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During revision of the genus Microphysogobio Mori, 1934, we discovered a new species of Huigobio from the Yangtze River Basin in China. The new species, named Huigobio heterocheilus sp. nov., can be distinguished from its congeners by a combination of the following characters: medial pad on lower lip not visible; ventral region scaleless before pelvic-fin insertion; lateral-line scales 39–40; caudal peduncle depth 49.2%–59.1% of length; barbel length 6.6%–10.7% of head length; black blotch between anterior margin of eye and upper lip. Using the K2P model and cytochrome b (cyt b) sequences, interspecific genetic distances between the new species and Huigobio exilicauda Jiang & Zhang, 2013 and Huigobio chenhsienensis Fang, 1938 were 13.2% and 15.1%, respectively. The new species is known from the upper reaches of the Xiangjiang River in the middle Yangtze River Basin. A diagnostic key for species of Huigobio Fang, 1938 is provided.

Wrasses are dominant components of major coral reef systems. Among wrasses, Cheilinus undulatus is an endangered species with high economic and ecological value that exhibits sex reversal of females to males, while sexual selection occurs in breeding aggregations. However, the molecular-associated mechanism underlying this remains unclear. Opsin gene diversification is regarded as a potent force in sexual selection. Here we present a genome assembly of C. undulatus, using Illumina, Nanopore and Hi-C sequencing. The 1.17 Gb genome was generated from 328 contigs with an N50 length of 16.5 Mb and anchored to 24 chromosomes. In total, 22,218 genes were functionally annotated, and 96.36% of BUSCO genes were fully represented. Transcriptomic analyses showed that 96.79% of the predicted genes were expressed. Transposons were most abundant, accounting for 39.88% of the genome, with low divergence, owing to their evolution with close species ~60.53 million years ago. In total, 567/1,826 gene families were expanded and contracted in the reconstructed phylogeny, respectively. Forty-six genes were under positive selection. Comparative genomic analyses with other fish revealed expansion of opsin SWS2B, LWS1 and Rh2. The elevated duplicates of SWS2B were generated by gene conversions via transposition of transposons followed by nonallelic homologous recombination. Amino acid substitutions of opsin paralogues occurred at key tuning sites, causing a spectral shift in maximal absorbance of visual pigment to capture functional changes. Among these opsin genes, SWS2B-3 and 4 and Rh1 are expressed in the retina. The genome sequence of C. undulatus provides valuable resources for future investigation of the conservation, evolution and behaviour of fishes.

Mitochondrial DNA cytochrome b and d-loop sequences (2,137 bp) in 65 specimens of Sarcocheilichthys sinensis from five populations were identified as two lineages (I and II). The pairwise genetic d...

The length–weight relationships (LWRs) were estimated for ten fish species from the Jingjiang reach of the Yangtze River, China. Samples were collected using a combination set‐net consisting of a 40‐meter net wall (mesh size: 1.8 cm) and two fyke nets (mesh size: 0.9 cm) on the 1st, 11th and 21st of each month from January 2012 to December 2017. The b values of all species were within the expected ranges, varying between 2.849 and 3.292. This study provides the LWR parameters for Distoechodon tumirostris, Microphysogobio microstomus, Saurogobio dumerili, Squalidus nitens, Acheilognathus gracilis, Sarcocheilichthys kiangsiensis, Sarcocheilichthys parvus, Rhodeus fangi, Micropercops swinhonis, Repomucenus olidus.

The genus Acrossocheilus is composed of small- to medium-sized barbine species and is distributed in Laos, Vietnam, Hainan, Taiwan and mainland China. To verify the molecular phylogeny of the genus Acrossocheilus, we report a new whole mitogenome of A. longipinnis, which provides new insights to better understand the taxonomic status of Acrossocheilus fishes. Phylogenetic trees presented two major clades based on whole mitogenomic data from sixteen Acrossocheilus species. Clade I is the ancestral group, including A. monticola and A. yunnanensis. The remaining species form clade II, which can be separated into two subclades (subclades A and B) with strong support. Subclade B clusters indicate that A. longipinnis forms a monophyletic group with A. iridescens and A. barbodon. Landscape evolution can strongly affect the evolutionary diversification of freshwater fishes. The Nanling and Wuyi Mountains, Taiwan Strait and Qiongzhou Strait played a key role in the geographical barriers for Acrossocheilus diversification. Our results improve our understanding of Acrossocheilus mitogenome structure and evolution, which will be useful for phylogenetic analysis and species identification.

