Cobitidae Research Articles

Complete mitochondrial genome of Lepidocephalichthysberdmorei and its phylogenetic status within the family Cobitidae (Cypriniformes).

In this study, the complete mitochondrial genome of Lepidocephalichthysberdmorei was first determined by the primer walking sequence method. The complete mitochondrial genome was 16,574 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (D-loop). The gene arrangement pattern was identical to that of other teleosts. The overall base composition was 29.9% A, 28.5% T, 25.5% C, and 16.1% G, with an A+T bias of 58.4%. Furthermore, phylogenetic analyses were conducted based on 13 PCGs from the mitochondrial genomes of 18 cobitid species using with three different methods (Neighbor-joining, Maximum likelihood, and Bayesian inference). All methods consistently showed that the four species of the genus Lepidocephalichthys form a monophyletic group. This study would provide effective molecular information for the Lepidocephalichthys species as well as novel genetic marker for the study of species identification.

Leveraging environmental DNA (eDNA) to optimize targeted removal of invasive fishes

Natural resource managers need innovative and cost-effective methodologies that enable the targeted removal of aquatic invasive species (AIS). Removing AIS before they establish and spread into critical habitat for native species can mitigate invasions in freshwater systems and preserve ecosystem integrity. To address this need, we established protocols using the detection of environmental DNA (eDNA) to guide deployment of traditional fisheries trapping methods for invasive fish species removal. In a pilot study during spring 2022, we set minnow traps (one per site) in a spatially stratified random design. We also developed a quantitative polymerase chain reaction (qPCR) assay to detect eDNA from multiple closely related invasive loach species (family Cobitidae) and compared detections of eDNA with detections of fish using minnow traps. At sites where both eDNA and minnow traps were deployed, the two methods agreed on the presence of loaches approximately 79% of the time (95% CI: 60%-90%). Based on the rate at which minnow traps failed to detect loaches when eDNA samples were positive (22%; 95% CI: 11%-40%), we estimated that setting three or more replicate traps per site would improve detections with gear. This information was used to inform a more comprehensive study in spring 2023. This main study consisted of two phases: (1) a fixed-point DNA study to calibrate a model of dispersal and attenuation rate, and (2) a loach removal phase. In the removal phase, we randomly selected sites to sample for loach eDNA, plotted eDNA concentration as a GIS layer to develop heatmaps, and then placed 10 replicate traps at sites with the highest concentrations. A total of 658 loaches were removed from 68 of 77 eDNA-positive trapped sites. Our results indicate that aquatic invasive species removal is more efficient when eDNA detection techniques are combined with traditional trapping methods.

A cyclical switch of gametogenic pathways in hybrids depends on the ploidy level

The cellular and molecular mechanisms governing sexual reproduction are conserved across eukaryotes. Nevertheless, hybridization can disrupt these mechanisms, leading to asexual reproduction, often accompanied by polyploidy. In this study, we investigate how ploidy level and ratio of parental genomes in hybrids affect their reproductive mode. We analyze the gametogenesis of sexual species and their diploid and triploid hybrids from the freshwater fish family Cobitidae, using newly developed cytogenetic markers. We find that diploid hybrid females possess oogonia and oocytes with original (diploid) and duplicated (tetraploid) ploidy. Diploid oocytes cannot progress beyond pachytene due to aberrant pairing. However, tetraploid oocytes, which emerge after premeiotic genome endoreplication, exhibit normal pairing and result in diploid gametes. Triploid hybrid females possess diploid, triploid, and haploid oogonia and oocytes. Triploid and haploid oocytes cannot progress beyond pachytene checkpoint due to aberrant chromosome pairing, while diploid oocytes have normal pairing in meiosis, resulting in haploid gametes. Diploid oocytes emerge after premeiotic elimination of a single-copied genome. Triploid hybrid males are sterile due to aberrant pairing and the failure of chromosomal segregation during meiotic divisions. Thus, changes in ploidy and genome dosage may lead to cyclical alteration of gametogenic pathways in hybrids.

