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The fragmentation and homogenization of habitats have seriously affected the fishery resources of the Pearl River. To protect the fishery resources, a novel artificial habitat, constructed using bamboo and palm slices, was deployed in the Youjiang River, a tributary of the Pearl River in China. The results of field and laboratory experiments showed that fish abundance, species richness and Shannon–Wiener diversity index were higher in the artificial habitats than at the control sites. There was no significant impact on fish biomass, as the artificial habitats attracted more Cultrinae and Gobioninae fish that are of a smaller size. Artificial habitats can serve as spawning grounds for fish that produce sticky eggs and refuges that improve the survival rates of juvenile fishes. This study revealed that this novel artificial habitat created suitable habitats and suitable spawning substrate for fish, improved fish richness and diversity in the structureless freshwater ecosystem like the Youjiang River., The fragmentation and homogenization of habitats have seriously affected the fishery resources of the Pearl River. To protect the fishery resources, a new type of artificial habitat, consisting of bamboo and palm slices, was deployed in the Youjiang River, a tributary of the Pearl River, China. This study revealed that the new type of artificial habitat can form new habitats for fish in the Youjiang River.

We assessed the relationship of Schizothoracinae species with other subfamilies Alburninae, Xenocyprinae, Cultrinae and Squaliobarbinae of family Cyprinidae by creating the phylogenetic trees using complete mitogenome and 12S and 16S RNA. Our representative species show the great affiliation with other but separated from a group composed of Metzia mesembrinum, Metzia longinasus, Metzia lineata and Metzia formosae of subfamily Alburninae while other subfamilies formed distinct group. The members of subfamily Schizothoracinae shows separate line of evolution from subfamily Barbinae.

In terms of taxonomic status, common carp ( Cyprinus carpio , Cyprininae) and crucian carp ( Carassius auratus , Cyprininae) are different species; however, in this study, a newborn homodiploid crucian carp-like fish (2 n =100) (2 n NCRC) lineage (F1–F3) was established from the interspecific hybridization of female common carp (2 n =100)×male blunt snout bream ( Megalobrama amblycephala , Cultrinae, 2 n =48). The phenotypes and genotypes of 2 n NCRC differed from those of its parents but were closely related to those of the existing diploid crucian carp. We further sequenced the whole mitochondrial (mt) genomes of the 2 n NCRC lineage from F1 to F3. The paternal mtDNA fragments were stably embedded in the mt-genomes of F1–F3 generations of 2 n NCRC to form chimeric DNA fragments. Along with this chimeric process, numerous base sites of F1–F3 generations of 2 n NCRC underwent mutations. Most of these mutation sites were consistent with the existing diploid crucian carp. Moreover, the mtDNA organization and nucleotide composition of 2 n NCRC were more similar to those of the existing diploid crucian carp than those of the parents. The inheritable chimeric DNA fragments and mutant loci in the mt-genomes of different generations of 2 n NCRC provided important evidence of the mtDNA change process in the newborn lineage derived from hybridization of different species. Our findings demonstrated for the first time that the paternal mtDNA were transmitted into the mt-genomes of homodiploid lineage, which provided new insights into the existence of paternal mtDNA in the mtDNA inheritance.

Distant hybridization is an effective tool to create offspring with different ploidy levels and is widely used in plants and lower organisms. In this study, the diploid gynogenetic grass carp (2nGGC, 2n = 48) and triploid hybrid (3nGT, 3n = 72) progenies of female grass carp (Ctenopharyngodon idellus, GC, Leuciscinae, 2n = 48) × male topmouth culter (Erythroculter ilishaeformis, TC, Cultrinae, 2n = 48) were successfully obtained by distant hybridization. The results regarding the chromosomal number, DNA content, 5S rDNA and fluorescence in situ hybridization (FISH) showed 2nGGC was derived from gynogenesis with 48 chromosomes and not a hybrid of GC and TC, while 3nGT was a triploid hybrid with 72 chromosomes. 3nGT exhibited significant phenotypic differences from GC and TC, but 2nGGC resembled GC. With regard to feeding, both 2nGGC and 3nGT were herbivorous. However, the total amino acid contents in the muscles of both 2nGGC and 3nGT were significantly higher than that in GC (P

The complete mitochondrial DNA genome of Anabarilius brevianalis was determined. The entire mitochondrial genome is 16,610 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA (rRNA) ...

