, GC percentage and 5mC level in the Indonesian coelacanth Latimeria menadoensis

The living fossil Latimeria menadoensis is important to understand sarcopterygian evolution. To gain further insights into this fish species we studied its genome size, GC% and 5mC level. The genome size and the GC% of the Indonesian coelacanth seem to be very similar to those of the African coelacanth. Moreover the GC%, the CpG frequency and the 5mC level of L. menadoensis are more similar to those of fish and amphibians than to those of mammals, birds and reptiles and this is in line with the hypothesis that two different DNA methylation and CpG shortage equilibria arose during vertebrate evolution. Our results suggest that the genome of L. menadoensis has remained unchanged for several million years, maybe since the origin of the lineage which from lobe-finned fish led to tetrapods. These data fit a conservative evolutionary landscape and suggest that the genome of the extant crossopterygians may be a sort of evolutionarily frozen genome.     

Close karyological kinship between the reptilian suborder serpentes and the class aves

Summary In contrast to the situation found in two classes of warm-blooded vertebrates, mammals and birds, the class Reptilia is not uniform with regard to total genetic content; rather, it contains two distinct categories. The close cytological kinship between snakes and birds was revealed. Both are almost identical in total genetic content, which is about 50 per cent that of placental mammals. Both have microchromosomes, as well as Z-chromosomes very similar in absolute size, comprising nearly 10 per cent of the homogametic haploid (AZ) set. This leads to the implication that snakes and birds originated from the same lineage, and that their Z-chromosomes have not changed substantially since the Jurassic period of the Mesozoic era, about 180 million years ago.Within the reptilian suborder Serpentes, the step-by-step differentiation from the primitive ZW pair to the grossly heteromorphic ZW pair could be observed. In the ancient family Boidae, the sex chromosomes were still homomorphic to each other. In the family Colubridae, the beginning of heteromorphism was manifested in two ways. In some species, a pericentric inversion on the W caused it to differ from the Z; in others, duplication of the W occurred. In the family Crotalidae, the W had apparently achieved its very specialized status; it was a distinctly smaller element.In Säo Paulo, this work was supported by Fundacão de Amparo a Pesquisa do Estado de São Paulo e Fundo de Pesquisas do Instituto Butantan. In Duarte, this work was supported in part by grant CA-05138-05, National Cancer Institute, U. S. Public Health Service. Contribution No. 36-64, Department of Biology, City of Hope Medical Center.     

Polyploidization in the fish family Cyprinidae,order Cypriniformes

Summary According to their chromosome sets, various members of the fish family Cyprinidae can be classified into two groups, one of which has about 50 chromosomes, the other about 100. In the species endowed with 50 chromosomes, the DNA content per cell ranges from 20 to 38% of that of mammals; this variability is attributed to regionally confined duplications. In the group having about 100 chromosomes, the DNA values comprise about 50% of that of mammals; these species apparently are tetraploid as compared to the former group.Supported by the Deutsche Forschungsgemeinschaft.Supported by a grant from the British Empire Cancer Campaign for Research.Supported in part by a grant from the U. S. Public Health Service (CA 05138).     

Comparative genomics of chondrichthyan Hoxa clusters

Background  

The chondrichthyan or cartilaginous fish (chimeras, sharks, skates and rays) occupy an important phylogenetic position as the sister group to all other jawed vertebrates and as an early lineage to diverge from the vertebrate lineage following two whole genome duplication events in vertebrate evolution. There have been few comparative genomic analyses incorporating data from chondrichthyan fish and none comparing genomic information from within the group. We have sequenced the complete Hoxa cluster of the Little Skate (Leucoraja erinacea) and compared to the published Hoxa cluster of the Horn Shark (Heterodontus francisci) and to available data from the Elephant Shark (Callorhinchus milii) genome project.     

The evolution of teleost pigmentation and the fish‐specific genome duplication

Teleost fishes have evolved a unique complexity and diversity of pigmentation and colour patterning that is unmatched among vertebrates. Teleost colouration is mediated by five different major types of neural‐crest derived pigment cells, while tetrapods have a smaller repertoire of such chromatophores. The genetic basis of teleost colouration has been mainly uncovered by the cloning of pigmentation genes in mutants of zebrafish Danio rerio and medaka Oryzias latipes. Many of these teleost pigmentation genes were already known as key players in mammalian pigmentation, suggesting partial conservation of the corresponding developmental programme among vertebrates. Strikingly, teleost fishes have additional copies of many pigmentation genes compared with tetrapods, mainly as a result of a whole‐genome duplication that occurred 320–350 million years ago at the base of the teleost lineage, the so‐called fish‐specific genome duplication. Furthermore, teleosts have retained several duplicated pigmentation genes from earlier rounds of genome duplication in the vertebrate lineage, which were lost in other vertebrate groups. It was hypothesized that divergent evolution of such duplicated genes may have played an important role in pigmentation diversity and complexity in teleost fishes, which therefore not only provide important insights into the evolution of the vertebrate pigmentary system but also allow us to study the significance of genome duplications for vertebrate biodiversity.     

Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions

Background  

One of the many gene families that expanded in early vertebrate evolution is the neuropeptide (NPY) receptor family of G-protein coupled receptors. Earlier work by our lab suggested that several of the NPY receptor genes found in extant vertebrates resulted from two genome duplications before the origin of jawed vertebrates (gnathostomes) and one additional genome duplication in the actinopterygian lineage, based on their location on chromosomes sharing several gene families. In this study we have investigated, in five vertebrate genomes, 45 gene families with members close to the NPY receptor genes in the compact genomes of the teleost fishes Tetraodon nigroviridis and Takifugu rubripes. These correspond to Homo sapiens chromosomes 4, 5, 8 and 10.     

Diploid-tetraploid relationship among old-world members of the fish family Cyprinidae

Evidence suggesting that the goldfish and the carp of the family Cyprinidae are tetraploid species in relation to other members of the same family were presented. The two barb species, Barbus tetrazona and Barbus jasciatus, were chosen as representatives of diploid members of the family Cyprinidae. These barbs had the diploid chromosome number of 50 and 52 and the DNA value 20–22% that of placental mammals, while the goldfish (Carassius auratus) and the carp (Cyprinus carpio) had the diploid chromosome number of about 104 and the DNA value 50–52% that of placental mammals.Supported in part by a grant (CA-05138) from the National Cancer Institute, U.S.Public Health Service, and in part by a research fund established in honor of General James H. Doolittle at Duarte, and by the British Empire Cancer Campaign for Research at Northwood. Contribution No. 11-67, Department of Biology, City of Hope Medical Center. Dr. Junichi Muramoto is a fellow of the Institute for Advanced Learning of the City of Hope Medical Center.     

Establishment of estrogen receptor 1 (ESR1)‐knockout medaka: ESR1 is dispensable for sexual development and reproduction in medaka,Oryzias latipes

Estrogens play fundamental roles in regulating reproductive activities and they act through estrogen receptor (ESR) in all vertebrates. Most vertebrates have two ESR subtypes (ESR1 and ESR2), whereas teleost fish have at least three (Esr1, Esr2a and Esr2b). Intricate functionalization has been suggested among the Esr subtypes, but to date, distinct roles of Esr have been characterized in only a limited number of species. Study of loss‐of‐function in animal models is a powerful tool for application to understanding vertebrate reproductive biology. In the current study, we established esr1 knockout (KO) medaka using a TALEN approach and examined the effects of Esr1 ablation. Unexpectedly, esr1 KO medaka did not show any significant defects in their gonadal development or in their sexual characteristics. Neither male or female esr1 KO medaka exhibited any significant changes in sexual differentiation or reproductive activity compared with wild type controls. Interestingly, however, estrogen‐induced vitellogenin gene expression, an estrogen‐responsive biomarker in fish, was limited in the liver of esr1 KO males. Our findings, in contrast to mammals, indicate that Esr1 is dispensable for normal development and reproduction in medaka. We thus provide an evidence for estrogen receptor functionalization between mammals and fish. Our findings will also benefit interpretation of studies into the toxicological effects of estrogenic chemicals in fish.     

Characterization of the neurohypophysial hormone gene loci in elephant shark and the Japanese lamprey: origin of the vertebrate neurohypophysial hormone genes

Background  

Vasopressin and oxytocin are mammalian neurohypophysial hormones with distinct functions. Vasopressin is involved mainly in osmoregulation and oxytocin is involved primarily in parturition and lactation. Jawed vertebrates contain at least one homolog each of vasopressin and oxytocin, whereas only a vasopressin-family hormone, vasotocin, has been identified in jawless vertebrates. The genes encoding vasopressin and oxytocin are closely linked tail-to-tail in eutherian mammals whereas their homologs in chicken, Xenopus and coelacanth (vasotocin and mesotocin) are linked tail-to-head. In contrast, their pufferfish homologs, vasotocin and isotocin, are located on the same strand of DNA with isotocin located upstream of vasotocin and separated by five genes. These differences in the arrangement of the two genes in different bony vertebrate lineages raise questions about their origin and ancestral arrangement. To trace the origin of these genes, we have sequenced BAC clones from the neurohypophysial gene loci in a cartilaginous fish, the elephant shark (Callorhinchus milii), and in a jawless vertebrate, the Japanese lamprey (Lethenteron japonicum). We have also analyzed the neurohypophysial hormone gene locus in an invertebrate chordate, the amphioxus (Branchiostoma floridae).