Integrated DNA barcoding methods to identify species in the processed fish products from Chinese market.

DNA-based methods are reliable for a precise identification of species in processed products. In this study, we assessed five typical DNA extraction methods from multiple aspects. Full-length and mini-length DNA barcoding were performed to detect the species substitution and mislabeling of 305 processed fish products from the Chinese market covering six processed fish products. The salt extraction method that exhibited the best overall performance was applied. All samples were successfully extracted; however, only 19.3 % of samples could be amplified using the full-DNA barcode primer set, and 90.2 % of samples could be amplified using the newly designed mini-DNA barcode primer sets (401 and 320 bp). Overall, the molecular identification results revealed that 36.4 % (111/305) of the samples were inconsistent with the labels, with commercial fraud observed in all six types of processed fish products. The survey findings provide technical references for effective fish authentication monitoring, offering insights into the seafood safety in markets.

Genome-wide identification and structural analysis of the BMP gene family in Triplophysa dalaica.

BACKGROUND: Bone morphogenetic proteins (BMPs) are part of the transforming growth factor beta (TGF-ß) superfamily and play crucial roles in bone development, as well as in the formation and maintenance of various organs. Triplophysa dalaica, a small loach fish that primarily inhabits relatively high elevations and cooler water bodies, was the focus of this study. Understanding the function of BMP genes during the morphogenesis of T. dalaica helps to clarify the mechanisms of its evolution and serves as a reference for the study of BMP genes in other bony fishes. The data for the T. dalaica transcriptome and genome used in this investigation were derived from the outcomes of our laboratory sequencing. RESULTS: This study identified a total of 26 BMP genes, all of which, except for BMP1, possess similar TGF-ß structural domains. We conducted an analysis of these 26 BMP genes, examining their physicochemical properties, subcellular localization, phylogenetic relationships, covariance within and among species, chromosomal localization, gene structure, conserved motifs, conserved structural domains, and expression patterns. Our findings indicated that three BMP genes were associated with unstable proteins, while 11 BMP genes were located within the extracellular matrix. Furthermore, some BMP genes were duplicated, with the majority being enriched in the GO:0008083 pathway, which is related to growth factor activity. It was hypothesized that genes within the BMP1/3/11/15 subgroup (Group I) play a significant role in the growth and development of T. dalaica. By analyzing the expression patterns of proteins in nine tissues (gonad, kidney, gill, spleen, brain, liver, fin, heart, and muscle), we found that BMP genes play diverse regulatory roles during different stages of growth and development and exhibit characteristics of division of labor. CONCLUSIONS: This study contributes to a deeper understanding of BMP gene family member expression patterns in high-altitude, high-salinity environments and provides valuable insights for future research on the BMP gene family in bony fishes.

Four new complete mitochondrial genomes of Gobioninae fishes (Teleostei: Cyprinidae) and their phylogenetic implications.

The subfamily Gobioninae is one of the most diverse fish groups within Cyprinidae. Their taxonomy and phylogenetic relationships are not completely resolved. In this study, the complete mitochondrial genomes (mitogenome) of four Gobioninae species (Microphysogobio elongatus, Microphysogobio chinssuensis, Gobio rivuloides and Rhinogobio nasutus) were sequenced and compared. The mitogenomes of four species ranges from 16603 bp to 16609 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. Most PCGs had significant codon usage bias. Except for the tRNASer (GCT), all the nucleotide substitutions of tRNA loops higher than the stems could fold into a stable secondary structure. The nucleotide compositions of Gobioninae mitogenome were biased toward A/T, and NAD4 was subjected to low purification selection and had a faster evolution rate among 13 PCGs. Bayesian inference and maximum likelihood phylogenetic analyses showed the consistent results. The four sequenced species clustered together with their congener species. However, more samples and mitogenome data are needed to untangle the phylogenetic relationships among genera Microphysogobio, Romanogobio, Hugobio, Biwia and Platysmacheilus.

Janus-type ionic conductive gels based on poly(N,N-dimethyl)acrylamide for strain/pressure sensors.

Strain/pressure sensors with high sensitivity and a wide operation range have broad application prospects in wearable medical equipment, human-computer interactions, electronic skin, and so on. In this work, based on the different solubilities of Zr4+ in the aqueous phase and the hydrophobic ionic liquid [BMIM][Tf2N], we used N,N-dimethylacrylamide (DMA) as a vinyl monomer to prepare a Janus-type ionic conductive gel with one-sided adhesion through "one-step" UV irradiation polymerization. The Janus-type gel has satisfactory mechanical properties (tensile strength: 217.06 kPa, elongation at break: 1121.01%), electrical conductivity (conductivity: 0.10 S m-1), one-sided adhesion (adhesion strength to glass: 72.35 kPa) and antibacterial properties. The sensor based on the Janus gel can be used not only for real-time monitoring of strain changes caused by various movements of the human body (such as finger bending, muscle contraction, smiling, and swallowing) but also for real-time monitoring of pressure changes (such as pressing, water droplets, and writing movements). Therefore, based on the simplicity of this method for constructing Janus-type ionic conductive gels and the excellent electromechanical properties of the prepared gel, we believe that the method provided in this study has broad application prospects in the field of multifunctional wearable sensors.