The Japanese grenadier anchovy ( Coilia nasus ) undergoes upstream migration to spawning annually but can also be observed in freshwater resident populations. It has been hypothesized that anadromous adult C. nasus may utilize olfactory cues to locate spawning grounds. We firstly performed a comparative proteome analysis about olfactory rosettes in two populations to hunt for the proteomic changes. Among 5 408 identified proteins, 1 515 proteins (629 up-regulated and 886 down-regulated) were differentially expressed. Especially, several proteins and pathways associated with olfactory signaling were found to be significantly differential. Compared with resident C. nasus, the expressions of Golf protein and the sodium/calcium exchanger were significantly up-regulated in anadromous C. nasus. The expression of adenylate cyclase and regulator of G-protein signaling (RGS) were decreased. Our findings suggest a decrease in the expression of cGMP-dependent protein kinase (PKG) in anadromous C. nasus compared to resident C. nasus. The expression of Calmodulin (CaM) was increased and CaM-dependent protein kinase II (CaMKII) was decreased. In addition, KEGG pathway enrichment analysis of up-regulated proteins indicated statistically significant difference not only in olfactory transduction but also in the cGMP-PKG signal pathway. Furtherly, we sought out some proteins expressed in the same trend occurring in DEGs (differentially expressed genes) and DEPs (differentially expressed proteins) by doing the integrative analysis of proteome and transcriptome in olfactory rosettes of C. nasus.

Populations of Yangtze finless porpoises (YFPs) have rapidly declined in recent decades, raising the specter of extinction. In order to protect YFPs, a greater understanding of their biology is needed, including studying how their immune functioning changes with age. Here, we systematically studied the hematologic and biochemical parameters, as well as mRNAs and miRNAs profiles of old, adult, and young YFPs. The lymphocyte (LYMPH), neutrophils (NEUT) and eosinophils (EOS) counts in old YFPs were lower than those in young or adult YFPs. When comparing old to adult YFPs, the latter showed higher expression of genes associated with the innate and adaptive immune systems, including complement components, major histocompatibility complex, interleukins, TNF receptors, and chemokines/cytokines. When comparing old to young YFPs, the most striking difference was in higher toll-like receptor signaling in the latter. When comparing adult to young YFPs, the former exhibited higher expression of genes related to adaptive immunity and the FoxO signaling pathway, but lower expression of genes associated with the PI3K-Akt signaling pathway. Negative miRNA-mRNA interactions were predicted in comparisons of the old and adult (326), old and young (316), adult and young (211) groups. Overall, these results delineate a progression from early innate immune function dominance to adaptive immune function enhancement (young to adult) and deterioration (adult to old), and the changes in miRNAs profile correlate with the effects of age on immune functions. This study is the first to observe the changes of immune function of Yangtze finless porpoise with age using transcriptome method, and the study's findings are of great significance for protecting this endangered species.

Mitochondrial DNA cytochrome

The rosy bitterling, Rhodeus ocellatus, is a small freshwater fish belonging to the family Cyprinidae. This species lives in ponds where freshwater mussels are abundant and female lays eggs inside mussels. To understand whether the reproduction mode influenced the phylogeography, our study examined the genetic structure of R. ocellatus using sequences from the mitochondrial DNA (cytochrome b gene and control region) and nuclear DNA (the first intron of ribosomal protein S7 gene). In total, 213 specimens were collected from twelve populations in south of Yangtze River, including Yangtze River, Taiwan and Hainan Islands. The phylogenetic analyses based on mitochondrial and nuclear sequences both showed the lack of a population genetic structure, but all results, including the approximate Bayesian computation approaches, showed that these two markers revealed incongruent historical signals. Our study found that (1) the discordance between these two markers were accounted for admixtures by introduced; (2) the phylogeographic pattern of R. ocellatus and that of other freshwater fish were identical; (3) the reproduction mode was due to that the gene flows among populations were limited; and (4) R. ocellatus colonized in south of the Yangtze River (including) after southeast coastal districts formed and before Taiwan Island reached its present shape by comparing our results with that of the previous studies.

The objective of this study was to investigate 4 aquaculture populations Shanghai (SH), Hangzhou (HZ), Kaihua (KH) and Xianju (XJ) and one wild population Yingshan (YS) of spotted barbell (Hemibarbus maculates) to assess their genetic diversity level and investigate the genetic structure of the populations. The dendrogram and STRUCTURE revealed that the populations XJ, KH, and HZ jointly formed one cluster, to which the populations SH and YS were sequentially adhered. The genetic diversity of the cultured populations maintained better, possible due to favourable hatchery conditions that decreased the effect of environmental selection present in wild populations. The results of the present study will contribute to the management of spotted barbell genetic resources, but also demonstrates how the genetic diversity of freshwater species is vulnerable to human activity.

Population genetic structure of Onychostoma lepturum on Hainan Island was investigated based on mitochondrial CR + cyt b region in 63 specimens collected from four populations. Population analyses indicated significant genetic structure (FST = 0.749) and displayed a significant relationship between phylogeny and geography (NST = 0.750 and GST = 0.140). Thirty-one mtDNA haplotypes were classified into four lineages, and these lineages had an almost allopatric distribution. The results of a statistical dispersal-vicariance analysis suggest that the ancestral populations were distributed widely on Hainan Island, and the rising of the central mountainous area of Hainan Island, the Wuzhi and Yinggeling Mountain Range, separated these four drainages into independent lineages. According to a spatial analysis of molecular variance analysis, we divided these populations into three units: ND, CH and WQ + LS, running into Qiongzhou Strait, the Gulf of Tokin and the South China Sea, respectively. According to our study, the exposure of straits and shelf under water retreat gave chances for population dispersion during the glaciations.

