[Nucleotide variation in the mitochondrial DNA cytochrome oxidase 1 gene in the Siberian sucker (Catostomus catostomus rostratus) from Kolyma River]

This study presents the data of the first molecular genetic analysis of the Siberian sucker from Kolyma River. Polymorphism of the mtDNA cytochrome oxidase 1 gene was established. Comparative sequence analysis of the gene examined and the GenBank variants characterizing suckers from the rivers of Canada enabled the suggestion that the sucker penetrated to Asia from North America approximately at the end of Early and the beginning of the Middle Pleistocene. It was demonstrated that intrapopulation genetic variation in the Siberian sucker accounted for 11.63% of total variation, while the proportion of the intergroup, component (Fst) constituted 88.37%. It seems likely that a considerable proportion of intergroup variation was caused by the long period of isolation of the Siberian sucker in Kolyma River. The prevalence of one common haplotype, CH-COI 1, in the sample examined indicates that the founder effect played an importaht role in the history of the formation of the Kolyma population.

[Genetic structure of the Siberian Sucker (Catostomus catostomus rostratus) according to data on sequence variation of the mtDNA cytochrome B gene]

Data regarding the structure and variation of the nucleotide sequence of the cytochrome b gene of mitochondrial DNA of the Siberian Sucker from the Kolyma River were obtained. Analysis of the median network revealed that evolutionary lines diverged from a common ancestor. Penetration of the sucker into Asia from Northern America took place between the Early and Middle Pleistocene. Prolonged reproductive isolation of the Siberian and Northern American suckers led to interspecies divergence with the appearance of amino acid substitutions, which, apparently, fixed due to positive selection. The Siberian Sucker appeared to have three modifications of the Cytb protein.

Distinguishing between incomplete lineage sorting and genomic introgressions: complete fixation of allospecific mitochondrial DNA in a sexually reproducing fish (Cobitis; Teleostei), despite clonal reproduction of hybrids

Distinguishing between hybrid introgression and incomplete lineage sorting causing incongruence among gene trees in that they exhibit topological differences requires application of statistical approaches that are based on biologically relevant models. Such study is especially challenging in hybrid systems, where usual vectors mediating interspecific gene transfers--hybrids with Mendelian heredity--are absent or unknown. Here we study a complex of hybridizing species, which are known to produce clonal hybrids, to discover how one of the species, Cobitis tanaitica, has achieved a pattern of mito-nuclear mosaic genome over the whole geographic range. We appplied three distinct methods, including the method using solely the information on gene tree topologies, and found that the contrasting mito-nuclear signal might not have resulted from the retention of ancestral polymorphism. Instead, we found two signs of hybridization events related to C. tanaitica; one concerning nuclear gene flow and the other suggested mitochondrial capture. Interestingly, clonal inheritance (gynogenesis) of contemporary hybrids prevents genomic introgressions and non-clonal hybrids are either absent or too rare to be detected among European Cobitis. Our analyses therefore suggest that introgressive hybridizations are rather old episodes, mediated by previously existing hybrids whose inheritance was not entirely clonal. Cobitis complex thus supports the view that the type of resulting hybrids depends on a level of genomic divergence between sexual species.

Correlation of gene expression and contaminant concentrations in wild largescale suckers: a field-based study

Toxic compounds such as organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether flame retardants (PBDEs) have been detected in fish, birds, and aquatic mammals that live in the Columbia River or use food resources from within the river. We developed a custom microarray for largescale suckers (Catostomus macrocheilus) and used it to investigate the molecular effects of contaminant exposure on wild fish in the Columbia River. Using Significance Analysis of Microarrays (SAM) we identified 72 probes representing 69 unique genes with expression patterns that correlated with hepatic tissue levels of OCs, PCBs, or PBDEs. These genes were involved in many biological processes previously shown to respond to contaminant exposure, including drug and lipid metabolism, apoptosis, cellular transport, oxidative stress, and cellular chaperone function. The relation between gene expression and contaminant concentration suggests that these genes may respond to environmental contaminant exposure and are promising candidates for further field and laboratory studies to develop biomarkers for monitoring exposure of wild fish to contaminant mixtures found in the Columbia River Basin. The array developed in this study could also be a useful tool for studies involving endangered sucker species and other sucker species used in contaminant research.