New Data on the Distribution of the Bulgarian Spined Loach <i>Cobitis strumicae</i> (Teleostei: Cobitidae) in Turkey

This study reports the presence of Cobitis strumicae Karaman, 1955 in Terme Stream (Samsun-Black Sea-Turkey). Molecular and morphometric approaches were used together to prove the existence of the species in Terme Stream. The family Cobitidae represents a unique element of ichthyofauna. Even while sexual dimorphism can take many different forms, taxonomy studies have only used a small number of morphological features, leaving many concerns unanswered. In addition to the assessments of phenotypic traits (Gambetta’s longitudinal zones, Canestrini’s scales, suborbital spine morphology, barbel and mental lobe morphology), mitochondrial cytochrome b gene (cyt b) (1140 bp) sequence variation was studied in molecular analysis. We present the phylogenetic relationships of morphologically diagnosable subgenus Bicanestrinia from Asia Minor and Balkans in here. Samples from Terme (Accession Numbers: ON116344 and ON116345) and GENBANK were combined in the phylogenetic analysis. Our findings offered a significant distribution update of C. strumicae from Terme Stream, a southern coastal Black Sea drainage, and support the vicariance theory, according to the results of this study.

The chromosome-level genome and key genes associated with mud-dwelling behavior and adaptations of hypoxia and noxious environments in loach (Misgurnus anguillicaudatus)

BackgroundThe loach (Misgurnus anguillicaudatus), the most widely distributed species of the family Cobitidae, displays a mud-dwelling behavior and intestinal air-breathing, inhabiting the muddy bottom of extensive freshwater habitats. However, lack of high-quality reference genome seriously limits the interpretation of the genetic basis of specialized adaptations of the loach to the adverse environments including but not limited to the extreme water temperature, hypoxic and noxious mud environment.ResultsThis study generated a 1.10-Gb high-quality, chromosome-anchored genome assembly, with a contig N50 of 3.83 Mb. Multiple comparative genomic analyses found that proto-oncogene c-Fos (fos), a regulator of bone development, is positively selected in loach. Knockout of fos (ID: Mis0086400.1) led to severe osteopetrosis and movement difficulties, combined with the comparison results of bone mineral density, supporting the hypothesis that fos is associated with loach mud-dwelling behavior. Based on genomic and transcriptomic analysis, we identified two key elements involved in the intestinal air-breathing of loach: a novel gene (ID: mis0158000.1) and heat shock protein beta-1 (hspb1). The flavin-containing monooxygenase 5 (fmo5) genes, central to xenobiotic metabolism, undergone expansion in loach and were identified as differentially expressed genes in a drug stress trial. A fmo5−/− (ID: Mis0185930.1) loach displayed liver and intestine injury, indicating the importance of this gene to the adaptation of the loach to the noxious mud.ConclusionsOur work provides valuable insights into the genetic basis of biological adaptation to adverse environments.

Baseline information and physiological modification of hill-stream fishes of Mahakali River, Nepal

This study was carried on the Mahakali River from October 2007 to October 2008, which flows in western region of Kanchanpur district of Mahakali zone of Nepal. The purpose of this study to provide baseline information of the hill-stream fishes of Mahakali River and physiological modification. The sampling stations were established along the 10 km stretch of this river and dividing into two sections, each sampling station were 10km far from each other. Each sampling station was visited three times during the study period. A total of 16 times samples were collected with the help of cast net, scoop net and hook line. Altogether 44 fish species collected including 19 hill stream fish species recorded from the study site. This includes 5 orders, 12 families, 29 genus which represents the total collected species. Among them, 5 species were exotic and 39 species were collected from Mahakali river and irrigation canal along with other associated area. The family Cyprinidae found to be dominating species with 21 species, followed by family Cobitidae with 5 species, Bagridae represented by 2 species, Clariidae with 2 species, Channidae with 2 species, Mastacembelidae 2 species, Siluridae 1 species, Chandidae 1 species, Nandidae 1 species, Gobiidae 1 species and finally Anguillidae represent 1 species. Among them, altogether 19 species were hill-stream fishes. The hill-stream fishes like Labeo dero, Barilius barna, Barilius bendelisis, Barilius vagra, Raiamas bola, Brachydanio rerio, Esomus danrica, Garra annandalei, Garra gotyla, Tor Crossocheilus latius, Schizothorax plagiostomus, Schizothoraichthys progastus, Botia lohachata, Lepidocephalus guntea, Acanthocobatis botia, Schistura rupecula, Schistura corica and Glossogobius giuris were found.