The Coilia nasus is an important fish species, which is of commercial values in China. In order to manage the fisheries resources and the development of sustainable fishing strategies to protect this species, 11 microsatellite loci polymorphisms and mtDNA COI sequences were used to examine the genetic diversity of C. nasus in Japan and China. In total, the 40 COI haplotypes and 93 microsatellite alleles were detected. The mtDNA phylogeny did not support population grouping, but the distribution patterns of mtDNA haplotypes and the results of STRUCTURE analysis based on microsatellite indicated a degree of genetic isolation in this species. Our study suggested that the lack of a population genetic structure might result in its amphidromous life cycle, and the geographical distance and habitat fragments might cause isolated populations. Thus, the sampling populations of C. nasus in Japan and China could be divided as four geographical/ecological populations.

The phylogeography of Coreoperca whiteheadi was studied using sequences from the mitochondrial cytochrome b (cytb) gene and first intron of the S7 ribosomal protein gene. The reciprocal monophyly mitochondrial cytb and nuclear sequences strongly suggest that C. whiteheadi has significantly reduced gene flow between populations and may be in the process of speciation. Phylogenetic analysis revealed phylogeographical structuring into two major clades (highly supported by bootstrap analysis) corresponding to the two regions divided by Nanling-Wuyi Mountain Range. Subsequent nested clade analysis confirmed this structure. The results suggest that Nanling-Wuyi Mountain Range represents a major phylogeographic barrier for C. whiteheadi . Six evolutionarily significant units of C. whiteheadi were designated from the genetic analysis for conservation and management.

Firstly, RAPD was conducted to analyze genetic diversity of Trachidermus fasciatus in the Fuchun River population (FR), Yellow River population (YR), Luan River population (LR), and Yalu River population (YL), with 32 polymorphic 10-bp random primers selected from 294 ones. Thirty wild individuals were detected in each population. The results indicated that the genetic diversity of T . fasciatus was relatively rich. The major results were as the following: 1) Altogether, 591 bands were detected and 515 of them were polymorphic, accounted for 87.14%. The range of proportion of polymorphic loci (P) was: FR(89.17%)>YR(87.99%)>YL(86.63%)>LR(83.25%). 2) The Shannon’s information index(IT) and Nei’s genetic diversity(HT) among populations were 0.3393−0.3566 and 0.2157−0.2279, respectively. Compare to other three populations, LR population had relative lower values. If took the populations as a whole, the total Nei’s genetic diversity(HT) and Shannon’s information index(IT) was 0.2336±0.1643 and 0.3710±0.2153, respectively. 3) The value of gene flow (Nm) (5.76103−19.84497) were high, indicating certain gene exchange existed among the four populations. But the AMOVA results exhibited significantly differentiation (P

The complete sequence of the mitochondrial DNA (mtDNA) of the East Asian finless porpoise (Neophocaena asiaeorientails sunamrei) has been completed and annotated in this study. The circular genome is 16 385 bp in length, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 2 non-coding areas. Ten protein-coding genes use ATG as the initiation codon, except that ND2 started with ATT, and ND3 and ND5 started with ATA. Canonical TAA and TAG termination codons are found in seven protein-coding genes, the remaining four (ND4, ND2, ND3, and COIII) have incomplete termination codons (T or TA), in addition, the COI ends with AGG, and the Cyt b ends with AGA. On the neighbor-joining phylogenetic tree, these results show that the relationship of Phocoenidae is closer with Delphinidae.

A number of studies have suggested that olfaction plays an important role in fish migration. Fish use several distinct families of olfactory receptors to detect environmental odorants, including MORs (main olfactory receptors), V1Rs (vomeronasal type-1 receptors), V2Rs (vomeronasal type-2 receptors), TAARs (trace amine-associated receptors), and FPRs (formyl peptide receptors). The V1Rs have been reported to detect pheromones, and a pheromone hypothesis for the spawning migration of anadromous fish has been proposed. Examining whether Coilia nasus relies on V1R-mediated olfaction for spawning migration is important for understanding the molecular basis of spawning migration behavior. Here, we explored the V1R gene family in anadromous C. nasus. Six V1R genes previously reported in other teleost fish were successfully identified. Interestingly, we detected the largest V1R repertoire in teleost fish from C. nasus and identified a species-specific expansion event of V1R3 gene that has previously been detected as single-copy genes in other teleost fish. The V1R loci were found to be populated with repetitive sequences, especially in the expanded V1R3 genes. Additionally, the divergence of V1R3 genetic structures in different populations of C. nasus indicates the copy number variation (CNV) in V1R3 gene among individuals of C. nasus. Most of the putative C. nasus V1R genes were expressed primarily in the olfactory epithelium, consistent with the role of the gene products as functional olfactory receptors. Significant differences in the expression levels of V1R genes were detected between the anadromous and non-anadromous C. nasus. This study represents a first step in the elucidation of the olfactory communication system of C. nasus at the molecular level. Our results indicate that some V1R genes may be involved in the spawning migration of C. nasus, and the study provides new insights into the spawning migration and genome evolution of C. nasus.