Combining morphology and genetics in resolving taxonomy--a systematic revision of spined loaches (Genus Cobitis; Cypriniformes, Actinopterygii) in the Adriatic watershed

Taxonomic investigation of spined loaches from Dalmatia and Herzegovina was conducted on specimens from 14 localities. The results of the detailed morphological investigations were combined with genetic data (based on one mitochondrial and two nuclear genes) in order to resolve the taxonomic status of each Cobitis population. Among the investigated features of external morphology, the appearance of spots on the caudal fin base turned out to have the greatest diagnostic value. Furthermore, the number of branched fin rays enabled the discrimination of several species. No morphometric character alone could ensure determination of any Cobitis species. Nevertheless, groups of populations that are more similar in their body shapes correspond to mitochondrial phylogenetic lineages. Based on molecular genetic markers, Dalmatian and Herzegovinian spined loaches form independent lineages inside the Adriatic phylogenetic group. Mitochondrial DNA phylogenetic reconstruction revealed six monophyletic lineages, corresponding to six species distributed in the investigated area. The population distributed in Mostarsko blato karstic field in Bosnia and Herzegovina is described as a new species based on a unique combination of morphological characters: a single triangular Canestrini scale; usually 5¹/₂ branched anal fin rays, 6¹/₂ branched dorsal fin rays, 14 branched caudal fin rays; no spots in the surface pigmentation layer on the caudal fin base; scales on the body very small.

cDNA cloning and expression characterization of serum transferrin gene from oriental weatherfish Misgurnus anguillicaudatus

In this study, the cDNA coding serum transferrin (stf) of Misgurnus anguillicaudatus (mastf) was cloned. mastf cDNA is composed of 2326 bp with a 2007 bp open reading frame encoding 668 amino acids. The deduced Mastf protein consists of a signal peptide, two lobes (N and C-lobes) and signature motifs of transferrin (Tf) family. The results of tissue distribution indicated that mastf mRNA was predominantly expressed in the liver. The results indicate that the mastf expression increased significantly in liver, blood, spleen and head kidney after the challenge with Aeromonas sobria, acting as a positive acute protein, suggesting that mastf is related to the immune response. The cloning and expression analysis of mastf further demonstrates the evolutionary conservation of Stf and immune function in vertebrates.

Comparative analysis of mitochondrial genomes in distinct nuclear ploidy loach Misgurnus anguillicaudatus and its implications for polyploidy evolution

Misgurnus anguillicaudatus has several natural ploidy types. To investigate whether nuclear polyploidy have an impact on mitochondrial DNA (mtDNA), the complete mitochondrial genomes (mitogenomes) of five distinct ploidy M. anguillicaudatus (natural diploid, triploid, tetraploid, pentaploid and hexaploid), which were collected in central China, were sequenced and analyzed. The five mitogenomes share the same gene arrangement and have similar gene size, base composition and codon usage pattern. The most variable regions of the mitogenome were the protein-coding genes, especially the ND4L (5.39% mutation rate). Most variations occurred in tetraploids. The phylogenetic tree showed that the tetraploid M. anguillicaudatus separated early from other ploidy loaches. Meanwhile, the mitogenomes from pentaploids, and hexaploids have the closest phylogenetic relations, but far from that of tetraploids, implying that pentaploids and hexaploids could not be formed from tetraploids, possibly from the diploids and triploids. The genus Misgurnus species were divided into two divergent inter-genus clades, and the five ploidy M. anguillicaudatus were monophyletic, which support the hypotheses about the mitochondrial introgression in loach species.