Taxonomic Status of the Genus Sabanejewia (Cobitidae) from Kura-Aras River System (Turkey)

Abstract Sabanejewia is a member of the family Cobitidae found in Europe and Asia. In previous studies, S. balcanica, S. caucasica, S. aurata and S. caspia were reported from Turkey. Of these S. aurata and S. caspia were reported from the Kura-Aras Basin. We examined morphological characters and molecular data of the Sabanejewia specimens from Turkish parts of the Kura-Aras river system to determine their taxonomic status. We found no differences between the Kura and Aras rivers’ populations in terms of morphology, but different populations showed a genetic distance of 0.1-1.9%. All the studied populations were identified as S. aurata. In addition, we could not find any evidence for the presence of S. caucasica and S. caspia in Turkey.

Species diversity, population structure and conservation status of fishes inhabiting in six different wetlands of Uttar Pradesh

The present study was carried out to investigate the species diversity and population structure of freshwater fishes of six wetlands (also called Bird Sanctuaries) of Uttar Pradesh viz., Patna, Nawabganj, Sandi, Lakh Bahosi, Saman and Sur Sarovar. The sampling was done from three years period 2017 to 2020. The results of present investigation revealed the occurrence of twenty fish species in all the study areas belonging to four orders viz. Cypriniformes, Mastacembeliformes, Perciformes and Siluriformes and 11 families i.e. Cyprinidae, Cobitidae, Nemachilidae, Mastacembelidae, Channidae, Osphronemidae, Heterorpnuestidae, Sisuridae, Bagaridae, Chichlidae and Ambassidae. In all the study wetlands Cyprinidae was found to be dominant (35%), Osphronemidae (20%), Mastacembelidae, (10%), followed by family Cobitidae, Nemacheilidae, Channidae, Sisuridae, Bagaridae, Heterorpnuestidae and Ambassidae showed least contribution of 5% each. The fish diversity indices i.e. Shannon weiner (H) and Evenness (e) at all the six wetlands were 1.31, 0.9084 & 0.5710, 1.2068 & 0.6202, 1.0961 & 0.6117, 1.1552 & 0.4649, 0.9080 & 0.5068, 1.3002 & 0.6682 at wetlands viz, Patna, Nawabganj, Sandi, Lakh Bahosi, Saman and Sur Sarovar respectively. Most of the species recorded in the present study were under 19 Least Concern (95%) and 1 species namely Chagunius chagunio were found to be under Near Threatened Category (5%) of the International Union for Conservation of Nature (IUCN).

Genetics of colour variation in wild versus cultured queen loach, Botia dario (Hamilton, 1822)

The Queen loach (Botia dario), an ornamental fish species having export potential, belongs to family Cobitidae of order Cypriniformes. The dull colouration in captive condition as compared to nature is a drawback in ornamental fisheries. We report the first comparative transcriptomic analysis of Cultured (CBD) and Natural (NBD) B. dario using bioinformatics tools. Total 26 and 7 key genes for melanin and carotenoid colouration were found, respectively. KEGG pathway annotations of the genes were carried out, to annotate and describe their relevance for pigmentation. The qPCR validation of genes confirmed their expression pattern in the skin and muscle. Differential expression of, slc7a11, asip1, mc1r, dct, tyrp1a, tyr, bcdo2, csf1r, plin2, gsta2, star3 and stard5 in the skin and muscle tissues revealed the reasons for wild versus cultured colour variation. The molecular data was further supported by low yellowness and redness values of CBD skin and muscle in a colorimeter.