The roughskin sculpin (Trachidermus fasciatus) is an endangered species. It has been listed as an “endangered aquatic wild animal under second class protection” since late 1980s in China. In this study, 19 polymorphic microsatellite loci were isolated and characterized. The markers were tested on 60 individuals collected from Yalu River (YL) and the mouth of Yellow River (YR) in China. The number of alleles in these 19 markers ranged from 10 to 20. The observed (HO) and expected (HE) heterozygosity ranged from 0.8000 to 1.000 in YL and from 0.8638 to 0.9497 in YR, respectively. The polymorphism information content varied from 0.8230 to 0.9300 in the two populations. These microsatellite loci could help in genetic studies on this species and may provide essential information for its conservation.

Coilia nasus is widely distributed in the Yangtze River, the coastal waters of China, Korea and the Ariake Sound of Japan. Several ecotypes exist and this provides a useful model for the study of comparative diversity between molecular markers. Here we analyze and compare the nucleotide sequences between single-copy ribosomal protein S7 gene intron 1 (rpS7) and multiple-copy ribosomal internal transcribed spacer 1 (ITS1) in this species to compare the phylogenetic signal of the two nuclear genes. Nucleotide substitutions among the two gene sequences and partial sequence of mitochondrial cytochrome c oxidase subunit I (COI) gene were also analyzed. A total of 115 clones for rpS7 and 122 clones for ITS1 were obtained from 37 specimens. The nucleotide sequence length is 741 to 743 bp for rpS7 and 334 to 348 bp for ITS1. Intra- and inter-specimen variation in rpS7 results from nucleotide substitution, while such variation in ITS1 is mainly due to different numbers of short base repeats. The content of G + C is lower in rpS7 (43.5%) than in ITS1 (68.2%). Our results indicate that the proportion of the sequence variable sites is higher in rpS7 (61) than in ITS1 (23); the informative parsimony of rpS7 is evidently higher than that of ITS1 (26 vs. 2); the overall ratio between transitions and transversions in ITS1 is slightly lower than in rpS7, but remarkably lower than in COI. These results suggest that rpS7 is more suitable than ITS1 as a marker for genetic divergence of this group. Furthermore, gene flow is observed between the different geographic populations of C. nasus from the phylogeny of this species based on rpS7, showing that rpS7 has more evolutionary characteristics for understanding the processes of genomic evolution at the intraspecific level.

Short interspersed nucleotide elements (SINEs), a type of retrotransposon, are widely distributed in various genomes with multiple copies arranged in different orientations, and cause changes to genes and genomes during evolutionary history. This can provide the basis for determining genome diversity, genetic variation and molecular phylogeny, etc. SINE DNA is transcribed into RNA by polymerase III from an internal promoter, which is composed of two conserved boxes, box A and box B. Here we present an approach to isolate novel SINEs based on these promoter elements. Box A of a SINE is obtained via PCR with only one primer identical to box B (B-PCR). Box B and its downstream sequence are acquired by PCR with one primer corresponding to box A (A-PCR). The SINE clone produced by A-PCR is selected as a template to label a probe with biotin. The full-length SINEs are isolated from the genomic pool through complex capture using the biotinylated probe bound to magnetic particles. Using this approach, a novel SINE family, Cn-SINE, from the genomes of Coilia nasus, was isolated. The members are 180-360 bp long. Sequence homology suggests that Cn-SINEs evolved from a leucine tRNA gene. This is the first report of a tRNA(Leu)-related SINE obtained without the use of a genomic library or inverse PCR. These results provide new insights into the origin of SINEs.

Background The South China landmass has been characterized by a complex geological history, including mountain lifting, climate changes, and river capture/reversal events. To determine how this complexity has influenced the landmass’s phylogeography, our study examined the phylogeography of Garra orientalis, a cyprinid widely distributed in South China, using sequences from the mitochondrial DNA control region and cytochrome b gene (1887 bp) and polymorphisms of thirteen microsatellite loci. Results In total, 157 specimens were collected from eight populations. All 88 mtDNA haplotypes were identified as belonging to three major lineages, and these lineages were almost allopatric in their distributions. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of G. orientalis were distributed south of the Yunkai Mountains, including on Hainan Island. The mtDNA data revealed a strong relationship between phylogeny and geography. In the microsatellite analysis, a total of 339 alleles with an average of 26 alleles per locus were observed across thirteen microsatellite loci. A clustering algorithm for microsatellite data revealed an admixture-like genetic structure. Although the mtDNA and microsatellite data sets displayed a discordant population structure, the results of an approximate Bayesian computation approach showed that these two markers revealed congruent historical signals. The population history of G. orientalis reflects vicariance events and dispersal related to the complex geological history of South China. Conclusion Our results (i) found that the discordances between mtDNA and microsatellite markers were accounted for by admixtures; (ii) showed that the Wuzhishan and Yinggeling mountain ranges and Qiongzhou Strait were important barriers limiting gene exchange between populations on both sides; (iii) indicated that during glaciation and inter-glacial periods, the strait and continental shelves were exposed and sank, which contributed with the dispersion and differentiation of populations; and (iv) displayed that the admixtures between lineages took place in coastal populations and then colonized the tributaries of the Pearl River.