Influence of introgression and geological processes on phylogenetic relationships of Western North American mountain suckers (Pantosteus, Catostomidae)

Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western USA and into northern Mexico. They are typically found in medium gradient, middle-elevation reaches of rivers over rocky substrates. This study (1) compares molecular data with morphological and paleontological data for proposed species of Pantosteus, (2) tests hypotheses of their monophyly, (3) uses these data for phylogenetic inferences of sister-group relationships, and (4) estimates timing of divergence events of identified lineages. Using 8055 base pairs from mitochondrial DNA protein coding genes, Pantosteus and Catostomus are reciprocally monophyletic, in contrast with morphological data. The only exception to a monophyletic Pantosteus is P. columbianus whose mtDNA is closely aligned with C. tahoensis because of introgression. Within Pantosteus, several species have deep genetic divergences among allopatric sister lineages, several of which are diagnosed and elevated to species, bringing the total diversity in the group to 11 species. Conflicting molecular and morphological data may be resolved when patterns of divergence are shown to be correlated with sympatry and evidence of introgression.

Identification and molecular characterization of an Akirin2 homolog in Chinese loach (Paramisgurnus dabryanus)

Akirin is a nuclear factor involved in innate immune responses of arthropods and mammals. In this study we have cloned an Akirin2 gene, pdakirin2, from freshwater Chinese loach (Paramisgurnus dabryanus) and characterized its biological functions. Phylogenetic analysis revealed deduced PdAkirin2 had high sequence identities to Akirin2 homologs from fish and mammals (70-91%), it contained two conserved nuclear localization signals (NLSs) with verified sub-cellular localization. Quantitative real-time (qRT)-PCR analysis indicated that PdAkirin2 was present in a wide range of loach tissues and showed up-regulation with challenges of Aeromonas hydrophila NJ-1, LPS and poly I:C. PdAkirin2 as an immune factor had significant effects on the expression of cytokines (TNFα, IFN-α, IFN-γ, IL-4 and IL-1β) and transcription factor NF-κB. This study provides insights into the potential role of PdAkirin2 in the innate immune system.

Hsp60 in caudal fin regeneration from Paramisgurnus dabryanus: molecular cloning and expression characterization

Heat shock protein 60 (Hsp60) is a kind of highly conserved immunogenic molecule involved in a wide range of biochemical processes in response to external stressors. Its multifunction in regulating immune responses and modulating signal pathway interests us in investigating its role in fin regeneration that has become an excellent and interesting model for studying the molecular basis of morphogenesis. We firstly clarified basical process and crucial period of caudal fins regeneration in Paramisgurnus dabryanus by histological analysis. Then we cloned full-length cDNA of hsp60 from P. dabryanus (designated as PdHsp60) by RACE method. The cDNA contains a 124 bp 5'UTR, a 1731 bp open reading frame (ORF) encoding 576 amino acids and a 510 bp 3'UTR (Accession no.: KF544774). The phylogenetic tree shows that the PdHsp60 fits within the hsp60 clade. And quantitative RT-PCR detected the PdHsp60 began to increase rapidly its expression at 1 dpa and reached its peak at 2 dpa. Next, spatial distribution analysis of PdHsp60 in fins showed that PdHsp60 located mainly in the deeper lay of regenerated epidermis when PdHsp60 expressed most. After the PdHsp60 had been cloned into the pET-32a vector, SDS-PAGE and Western blotting analysis confirmed that the PdHsp60 protein was efficiently expressed in Escherichia coli BL21. These findings have revealed that PdHsp60, a highly conserved gene related to the innate immune system and stress response during vertebrate evolution, is involved in response to wounding stimulation--in the formation of wound epidermis which occurs as the first phase of fin regeneration after fin amputation in caudal fin regeneration.

The complete mitochondrial genome of Cobitis lutheri (Cypriniformes: Cobitidae: Cobitis)

The traditional polymerase chain reaction method was employed to obtain the complete mitochondrial genome of Cobitis lutheri from Fuyuan country, Heilongjiang province, China. The mitogenome was determined to be 16,639 bp in length. It contains 13 protein-coding genes, 2 rRNAs and 22 tRNAs. This is the first report on the complete mitogenome sequence of C. lutheri.

Complete mitochondrial genome of Sarcocheilichthys lacustris (Cypriniformes, Cyprinidae)

In this study, we sequenced and characterized the complete mitochondrial genome of Sarcocheilichthys lacustris from Heilongjiang River (Amur River) at fuyuan county, Heilongjiang province, China. The circular mitochondrial genome of S. lacustris was determined to be 16,684 bp in length. It contains typical complement of 13 protein coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 control region.