Complete mitochondrial genome of Iksookimia hugowolfeldi and its phylogenetic position within genus Iksookimia

In this study, the complete mitochondrial genome sequences of Iksookimia hugowolfeldi, Korean loach species, was determined using next-generation sequencing analysis. The complete mitogenome of I. hugowolfeldi has 16,634 bp in length and consists of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and one control region (D-loop). Both gene orders and characteristics were exactly accord with mitochondrial genome of other species those belong to the family Cobitidae. Phylogenetic analysis revealed that the establishment of taxonomic relationship between Iksookimia and Cobitis has still uncompleted because of the not distinguished as monophyletic status.

Cobitidae (Вьюновые) и Balitoridae (Балиторовые) Среднего Амура в водоёмах Еврейской автономной области и сопредельных приграничных территорий Китая

The article reports on the results of a study on the ichthyological diversity observed in the middle part of the Amur basin on the territory of the Jewish Autonomous Region (JAO) and the adjacent border territory of the People's Republic of China. The research covers the issues of diversity, distribution and ecological specificity of fish for the families Cobitidae and Balatoridae in the water bodies and watercourses of the region. The research summarizes and amends information on the distribution of the Cobitidae and Balatoridae families in the Bastak Nature Reserve (Russian Federation), and in the Honghe and the Bachadao reserves (China), as well as in a number of rivers of the JAO (Amur, Dobraya, Bijan, Bira, Ikura, Tunguska, In, Zabelovka, Gari, etc.), and rivers of the adjacent Chinese territory (Amur, Yalu, Sungari). The paper confirms the families’ habitat within the location under study, and provides information on the distribution of eight members of the family Cobitidae: Cobitis lutheri (Rendahl, 1935), Cobitis melanoleuca (Nichols, 1925), Cobitis choii (Kim et Son, 1984), Misgurnus anguillicaudatus (Cantor, 1842), Misgurnus nikolskiy (Vasilieva, 2001), Misgurnus mohoity (Cantor, 1842), Paramisgurnus dabrianus (Dabry de Thiersant, 1872), Parabotia mantschurica (Berg, 1907), and three members of the family Balatoridae: Barbatula toni (Dybowski, 1869), Lefua costata (Kessler, 1876), Lefua pleskei (Herzenstein, 1887). The article contains data for the observation period from 2001 to 2019. The information is new for the area under investigation.

Рыбы семейств Cobitidae (вьюновые) и Balitoridae (балиторовые) в экотопах заповедника «Бастак»

The article provides the results of studying the fish fauna of the Bastak reserve. Based on the analysis of field ichthyologic collections in 2001-2019, the author described the species composition, distribution and habitat specificity in the nature reserve reservoirs - of the fish from the Cobitidae and Balitoridae families. Within the reserve and its conservation zone, it was found the habitat of four representatives of the family Cobitidae and two fish from the family Balitoridae. The research, made in 2019, first discovered the Paramisgurnus dabrianus (Dabry de Thiersant, 1872) and the round-tailed form of Barbatula toni (Dybowski, 1869) in the territory and protection zone of the Bastak nature reserve. There, it was also found some new habitats of species belonging to the families.

Development and characterization of 10 novel polymorphic microsatellite loci in Homatula potanini (Günther, 1896)

Homatula potanini is a genus Paracobitis which belongs to the family Cobitidae, subfamily Nemacheilinae. We first isolated ten novel microsatellite DNA loci using the FIASCO protocol. The number of observed alleles per locus ranged from 5 to 14. The observed heterozygosity and expected heterozygosity ranged from 0.3750 to 0.9375 and 0.4028 to 0.8819 respectively. The polymorphic information content ranged from 0.3515 to 0.8556 (M = 0.6170). No significant linkage disequilibrium was detected among the loci. In the present study, we have identified 10 new markers for H. potanini. These loci should provide sufficient levels in the evaluation of genetic diversity and designing effective conservation programs of H. potanini.