The complete mitochondrial DNA genome of Anabarilius grahami was determined by the primer walking sequence method. The entire mitochondrial genome is 16,612 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one control region (CR). As in other teleosts, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall nucleotide composition was 28.9% A, 24.8% T, 27.9% C, and 18.3% G, respectively, with a slight A+T bias (53.7%). Phylogenetic analysis based on 12 concatenated protein-coding genes of the heavy strand shows the evolutionary position of A. grahami is more closely related to two species of the genus Hemiculter within the subfamily Cultrinae.

It is commonly believed that hybridization might lead to the formation of new polyploidy species, but it is unclear whether hybridization can produce a new homodiploid species. Here, we report the spontaneous occurrence of a new crucian carp-like homodiploid fish (2n = 100) that originated from the interspecific hybridization of female common carp (Cyprinus carpio, Cyprininae, 2n = 100) × male blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n = 48). The phenotype and reproductive traits of this new crucian carp-like homodiploid fish were found to be very similar to those of the existing diploid species (diploid crucian carp; Carassius auratus). FISH and 5S rDNA analyses revealed that the genotype of the crucian carp-like homodiploid fish differs from those of its parents but is closely related to that of diploid crucian carp. The results provide evidence of the existence of a possible route through which the distant hybridization of this cross can generate crucian carp. The new type of homodiploid fish is of great value in fish genetic breeding and for studying the early evolutionary process.

Studies on fish eggs and larvae are important for understanding the recruitment dynamics of fish assemblages and their relationships with environmental conditions. Located in the upper reaches of the Yangtze River, China, the Three Gorges Reservoir (TGR) is one of the largest reservoirs in the world, where the fish resource ecology has drawn great attention. With the purpose of evaluating fish recruitment in the TGR, in the present study, samples of fish eggs and larvae were collected at Luoqi County, the upper end of the TGR, from April 15th to July 29th 2011. From the samples collected, we identified 46 fish species belonging to nine families and five orders. The most abundant species were in the Cultrinae, Gobiidae, and Gobioninae. An estimated 12.4 billion fish eggs and larvae drifted into the TGR. There were approximately 2.6 billion Pseudolaubuca sinensis, 1.9 billion Hemiculter leucisculus, and 1.8 billion Gobiidae. The spawning grounds of fishes that release pelagic eggs are in the reaches 13-162 km upstream from our sampling site. More attention should be paid to protecting the habitat in large free stretches upstream of the reservoir, since these areas are important spawning grounds for many fishes. Also, an ample natural flooding regime should be retained in this region.

We describe the complete mitochondrial genome of the Endangered fish Anabarilius liui yalongensis. It is a circular molecule of 16,608 bp in size, and all genes show the typical gene arrangement conforming to the vertebrate consensus. The cytochrome c oxidase subunit I (COI) sequence of A. liui yalongensis and other 21 species from 14 genera were used for phylogenetic analysis by Bayesian inference and maximum likelihood methods. The topology demonstrated that the A. liui yalongensis clustered with A. grahami are closely to Hemiculter branch within the subfamily Cultrinae.

Specimens of the nematode genus Rhabdochona Railliet, 1916 (Rhabdochonidae) were collected during helminthological examination of four species of cyprinid fishes in two rivers of the Amur River basin in the Russian Far East (Primorsky Region) in June 2011. Detailed light microscopical (LM) and scanning electron microscopical (SEM) examinations (the latter used for the first time for the reported nematode species) of the available material revealed the presence of three inadequately described nominal species of this genus: R. (Rhabdochona) denudata (Dujardin, 1845) from the spotted steed Hemibarbus maculatus Bleeker (Gobioninae), and R. (Rhabdochona) longispicula Belous in Roytman, 1963 and R. (Globochonoides) coronacauda Belous, 1965 from Culter alburnus Basilewsky (Cultrinae) in the Ilistaya River. Detailed morphological study of these worms, especially SEM examination, made it possible to reveal some previously unreported morphological features (e.g., the presence of sublabia or the character of ventral precloacal ridges) and to confirm other taxonomically important characters such as the shape of deirids, number of anterior prostomal teeth, number and situation of lateral preanal and postanal papillae or the detailed structure of the crown-like formation on the female tail tip in R. coronacauda. Unidentifiable Rhabdochona (Rhabdochona) gravid females were recorded from the humpback Chanodichthys dabryi (Bleeker) (Cultrinae) in the Ilistaya River and from the Amur minnow Rhynchocypris lagowskii (Dybowski) (Leuciscinae) in the Komissarovka River.