The complete mitochondrial genome of Chinese sucker Myxocyprinus asiaticus (Cypriniformes, Catostomidae)

In this study, the complete mitogenome sequence of Chinese sucker Myxocyprinus asiaticus (Cypriniformes, Catostomidae) has been amplified and sequenced by employing long polymerase chain reaction method. The mitogenome, consisting of 16,636 base pairs (bp), had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes, and a noncoding control region (CR). CR of 944 bp length is located between tRNA(Pro) and tRNA(Phe). The overall base composition of M. asiaticus is 28.62% for A, 27.90% for C, 24.8% for T, and 18.70% for G, with a slight AT bias of 53.40%. The complete mitogenome may provide important DNA molecular data for further phylogenetic analyses for higher taxa of teleost fishes especially for the members of Cypriniformes.

Homologue of Sox10 in Misgurnus anguillicaudatus: sequence, expression pattern during early embryogenesis

A number of genetic studies have established that Sox10 is a transcription factor associated with neurogenesis in vertebrates. We have isolated a homologue of Sox10 gene from the brain of Misgurnus anguillicaudatus by using homologous cloning and RACE method, designated as MaSox10b. The full-length cDNA of MaSox10b contained a 311 bp 5'UTR, a 312 bp 3'UTR and an ORF encoding a putative protein of 490 amino acids with a characteristic HMG-box DNA-binding domain of 79 amino acids (aa: 105-183). Phylogenetic tree shows that the MaSOX10b fits within the Sox10 clade and clusters firmly into Sox10b branches. During embryogenesis, MaSox10b was first detected in gastrulae stage. From somitogenesis stage and thereafter, distinct expression was observed in the medial neural tube, extending from the hindbrain through the posterior trunk. Taken together, these preliminary findings suggested that MaSox10b is highly conserved during vertebrate evolution and involved in a wide range of developmental processes including embryogenesis and neurogenesis.

Identification, expression and bioactivity of Paramisgurnus dabryanus β-defensin that might be involved in immune defense against bacterial infection

β-defensins are a large family of multi-disulfide-bonded peptides with broad-spectrum antimicrobial activities that contribute to innate host defense in many organisms, but little information is available about β-defensins produced by freshwater fish lacking scales. We therefore cloned and identified a β-defensin gene from Chinese loach (Paramisgurnus dabryanus) by designing degenerate primers and using thermal asymmetric interlaced PCR. This gene is the first defensin gene ever identified in a non-scaled freshwater fish. Annotation of the protein domain architecture showed that the putative Chinese loach β-defensin contains the signature motif of six conserved cysteines within the mature peptide, an aspect similar to β-defensins of other marine fish. We also used quantitative real-time PCR to investigate the expression pattern of the Chinese loach β-defensin gene, mRNA of which could be observed in various tissues. After challenge with the pathogenic bacterium Aeromonas hydrophila, β-defensin expression was induced in the eye, gill, skin, and spleen of the adult loach. The bioactivity of the recombinant P. dabryanus β-defensin was examined against pathogenic bacteria, and the results suggest that this class 2 β-defensin has potential applications for treatment of bacterial infections.

Complete mitochondrial genome of Osteochilus salsburyi (Cypriniformes, Cyprinidae)

Osteochilus salsburyi (Cypriniformes, Cyprinidae) is a small-sized fish of significant economic value. In this paper, the complete mitogenome sequence of O. salsburyi was first determined. It is 16,599 bp in length and consists of a typical vertebrate genome structure including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA (tRNA) genes, and a control region. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The overall base composition of the heavy strand in descending order is A (33.0%), T (26.5%), C (25.4%), and G (15.0%), with a slight AT bias of 59.5%. This information of O. salsburyi mitogenome could contribute not only to the development of efficient conservation strategy on vulnerable genetic diversity but also to the identification of useful genetic markers for distinction across species boundary.