Squalidus argentatus (Sauvage and Dabry de Thiersant 1874) is a small-sized freshwater fish which is distributed in Mainland China, Hainan Island and Taiwan. The populations of S. argentatus have dropped sharply probably due to overharvesting and water pollution recently. Eleven polymorphic microsatellite markers were developed for the cyprinid fish S. argentatus. These new markers were tested on 43 individuals collected from Yangtze River and Qiantang River. The number of alleles, observed and expected heterozygosity per locus, in two populations ranged from 3 to 14, from 0.333 to 0.954 and from 0.480 to 0.928, respectively. Only two loci are significantly deviated from Hardy–Weinberg expectations due to the heterozygote deficiency. No significant linkage disequilibrium was detected between the pairwise comparisons of these loci. These polymorphic microsatellite loci will enable us to study the genetic variation, population structure, and conservation genetics of this species in the future.

Transposable elements widely disseminate in genomes of various organisms. Transpositions of these elements take place from one position in the chromsome to another, and their amplification also occurs in genomes. Activities of transposable elements create genomic rearrangements and gene mutations, and contribute to cause biological diversity and promote evolutionary transitions, indicating that transposable elements are major drivers of genomic evolution. Transposable elements fall into two major classes: retrotransposons and DNA transposons. Tc1-like transposons that belong to DNA transposon class are the most abundant and most ubiquitous group in nature. This review focuses on Tc1-like transposon’s structure characteristics, their amplification and transposition mechanisms, and their burst dynamics, and also prospects to the application of these elements as a tool for molecular biology and the research on these elements in the future.

The study analyzed 30 exterior meristic characters for 255 silver and bighead carp samples of 1- to 5-year-old collected from the National Primary Breeding Farm at Laojianghe Lake at the Middle Reach of the Yangtze River. Multivariate analysis was performed. In silver carp, the Euclidean distance was the greatest between the 1-year-old group and other age groups. Silver carp individuals were correctly classified at 98.0% accuracy with a discriminant function established by discriminant analysis based on meristic measurements. Similarly, bighead carp had the greatest distance between 1- to 2-year-old group and other age groups. Individuals of bighead carp were correctly classified at 90.7% accuracy by the discrimination function. The data showed that morphological transformation occurred during the life history of silver and bighead carp development. Eighteen meristic measurements showed highly significant differences, while four showed a significant difference between the two silver carp groups. Ten parameters decreased, while twelve measurements increased during development. In bighead carp, fourteen parameters were significantly different, while three parameters were significantly different between the two groups. Twelve parameters were significantly decreased and another five were increased during development. The results suggest allometric growth should be taken into account when identifying species, analyzing population differences and establishing germplasm standards based on morphology.

In order to analysis the genetic structure and demographic history of Beleophthalmus petinirostris , the random amplified polymorphic DNA (RAPD) technology and mitochondrial cytochrome b (Cyt b) gene sequences were used in the study. The results showed that there was high level genetic diversity in the populations of B. pecinirostris in Yangtze River estuary and its southern wet-land adjacent regions. (1) RAPD was conducted to analysis the genetic variation of B. pecinirostris in Jiuduansha (JDS), Dinghai（DH）and Xiapu（XP）for 20 individuals per population, with 30 polymorphic 10-based random primers selected from 100 ones. In total, 236, 270 and 274 bands were obtained for JDS, DH and XP, respectively and there was 301useful loci. The range of proportion of polymorphic loci (P), Nei’s gene diversity (H) and Shannon diversity index (I ) was: 93.02%–96.3%, 0.3890–0.4219, 0.5618–0.6044, respectively. The results of AMOVA showed significantly genetic differentiation (Fst=0.03004-0.03254, P0.05) all revealed that the B. pecinirostris had no obviously geographical differentiation. However, the phylogenetic tree estimated by neighbor-joining (NJ) method indicated that the individuals of B. pecinirostris formed two monophyletic lineages, and the two lineages were not correlated with geographical populations. Neutrality tests, mismatch distribution and network analysis suggested a late Pleistocene population expansion for B. pecinirostris (0.057–0.023 million years ago).