The genus Culter, found only in East Asia (China, Vietnam, Korea and Russia), is a primary group of freshwater fishes in the subfamily Cultrinae (Cyprinidae). Of a total of 517 specimens studied, 235 were Culter alburnus from different localities and were used for morphometric analysis in this study. 17 landmarks were used in geometric morphometrics (GM) analysis of shapes. 13 traditional morphometrics (TM) and 21 truss-based morphometrics (TBM) characteristics were measured. The results of discriminant analysis and cluster analysis showed that four species-groups could be divided into separate groups. They were (1) C. alburnus + C. recurviceps, (2) C. dabryi dabryi + C. oxycephalus + C. dabryi shinkainensis, (3) C. oxycephaloides, (4) C. mongolicus mongolicus + C. mongolicus elongates + C. mongolicus qionghaiensis. The six populations of C. alburnus (Basilewsky, Nouv Mem Soc Imp Nat Moscou, 10:215–263, 1855), from Lake Poyanghu, River Songhuajiang, River Liaohe, River Jialingjiang, River Lijiang and Lake Taihu, should be classified as different geographical populations, but not subspecies. C. mongolicus elongates (He and Liu, Zool Res, 1(4):483–485, 1980) from Lake Chenghaihu and C. mongolicus qionghaiensis (Ding, Acta Zootaxon Sin, 15(2):246–250, 1990) from Lake Qionghaihu should be classified as subspecies. C. dabryi shinkainensis differed greatly from C. dabryi dabryi in body forms, and we suggest that C. dabryi shinkainensis should be changed to species, instead of subspecies, namely Culter shinkainensis (Yih and Chu, Acta Hydrobiol Sin, 2:170–199, 1959).

The family Cyprinidae is one of the largest fish families in the world, which is widely distributed in East Asian, with obvious difference in characteristic size among species. The phylogenetic analysis of cyprinid taxa based on the functionally important genes can help to understand the speciation and functional divergence of the Cyprinidae. The c-myc gene is an important gene regulating individual growth. In the present study, the sequence variations of the cyprinid c-myc gene and their phylogenetic significance were analyzed. The 41 complete sequences of the c-myc gene were obtained from cyprinids and outgroups through PCR amplification and clone. The coding DNA sequences of the c-myc gene were used to infer molecular phylogenetic relationships within the Cyprinidae. Myxocyprinus asiaticus (Catostomidae), Misgurnus anguillicaudatus (Cobitidae) and Hemimyzon sinensis (Homalopteridae) were assigned to the outgroup taxa. Phylogenetic analyses using maximum parsimony (MP), maximum likelihood (ML), and Bayesian retrieved similar topology. Within the Cyprinidae, Leuciscini and Barbini formed the monophyletic lineage respectively with high nodal supports. Leuciscini comprises Xenocyprinae, Cultrinae, East Asian species of Leuciscinae and Danioninae, Gobioninae and Acheilognathinae, and Barbini contains Schizothoracinae, Barbinae, Cyprininae and Labeoninae. Danio rerio, D. myersi and Rasbora trilineata were supposed to separate from Leuciscinae and Barbini and to form another lineage. The positions of some Danioninae species were still unresolved. Analyses of both amino acid variation with parsimony information and two high variation regions indicated that there is no correlation between variations of single amino acid or high variation regions and characteristic size of cyprinids. In addition, the species with smaller size were usually found to be basal within clades in the tree, which might be the results of the adaptation to the primitive ecology and survival pressure.

Toxabramis houdemeri belongs to the genus Toxabramis in the subfamily of Cultrinae (Cyprinidae). We first determine the complete mitochondrial genome of T. houdemeri in this study. It is 16 618 bp in length, with the base composition on the heavy strand: 30.79% A, 16.61% G, 27.29% C, and 25.31% T. It has the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a D-loop region. Phylogenetic analysis showed that T. houdemeri was clustered into one branch of the subfamily of Cultrinae, and closely related to Hemiculter leucisculus. The present study will contribute to genetic resources conservation of T. houdemeri and studying its population genetic structure and phylogenetic relationships.