De novo assembly of mud loach (Misgurnus anguillicaudatus) skin transcriptome to identify putative genes involved in immunity and epidermal mucus secretion

Fish skin serves as the first line of defense against a wide variety of chemical, physical and biological stressors. Secretion of mucus is among the most prominent characteristics of fish skin and numerous innate immune factors have been identified in the epidermal mucus. However, molecular mechanisms underlying the mucus secretion and immune activities of fish skin remain largely unclear due to the lack of genomic and transcriptomic data for most economically important fish species. In this study, we characterized the skin transcriptome of mud loach using Illumia paired-end sequencing. A total of 40364 unigenes were assembled from 86.6 million (3.07 gigabases) filtered reads. The mean length, N50 size and maximum length of assembled transcripts were 387, 611 and 8670 bp, respectively. A total of 17336 (43.76%) unigenes were annotated by blast searches against the NCBI non-redundant protein database. Gene ontology mapping assigned a total of 108513 GO terms to 15369 (38.08%) unigenes. KEGG orthology mapping annotated 9337 (23.23%) unigenes. Among the identified KO categories, immune system is the largest category that contains various components of multiple immune pathways such as chemokine signaling, leukocyte transendothelial migration and T cell receptor signaling, suggesting the complexity of immune mechanisms in fish skin. As for mucin biosynthesis, 37 unigenes were mapped to 7 enzymes of the mucin type O-glycan biosynthesis pathway and 8 members of the polypeptide N-acetylgalactosaminyltransferase family were identified. Additionally, 38 unigenes were mapped to 23 factors of the SNARE interactions in vesicular transport pathway, indicating that the activity of this pathway is required for the processes of epidermal mucus storage and release. Moreover, 1754 simple sequence repeats (SSRs) were detected in 1564 unigenes and dinucleotide repeats represented the most abundant type. These findings have laid the foundation for further understanding the secretary processes and immune functions of loach skin mucus.

Estimation of parameters in a Bertalanffy type of temperature dependent growth model using data on juvenile stone loach (Barbatula barbatula)

Parameters of a Bertalanffy type of temperature dependent growth model are fitted using data from a population of stone loach (Barbatula barbatula). Over two periods respectively in 1990 and 2010 length data of this population has been collected at a lowland stream in the central part of the Netherlands. The estimation of the maximum length of a fully grown individual is given special attention because it is in fact found as the result of an extrapolation over a large interval of the entire lifetime. It is concluded that this parameter should not at forehand be set at one fixed value for the population at that location due to varying conditions over the years.

Molecular characterization of estrogen receptor genes in loach Paramisgurnus dabryanus and their expression upon 17α-ethinylestradiol exposure in juveniles

The full-length cDNAs for estrogen receptor 1 (esr1), esr2a and esr2b were isolated and characterized from the loach (Paramisgurnus dabryanus, Cobitidae, cypriniformes). P. dabryanus Esr1, Esr2a and Esr2b share high amino acids identities with their counterparts of cyprinid species. Quantitative real-time PCR (qRT-PCR) was used to analyze the tissue distribution of esr mRNAs in one-year-old P. dabryanus. The mRNA expression of esr1 in female liver was extremely higher than that in other tissues. esr2a mRNA expression in female intestine and in male muscle was higher than that in other tissues. esr2b mRNA expression was the highest in both male and female intestine. Two-month-old P. dabryanus were exposed to 17α-ethinylestradiol (EE2) for 3weeks and the changes of esr mRNA expression in brain, gonad and liver were analyzed by qRT-PCR. Results showed that EE2 at 1, 5 and 25 ng/L significantly suppressed testicular esr1 mRNA expression in male. The ovarian esr2a mRNA expression was significantly up-regulated at 1 ng/L EE2. In female brain, esr1 mRNA expression was significantly down-regulated at 5 ng/L EE2. Both in males and females, EE2 exposure increased the hepatic esr1 mRNA expression in a concentration-dependent manner. The present study suggests that different esrs in different tissues have differential responsiveness to EE2 and the hepatic esr1 is a sensitive biomarker to EE2 at environmental concentrations in P. dabryanus juveniles. So, the loach P. dabryanus, a typical demersal fish, is a promising ecological model organism to detect estrogenic chemicals in the sediment of aquatic environment by using molecular biomarkers.