Osteochilus salsburyi (Cypriniformes, Cyprinidae) is a small-sized fish of significant economic value. In this study, thirteen polymorphic microsatellite markers were developed in O. salsburyi and were examined on twenty individuals collected from the Wanquan River in the Hainan Island. The number of alleles (NA), polymorphism information content, observed and expected heterozygosity per locus ranged from 10 to 21, 0.8020 to 0.9354, 0.7500 to 1.0000 and 0.8436 to 0.9628, respectively. No locus was found to significantly deviate from Hardy–Weinberg equilibrium. These markers would be suitable for studies on conservation genetics and population structure of O. salsburyi.

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.

14 Polymorphic microsatellite markers were developed in the Garra orientalis. These new markers were tested in 23 individuals collected from the Wanquan River in the Hainan Island. The number of alleles (NA), polymorphism information content, observed and expected heterozygosity per locus ranged from 8 to 25, 0.6788 to 0.9342, 0.5652 to 1.0000 and 0.7179 to 0.9585, respectively. Four loci are deviated from Hardy–Weinberg equilibrium due to the heterozygote deficiency. These markers can be used to study genetic diversity, population structure, conservation and rational utilization of this species.

In this study, the complete mitochondrial genome of the endangered roughskin sculpin, Trachidermus fasciatus, was first determined. The mitogenome (16,536 bp) consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. Except for the eight tRNA and ND6 genes, all other mitochondrial genes were encoded on the heavy strand. Mitochondrial DNA information can assist in species identification and conservation of the species' natural resources.

The mudskipper, Boleophthalmus pectinirostris (Perciformes, Gobiidae), is an amphibious gobioid fish and a good species for marine culture in China. In this paper, 16 polymorphic microsatellite loci were isolated and characterized. The markers were tested on 60 individuals collected from Beihai (BH) and Lianyungang (LYG) coast in China. The number of alleles (N A ) in these markers ranged from 5 to 11. The polymorphism information content varied from 0.5946 to 0.8567 in the two populations. The observed (H O ) and expected (H E ) heterozygosity ranged from 0.5333 to 0.9000 in BH and from 0.5333 to 0.8729 in LYG, respectively. No significant linkage disequilibrium was detected at any pair of loci (P > 0.01). These microsatellite loci will be useful for population genetic studies of B. pectinirostris.

The mudskipper, Boleophthalmus pectinirostris (Perciformes, Gobiidae), is an amphibious gobioid fish. In this paper, the complete mitochondrial genome of B. pectinirostris was firstly determined. The mitogenome (17,111 bp) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 putative control region. 130-bp tandem repeat was identified in the control region, which was almost identical among the 10 individuals examined, and three different frequencies of the repeat unit (five, six or seven) were found among these individuals.

We isolated and characterized 12 novel polymorphic microsatellite loci for the Japanese grenadier anchovy (Coilia nasus) using the method of PCR-based isolation of microsatellite arrays. Sixteen individuals of C. nasus from Ariake Bay in Japan were genotyped using 24 PCR primers to characterize the polymorphism at each locus. The average number of the observed alleles per locus was 11.08 (ranging from 8 to 20). The observed heterozygosity values ranged from 0.562 to 1.0, and the expected heterozygosity values ranged from 0.647 to 0.969. Only one of the twelve loci deviated significantly from Hardy–Weinberg equilibrium, and linkage disequilibrium was not found in any pairs of the loci. These markers can be used to investigate the genetic structure of the C. nasus population.

Background Coilia nasus (Japanese grenadier anchovy) undergoes spawning migration from the ocean to fresh water inland. Previous studies have suggested that anadromous fish use olfactory cues to perform successful migration to spawn. However, limited genomic information is available for C. nasus. To understand the molecular mechanisms of spawning migration, it is essential to identify the genes and pathways involved in the migratory behavior of C. nasus. Results Using de novo transcriptome sequencing and assembly, we constructed two transcriptomes of the olfactory epithelium from wild anadromous and non-anadromous C. nasus. Over 178 million high-quality clean reads were generated using Illumina sequencing technology and assembled into 176,510 unigenes (mean length: 843 bp). About 51% (89,456) of the unigenes were functionally annotated using protein databases. Gene ontology analysis of the transcriptomes indicated gene enrichment not only in signal detection and transduction, but also in regulation and enzymatic activity. The potential genes and pathways involved in the migratory behavior were identified. In addition, simple sequence repeats and single nucleotide polymorphisms were analyzed to identify potential molecular markers. Conclusion We, for the first time, obtained high-quality de novo transcriptomes of C. nasus using a high-throughput sequencing approach. Our study lays the foundation for further investigation of C. nasus spawning migration and genome evolution.