Genetic diversity and population structure of Kichulchoia multifasciata in South Korea

Kichulchoia multifasciata, a small-sized loach (Family Cobitidae) inhabiting only the Nakdong River on the Korean Peninsula, is generally found around well-oxygenated minor tributaries. Despite the scarcity, this species is not yet a legally protected species in South Korea, and the spatial pattern of genetic diversity, which is essential to create management strategies, has never been studied. In this study, three mitochondrial loci and ten microsatellites were used to analyze the genetic diversity and the structure among eight K. multifasciata populations collected from different tributaries. K. multifasciata populations showed a high level of mitochondrial variability, with above 0.9 of average haplotype diversity in all three loci analyzed. A substantial microsatellite polymorphism was also found. Weak genetic structuring among populations and isolation by distance were clearly revealed in both mitochondrial and microsatellite data, indicating the high levels of gene flow among the tributaries. However, a few of the populations exhibited a genetic signature that they have experienced the historical size decline. Our data suggest that unequal gene flow might be one of the causes; nevertheless, the possibility of effective population size reduction by other factors could not be completely excluded. Our genetic evidence can be the critical information needed to protect the populations from the genetic erosion in the Nakdong River that has been destroyed and fragmented with increasing anthropogenic interferences.

The complete mitochondrial genome of Triplophysa tibetana

Triplophysa tibetana belongs to the family Cobitidae, which is popular in Tibet. We first published the complete mitochondrial genome of T. tibetana. The mitogenome sequence was 16,607bp long and composed of 13 protein-coding genes, 22tRNA genes, and 2 rRNA genes. The protein-coding genes started with a traditional ATG except for COX1, which started with one infrequent GTG instead, and terminated with stop codons TAA, TGG, TGA, or a single T— base. The overall GC content is lower than AT. We constructed the phylogenetic tree to verify the accuracy and utility of newly determined mitogenome sequences using the full mitogenome-related evolution events.

Bidirectional mitochondrial introgression between Korean cobitid fish mediated by hybridogenetic hybrids.

Genomic introgression through interspecific hybridization has been observed in some species of the freshwater fish family Cobitidae. Within this family, a Cobitis hankugensis–Iksookimia longicorpa diploid–triploid hybrid species complex on the Korean peninsula is unique in displaying hybridogenesis, a unisexual reproduction mode that allows hybrids to mediate the transfer of mitochondrial DNA (but not nuclear DNA) between the two parent species. However, populations of the parental species in the wild have never been examined for the potential effect of introgression on their genomes. To address the genetic consequences of unisexual hybridization on the parental species, we examined genetic structure of the two parental species, C. hankugensis and I. longicorpa, in three independent natural habitats where they coexist with their hybrid complex using DNA sequence data of one mitochondrial gene and three nuclear genes. We found that mitochondrial introgression between the two species was extensive in all the examined localities, while there was no evidence of nuclear introgression across the species boundary. This result indicates that the hybridogenetic individuals mediate mitochondrial introgression from one species to the other, producing mito‐nuclear mosaic genomes such as C. hankugensis nuclear genomes associated with I. longicorpa mitochondrial DNA and the reverse. The direction and degree of introgression varied among the three localities, but the underlying mechanisms for this observation proved elusive. Introgression might depend on which species serves as the predominant sperm or ovum donor or the environmental conditions of the localities. The present study suggests that introgressive hybridization between pure C. hankugensis and I. longicorpa species is highly likely where the two species co‐occur with hybridogenetic individuals, but the consequence of introgression could be variable due to the history and environmental characteristics of particular populations across the parental species’ ranges.