Complete mitochondrial genome of Acheilognathus signifer (Cypriniformes, Cyprinidae): comparison of light-strand replication origins from six Acheilognathus species

Acheilognathus signifer (Cypriniformes, Cyprinidae) is an endemic, endangered fresh water fish species in the Korean peninsula. In this study, the mitochondrial genome of A. signifer was completely sequenced, which is 16,566 bp in length. The characteristics of the complete mitochondrial genome were described in detail.

Morphological taxonomy and molecular divergence of four balitorid species (subfamily: Nemachelinae) from Central Himalaya, India

The fishes in this study belong to the difficult group. It is difficult to identify about more than 50 nemacheilid loach species in India, mainly due to the poor quality of the original descriptions, the lack of good reviews, and the similarity of a number of the banded species. In view of this, a morphometric and genetic study was conducted on four species that have been documented in Central Himalayan region of India. Using comparative methods, a contribution to the knowledge about the variability of four Himalayan hillstream loaches, a molted loach Acanthocobitis botia (Hamilton, 1822), Nemacheilus corica (Hamilton, 1822), a creek loach Schistura beavani (Gunther, 1868), and Schistura montana (McClelland, 1838), was accomplished. Morphometric data were analyzed by univariate (CV and analysis of variance) and multivariate analyses (discriminant function analysis and cluster analysis). Based on the results of these statistical analyses, generally all four species grouped into their own species cluster with minimal overlap between two species of genus Schistura. Mitochondrial DNA cytochrome b (Cyt b) gene analysis revealed 7.7-17.6% genetic distances among the four species. Molecular phylogenetic relationship among these species and other Balitoridae species was investigated using published mitochondrial Cyt b sequences. Dendrograms obtained by the maximum likelihood and maximum parsimony method analyses exhibited the same topology. According to this topology, all the four species represented distinct species group and A. botia form the most distinct species while S. beavani and S. montana are clustered together with Nemacheilus species to form a single group. This work may build the base for the revision of taxonomic identity of fishes of the family Balitoridae. The results may further help to enhance the knowledge of the ichthyologists in understanding the fish fauna of India and assist them in planning conservation and management strategies for the propagation of these less studied small indigenous species along their natural range of distribution.

Modulation of warm-temperature-acclimation-associated 65-kDa protein genes (Wap65-1 and Wap65-2) in mud loach (Misgurnus mizolepis, Cypriniformes) liver in response to different stimulatory treatments

Two paralogous isoform cDNAs of warm-temperature-acclimation-associated 65-kDa protein (Wap65-1 and Wap65-2) were isolated from the cypriniform species, mud loach (Misgurnus mizolepis), and characterized. The deduced amino acid sequences of the two mud loach Wap65 isoforms (mlWap65-1 and mlWap65-2) share moderate levels of sequence homology with their corresponding orthologues from teleosts and with human hemopexin, a possible mammalian homologue. Both isoforms display conserved features, including essential motifs and/or residues that are important for the protein structure of hemopexin. In overall, mlWap65-2 is more homologous to human hemopexin than is mlWap65-1. Both mud loach Wap65 transcripts are predominantly expressed in liver, although the transcripts are ubiquitously detectable in most tissues with variable basal expression. Both mlWap65 isoforms are differentially regulated during embryonic development, and the changes in transcript levels during embryogenesis are greater for mlWap65-2 than for mlWap65-1. The transcription of the mlWap65 genes is differentially modulated by various stimuli, including thermal changes, immune challenge (lipopolysaccharide injection or bacterial infection), and heavy metal exposure (cadmium, copper, or nickel). The isoform mlWap65-1 is more responsive to warm temperature treatments than mlWap65-2, whereas mlWap65-2 is much more strongly stimulated by immune and heavy metal challenges than is mlWap65-1. Taken together, the results of this study suggest that mud loach Wap65 isoforms are potentially involved in multiple cellular pathways and that the two mud loach Wap65 isoforms undergo functional partitioning or subfunctionalization.