The complete mitochondrial genome of Osteobrama belangeri was obtained, using Illumina high-throughput NextSeq 500 with 2 × 150 bp sequencing of mitochondrial DNA. The mitochondrial genome of O. belangeri was 16,602 bp in length (GenBank Accession No. KY887473), comprised of 13 protein coding genes, 22 tRNA genes, 2 rRNA genes and a control region, i.e. D-loop. In present mitogenome, 11 short sequence repeats were identified and validated in silico. The arrangement of genes was found identical to other Cypriniformes fish mitogenomes, available in NCBI database. Phylogenetic relationship established in the present study also supported that genus Osteobrama is member of subfamily Cyprininae (tribe: smiliogastrini) not Cultrinae, which provide useful insights into taxonomic status of the genus.

The complete mitogenome was first determined for a minnow Hemiculter leucisculus in this study. It is 16,622 bp in length and has 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. Overall nucleotide base composition is 30.4% A, 27.10% C, 17.10% G and 25.40% T. All the tRNA genes can fold into the typical clover-leaf secondary structures, except the tRNA-Ser2 which loses the dihydrouridine arm and is replaced with one 11 bp loop. The origin of light-strand replication (OL) was found between the tRNA-Asn and tRNA-Cys genes while the termination associated sequence (TAS) and the conserved sequence blocks (CSB1-3) were found in the control region.

The species boundaries and evolutionary relationships of two closely related genera, Megalobrama and Parabramis, were inferred from the partial mitochondrial cytochrome oxidase subunit I (COI) gene, NADH dehydrogenase subunit 2 (ND2) gene and their concatenated segment. Phylogenetic reconstructions showed that among the three breams, Megalobrama amblycephala and Megalobrama skolkovii are more closely related to each other than either is to Megalobrama terminalis. The taxonomy of M. pellegrini should be reconsidered. The divergence time estimation based on the assumption of a global molecular clock indicated that speciation and dispersal of the two genera might have occurred at approximately Pliocene to Late Pleistocene, due to major paleo-environmental events associated with monsoon evolution and the formation of the Three Gorges of the Yangtze River.

The complete mitochondrial genome of Sinibrama macrops was first determined in this study. The genome is 16,626 bp in length, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 control region. Its gene arrangement and translation direction were identical to those of other typical vertebrates. The overall base composition is 30.7% A, 27.9% C, 16.7% G and 24.7% T, with the negative GC skew value ( - 0.251). In a long term, S. macrops was confused with Sinibrama wui, which was confirmed as an invalid species by recent morphological study. Therefore, the mitochondrial genome of S. macrops can contribute to the molecular identification of the species and further phylogenetic study of Cyprinidae.

Through distant crossing, diploid, triploid and tetraploid hybrids of red crucian carp (Carassius auratus red var., RCC♀, Cyprininae, 2n = 100) × topmouth culter (Erythroculter ilishaeformis Bleeker, TC♂, Cultrinae, 2n = 48) were successfully produced. Diploid hybrids possessed 74 chromosomes with one set from RCC and one set from TC; triploid hybrids harbored 124 chromosomes with two sets from RCC and one set from TC; tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from TC. The 5S rDNA of the three different ploidy-level hybrids and their parents were sequenced and analyzed. There were three monomeric 5S rDNA classes (designated class I: 203 bp; class II: 340 bp; and class III: 477 bp) in RCC and two monomeric 5S rDNA classes (designated class IV: 188 bp, and class V: 286 bp) in TC. In the hybrid offspring, diploid hybrids inherited three 5S rDNA classes from their female parent (RCC) and only class IV from their male parent (TC). Triploid hybrids inherited class II and class III from their female parent (RCC) and class IV from their male parent (TC). Tetraploid hybrids gained class II and class III from their female parent (RCC), and generated a new 5S rDNA sequence (designated class I-N). The specific paternal 5S rDNA sequence of class V was not found in the hybrid offspring. Sequence analysis of 5S rDNA revealed the influence of hybridization and polyploidization on the organization and variation of 5S rDNA in fish. This is the first report on the coexistence in vertebrates of viable diploid, triploid and tetraploid hybrids produced by crossing parents with different chromosome numbers, and these new hybrids are novel specimens for studying the genomic variation in the first generation of interspecific hybrids, which has significance for evolution and fish genetics.