Rapid detection of alien DNA in the loach genus Misgurnus (family Cobitidae) using real-time PCR

Rapid detection of alien DNA in the loach genus Misgurnus (family Cobitidae) using real-time PCR

Early life history of the eastern Korean tetraploid spined loach,iksookimia yongdokensis(Pisces: Cobitidae)

We investigated whether tetraploidy in Iksookimia yongdokensis adds more species specific variation in its early life history characteristics. To this end, morphological and temporal characteristics were analysed using artificial fertilisation and laboratory culture, and the results were compared to seventeen other species of the family Cobitidae. Extensive comparison of these characteristics among the cobitid species showed that tetraploid I. yongdokensis was apparently longer in egg diameter (1.54 ± 0.08 mm), hatching size (5.8 ± 0.15 mm in total length), and time to hatching (65 hours after fertilisation) than the other diploid cobitid species. With respect to these characteristics, I. yongdokensis was most similar to the congeneric species of Iksookimia (except I. pacifica). Next closest in similarity, were the other two species of different genera, Kichulchoia brevifasciata and Cobitis takatsuensis. Notably, all of the species with similar characteristics to I. yongdokensis were coincident in that they prefer a similar habitat, that being a bottom of pebbles and cobbles in middle to upper streams. In conclusion, the present study indicates that characteristics of the early life history of cobitid species are associated with both taxonomic closeness and habitat type.

Evolution and phylogenetic application of the MC1R gene in the Cobitoidea (Teleostei: Cypriniformes).

Fish of the superfamily Cobitoidea sensu stricto (namely loaches) exhibit extremely high diversity of color patterns, but so far little is known about their evolutionary mechanism. Melanocortin 1 receptor gene (MC1R) plays an important role during the synthesis of melanin and formation of animal body color patterns. In this study, we amplified and sequenced the partial MC1R gene for 44 loach individuals representing 31 species of four families. Phylogenetic analyses yielded a topology congruent with previous studies using multiple nuclear loci, showing that each of the four families was monophyletic with sister relationships of Botiidae+ (Cobitidae+(Balitoridae+Nemacheilidae)). Gene evolutionary analyses indicated that MC1R in loaches was under purifying selection pressure, with various sites having different dN/dS values. Both Botiidae and Cobitidae had lower dN/dS values than those of background lineages, suggesting their evolution might be strongly affected by purifying selection pressure. For Balitoridae and Nemacheilidae, both had larger dN/dS values than those of background lineages, suggesting they had a faster evolutionary rate under more relaxed selection pressure. Consequently, we inferred that the relatively stable color patterns in Botiidae and Cobitidae might result from the strong purifying selection pressure on the MC1R gene, whereas the complicated and diverse color patterns in Balitoridae and Nemacheilidae might be associated with the relaxed selection pressure. Given the easy experimental procedure for the partial MC1R gene and its excellent performance in reconstructing phylogeny, we suggest this gene could be used as a good molecular marker for the phylogenetic study of fish species.

Developmental transcriptome analysis and identification of genes involved in formation of intestinal air-breathing function of Dojo loach, Misgurnus anguillicaudatus.

Dojo loach, Misgurnus anguillicaudatus is a freshwater fish species of the loach family Cobitidae, using its posterior intestine as an accessory air-breathing organ. Little is known about the molecular regulatory mechanisms in the formation of intestinal air-breathing function of M. anguillicaudatus. Here high-throughput sequencing of mRNAs was performed from six developmental stages of posterior intestine of M. anguillicaudatus: 4-Dph (days post hatch) group, 8-Dph group, 12-Dph group, 20-Dph group, 40-Dph group and Oyd (one-year-old) group. These six libraries were assembled into 81300 unigenes. Totally 40757 unigenes were annotated. Subsequently, 35291 differentially expressed genes (DEGs) were scanned among different developmental stages and clustered into 20 gene expression profiles. Finally, 15 key pathways and 25 key genes were mined, providing potential targets for candidate gene selection involved in formation of intestinal air-breathing function in M. anguillicaudatus. This is the first report of developmental transcriptome of posterior intestine in M. anguillicaudatus, offering a substantial contribution to the sequence resources for this species and providing a deep insight into the formation mechanism of its intestinal air-breathing function. This report demonstrates that M. anguillicaudatus is a good model for studies to identify and characterize the molecular basis of accessory air-breathing organ development in fish.