The mudskipper Boleophthalmus pectinirostris is an important aquaculture species in China. It is endangered due to the loss and fragmentation of natural habitat, seawater pollution and overfishing. In this study, ten polymorphic microsatellite loci were isolated by the 5′-anchored polymerase chain reaction technique. Population genetic parameters were estimated on 60 wild individuals collected from Jiuduansha wetland in Yangtze River estuary. The number of alleles ranged from 3 to 14. The observed(HO) and expected(HE) heterozygosities ranged from 0.2500 to 0.8500 and from 0.3679 to 0.8692, respectively. This suite of microsatellite loci will facilitate future studies of the genetic status of wild and hatchery bred populations of B. pectinirostris.

The oriental sucking barb, Garra orientalis, is a small to moderate-sized freshwater fish. In this study, the complete mitochondrial genome of G. oriental was successfully sequenced for the first time with total length of 17,288 bp. The genome structure consists of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA (tRNA) genes and a control region. Moreover, tandem repeat unit ranged from 259 to 260 bp (repeated 3–4 times) was identified in the control region among G. orientalis individuals.

We reviewed the taxonomy and systematics research history of freshwater fish in China based on 1 236 taxonomic literature records on Chinese freshwater fish. The research was divided into five research periods according to specific historical events: (1) period by foreign scholars, (2) period with Chinese scholars, (3) period during World War II and Civil War, (4) recovery period and (5) period of rapid development. There were representative studies and innovations in all periods. We also discuss here the characteristics of each period on the basis of literature analysis.该文回顾了我国近、现代内陆水域鱼类系统分类学研究的历史。基于收集到的1758—2011年1 230余篇与中国内陆水域鱼类系统分类研究相关的中外文著作、文献等, 并根据特定的研究历史事件, 对我国内陆水域鱼类研究历程进行了断代分析。将这一历程划分为5个时期:外国学者研究时期(1758—1927年)、中国学者开始自主研究时期(1927—1937年)、抗日战争和国内战争影响时期(1937—1949年)、恢复时期(1950—1980年)和加速发展时期(1980年至今), 并分析了各时期的代表性研究以及时代特点。

We determined the complete mitochondrial genome (mitogenome) sequence of Sarcocheilichthys nigripinnis by using long polymerase chain reaction method. The total length of S. nigripinnis mitogenome is 16,680 bp, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a noncoding control region. The overall base composition of S. nigripinnis is 26.36% for T, 26.67% for C, 30.07% for A, and 16.90% for G, with a slight AT bias of 56.43%.

Firstly, RAPD was conducted to analyze genetic diversity of Trachidermus fasciatus in the Fuchun River population (FR), Yellow River population (YR), Luan River population (LR), and Yalu River population (YL), with 32 polymorphic 10-bp random primers selected from 294 ones. Thirty wild individuals were detected in each population. The results indicated that the genetic diversity of T . fasciatus was relatively rich. The major results were as the following: 1) Altogether, 591 bands were detected and 515 of them were polymorphic, accounted for 87.14%. The range of proportion of polymorphic loci (P) was: FR(89.17%)YR(87.99%)YL(86.63%)LR(83.25%). 2) The Shannon's information index(I(T)) and Nei's genetic diversity(H(T)) among populations were 0.3393-0.3566 and 0.2157-0.2279, respectively. Compare to other three populations, LR population had relative lower values. If took the populations as a whole, the total Nei's genetic diversity(H(T)) and Shannon's information index(I(T)) was 0.2336±0.1643 and 0.3710±0.2153, respectively. 3) The value of gene flow (N(m) ) (5.76103-19.84497) were high, indicating certain gene exchange existed among the four populations. But the AMOVA results exhibited significantly differentiation (P0.05 or P0.01) among the populations. 4) In the UPGMA tree constructed according to genetic distance, YL and YR populations clustered firstly, then with FR population, and finally they joined to LR population. Obviously, the YL, YR and FR populations had relatively close relationship according to their geographic distance, whereas LR population showed clear divergence to the other three populations. Secondly, out of the five special RAPD bands (S(1225)(525 bp), S(1225)(605 bp), S(1225)(841 bp), S(1345)(695 bp) and S(1345)(825 bp)), SCAR maker SCAR01(560 bp) and SCAR02(443 bp) were successfully transformed from S(1255)(605 bp) and S(1255)(841 bp), respectively. After large samples examination of the two markers, we found the highest frequency (96.67% and 93.33%) in the YL population, higher frequency (83.33% and 90%) in the FR population, high frequency (56.67% and 66.67%) in the YR population, and the lowest frequency (13.33% and 20 %) in the LR population. Therefore, SCAR01(560 bp) and SCAR02(443 bp) can be used as special molecular markers for the population identification between LR and other three populations.

Microphysogobio wulonghensis sp. nov. is described based on 15 specimens collected from the Wulonghe River in Laiyang County of Shandong Province in eastern China. The new species can be distinguished from all congeners by the combination of the following characteristics: upper lip with one row of well-developed and compressed triangular papillae; two lateral pads of lower lip well-developed, contacting each other behind medial pad; two-thirds of area between pectoral-fin origin and pelvic-fin origin scaleless.