In this study, the complete mitochondrial DNA genome sequence of Sinibrama taeniatus was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial DNA (mtDNA) genome sequence of S. taeniatus was a circular molecule of 16,623 bp in length. It consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of S. taeniatus was 31.3% A, 26.8% C, 16.1% G, and 25.8% T, with a relatively high A + T content (57.1%). The results could provide useful data for studying genetic diversity and phylogenetics in S. taeniatus and related species.

This study provides genetic evidences at the chromosome, DNA content, DNA fragment and sequence, and morphological levels to support the successful establishment of the polyploid hybrids of red crucian carp × blunt snout bream, which belonged to a different subfamily of fish (Cyprininae subfamily and Cultrinae subfamily) in the catalog. We successfully obtained the sterile triploid hybrids and bisexual fertile tetraploid hybrids of red crucian carp (RCC) (♀) × blunt snout bream (BSB) (♂) as well as their pentaploid hybrids. The triploid hybrids possessed 124 chromosomes with two sets from RCC and one set from BSB; the tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from BSB. The females of tetraploid hybrids produced unreduced tetraploid eggs that were fertilized with the haploid sperm of BSB to generate pentaploid hybrids with 172 chromosomes with three sets from BSB and two sets from RCC. The ploidy levels of triploid, tetraploid, and pentaploid hybrids were confirmed by counting chromosomal number, forming chromosomal karyotype, and measuring DNA content and erythrocyte nuclear volume. The similar and different DNA fragments were PCR amplified and sequenced in triploid, tetraploid hybrids, and their parents, indicating their molecular genetic relationship and genetic markers. In addition, this study also presents results about the phenotypes and feeding habits of polyploid hybrids and discusses the formation mechanism of the polyploid hybrids. It is the first report on the formation of the triploid, tetraploid, and pentaploid hybrids by crossing parents with a different chromosome number in vertebrates. The formation of the polyploid hybrids is potentially interesting in both evolution and fish genetic breeding.

The complete mitogenome of Pseudolaubuca engraulis was determined using long-distance polymerase chain reaction and sequenced by primer walking method. It is 16,612 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA (tRNA) genes and 1 A + T-rich control region. The gene arrangement and characterization of P. engraulis are similar to most vertebrates. The overall base composition of the heavy strand is 27.1% A, 27.5% C, 25.9% T and 19.5% G, with a slight A + T bias. The shortest tRNA-Ser2 lacks the dihydrouridine arm and is replaced with a simple loop. The termination-associated sequence and the conserved sequence blocks (1–3) are found in the control region.

Culter dabryi, a medium-sized economic cyprinid fish, is widely distributed in East Asia. We sequenced the complete mitochondrial genome of this species. The genome is 16,622 bp in length, and consists of 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and the non-coding control region with a structural organization conserved relative to that of other fishes. The overall base composition of C. dabryi in descending order is A 31.51%, C 27.60%, T 24.95% and G 15.94%, with a slight A + T bias. The mitogenome sequence data may provide useful information to the population genetics analysis of C. dabryi and the elucidation of evolutionary mechanisms in the endemic clade of East Asian Cyprinidae.

Complete mitochondrial cytochrome b sequences of 54 species, including 18 newly sequenced, were analyzed to infer the phylogenetic relationships within the family Cyprinidae in East Asia. Phylogenetic trees were generated using various tree-building methods, including Neighbor-joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods, with Myxocyprinus asiaticus (family Catostomidae) as the designated outgroup. The results from NJ and ML methods were mostly similar, supporting some existing subfamilies within Cyprinidae as monophyletic, such as Cultrinae, Xenocyprinae and Gobioninae (including Gobiobotinae). However, genera within the subfamily "Danioninae" did not form a monophyletic group. The subfamily Leuciscinae was divided into two unrelated groups: the "Leuciscinae" in East Asia forming as a monophyletic group together with Cultrinae and Xenocyprinae, while the Leucisciriae in Europe, Siberia, and North America as another monophyletic group. The monophyly of subfamily Cyprininae sensu Howes was supported by NJ and ML trees and is basal in the tree. The position of Acheilognathinae, a widely accepted monophyletic group represented by Rhodeus sericeus, was not resolved.