Phylogeographical analyses on Squalidus argentatus samples from thirteen localities within mainland China and Taiwan were conducted for biogeographic studies, as their dispersal strictly depends on geological evolution of the landmasses. A total of 95 haplotypes were genotyped for mtDNA cyt b gene in 160 specimens from nine river systems. Relatively high levels of haplotype diversity (h = 0.984) and low levels of nucleotide diversity (π = 0.020) were detected in S. argentatus. Two major phylogenetic haplotype groups, A and B, were revealed via phylogenetic analysis. The degree of intergroup divergence (3.96%) indicates that these groups diverged about 4.55 myr (million years) ago. Haplotype network and population analyses indicated significant genetic structure (F(ST) = 0.775), largely concordant with the geographical location of the populations. According to SAMOVA analysis, we divided these populations into four units: Yangtze-Pearl, Qiantang-Minjiang, Jiulong-Beijiang and Taiwan groups. Mismatch distribution analysis, neutrality tests and Bayesian skyline plots indicated a significant population expansion for lineage A and B, approximately dated 0.35 and 0.04 myr ago, respectively. We found strong geographical organization of the haplotype clades across different geographic scales that can be explained by episodes of dispersal and population expansion followed by population fragmentation and restricted gene flow.

The Yangtze River estuary is the main production area of Anguilla japonica in China, as well as the only existing fishery area for adult eels. Japanese eels are distributed in the main rivers and many tributaries from the Yangtze River estuary to the upper Jinsha River, which extend to nearly 3 000 km. However, their migration behaviors remain relatively unknown. We analyzed the biological characteristics of 153 specimens of silver eels collected from the Jingjiang section of Yangtze River (31(o)30'N, 120(o)42'E) between September and November, 2008, and tested the sagittal Sr/Ca ratios of 27 specimens. Among the 153 specimens examined, 85 were female and 68 were male, which translated to a female-male ratio of 1 : 0.8. The ages of the female specimens ranged from 3 to 7 a (average 5.52) with an average total length (TL) of (669 ± 80) mm, average body weight (BW) of (555 ± 229)g, average condition factor of 1.77 ± 0.22, and average gonad somatic index (GSI) of 1.32 ± 0.31. The ages of the males ranged from 3 to 5 a (average:4.38) with an average TL of (518 ± 51) mm, average BW of (234 ± 76) g, average condition factor of 1.62 ± 0.18, and average GSI of 0.21 ± 0.11. All biological parameters of females were significantly larger than those of the male specimens (P0.05). According to the average Sr/Ca ratio (7.99 ± 1.05) × 10(-3) of the elver mark of sagitta, 17 individuals (62.96%) were river eels and 10 individuals (37.04%) were estuarine eels. Of 16 females, 13 individuals (81.25%) were river eels and 3 were estuarine eels, while of 11 males, 36.36% were river eels and 63.64% were estuarine eels. The analysis on Sr/Ca ratios for every growth layer group (GLG) indicated there were no significant differences between second-age males and females. However, significant differences were observed between the third-age, fourth-age, and migration-age male and female specimens. This was likely related to the fact that second-age eels of both sexes stay in the same inhabitation waters; however, as they grow older, they move to different areas.

A new record species of Chaetodontidae, Heniochus diphreutes, was found by comparative analysis of the morphological characteristics in a taxonomic revision of the family Chaetodontidae in China. It was distinguished from its relative species H. acuminatus by a combination of the following: Dorsal fin usually with 12 spines (vs. 11); 2-3 rows of teeth on both jaws (vs. 5-7); ventral profile of head convex (vs. almost straight); anal fin more angular, and black area on posterior part of anal fin usually extending anteriorly to longest soft ray (vs. more round, and usually not extending anteriorly to longest soft ray); and snout shorter than eye (vs. longer).

Multivariate analysis was adopted to analyze 30 morphometrical characteristics of 121 one-year-old juvenile silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichthys nobilis) bred during the 1950s ("the former population") and 2008 ("the current population") and collected from the middle reach of the Yangtze River. The average discriminant accuracies of the former and current silver and bighead carp population were 94.2% and 98.0%, respectively. Discriminant analysis also revealed that significant differences in morphology occurred between the former and current populations of both carp in overall characteristics. One-way analysis of variance indicated that between former and current populations, silver carp showed highly significant differences (P0.01) in twelve of their characteristics and significant differences (P0.05) in eight of their characteristics, while bighead carp showed highly significant differences (P0.01) in eight of their characteristics and significant differences (P0.05) in eight of their characteristics. Six head morphology variables of the current silver and bighead carp were significantly or highly significantly larger than the former populations; fourteen characteristics of silver carp and ten characteristics of bighead carp of the current populations, mainly reflecting truck and tail morphology, were significantly or very significantly smaller than the former populations. Our results indicate that silver and bighead carp have developed a larger head and smaller truck and tail during the last 50 years. Due to such morphological changes, it seems apparent that the heads of these fish species need to be considered in regards to human diets, particularly in relation to economic and nutritious value.