Integrating regular and transcriptomic analyses reveal resistance mechanisms in Corbicula fluminea (Müller, 1774) in response to toxic Microcystis aeruginosa exposure.

The frequent occurrence of cyanobacterial blooms (CYBs) caused by toxic Microcystis aeruginosa poses a great threat to aquatic organisms. Although freshwater benthic bivalves have proven to be capable of uptake high levels of microcystins (MCs) due to their filter-feeding habits, there is a paucity of information concerning their systemic resistance mechanisms to MCs. In this study, the resistance mechanisms in Corbicula fluminea (O. F. Müller, 1774) in response to the exposure of toxic M. aeruginosa were explored through transcriptional analysis combined with histopathological and biochemical phenotypic analysis. Toxic M. aeruginosa exposure caused dose-dependent histological damage in the hepatopancreas. The conjugation reaction catalyzed by glutathione S-transferases was vulnerable to being activated by high concentrations of M. aeruginosa (10 ×105 cells mL-1). Additionally, reactive oxygen species scavenging processes mediated by superoxide dismutase and catalase were active in the initial stage of toxic M. aeruginosa exposure. The results of the integrated biomarker response index suggested that the biotransformation and antioxidant defense system in C. fluminea could be continuously activated after acute exposure to the high concentration of toxic M. aeruginosa. The eggNOG and GO analysis of the differentially expressed genes (DEGs) indicated that DEGs were significantly enriched in transporter activity, oxidant detoxification and response to oxidative stress categories, which were consistent with the alterations of biochemical indices. Besides, DEGs were significantly annotated in a few KEGG pathways involved in biotransformation (oxidation, cooxidation and conjugation) and immunoreaction (lysosome and phagosome responses), which could be responsible for the tolerance of C. fluminea to toxic M. aeruginosa. These findings improve our understanding of potential resistance mechanisms of freshwater bivalves to MCs.

Mitochondrial genome of Acheilognathusbarbatulus (Cypriniformes, Cyprinidae, Acheilognathinae): characterisation and phylogenetic analysis.

Acheilognathusbarbatulus is distributed in Yangtze River, Yellow River and Pearl River systems in China. Genome data can help to understand the phylogenetic relationships of A.barbatulus, but its complete mitochondrial genome has not been published. We determined the complete mitochondrial genome structure and characteristics of this species and constructed a comprehensive phylogenetic tree, based on mitochondrial genome data of several species of Acheilognathus, Rhodeus and Pseudorasboraparva. The complete length of the mitochondrial genome of A.barbatulus is 16726 bp. The genome is a covalently closed double-stranded circular molecule containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, a D-loop and a light strand replication initiation region. The base composition of the complete mitochondrial genome is A (29.33%) > T (27.6%) > C (26.12%) > G (16.95%), showing a strong AT preference and anti-G bias. All 13 PCGs have different degrees of codon preference, except for cytochrome c oxidase 1, which uses GTG as the start codon. All the PCGs use ATG as the start codon and the stop codon is dominated by TAG. The encoded amino acids Leu and Ser exist in two types, whereas the rest are all present as one type, except for tRNASer (GCT), which lacks the D-arm and has an incomplete secondary structure, all other tRNAs can be folded to form a typical cloverleaf secondary structure. Based on the 13 PCG tandems, the Maximum Likelihood and Bayesian trees were constructed, based on the concatenated sequence of 13 PCGs for the genera Acheilognathus and Rhodeus, with Pseudorasboraparva as the outgroup. Acheilognathusbarbatulus, Acheilognathustonkinensis and Acheilognathuscf.macropterus were clustered together and the most closely related. The results of this study enrich the mitochondrial genomic data of Acheilognathus and provide molecular and genetic base information for species conservation, molecular identification and species evolution of Acheilognathinae.

Genome-wide characterization of the Triplophysa dalaica slc4 gene family and expression profiles in response to salinity changes.

BACKGROUND: The solute carrier 4 (SLC4) gene family is involved in a variety of physiological processes in organisms and is essential for maintaining acid-base balance in the body. The slc4 genes have been extensively studied in mammals, and they play important roles in intracellular and extracellular pH regulation and in the secretion and uptake of HCO3- and other ions (Na+ and Cl-) between transepithelial cells in different tissues. This study identified and characterized the entire slc4 gene family of Triplophysa dalaica. RESULTS: Fifteen slc4 genes were identified in the whole genome of Triplophysa dalaica in this study, including five copies of Na+-independent Cl-/HCO3- transporters, eight members of Na+-dependent HCO3- transporters, and two genes coding Na+-coupled borate transporters. The chromosomal location information, isoelectric points, and molecular weights of the 15 slc4 genes were analyzed. The results for gene structure, domain analysis, and phylogenetic relationships of this gene family showed that the slc4 genes (except for slc4a9, which is missing in teleosts) are significantly expanded in teleosts compared to higher vertebrates. This phenomenon suggests that the slc4 gene family played an important role in the transition from aquatic to terrestrial animals. RT-PCR results showed that different slc4 genes showed diversified expression patterns in the tissues of T. dalaica. For osmotic pressure regulating organs, slc4a1b, slc4a4b, slc4a7, and slc4a11a were highly expressed in gills. In the kidney, slc4a1a, slc4a3, and slc4a10b were highly expressed, suggesting that the slc4 genes play a specific role in the salinity adaptation of T. dalaica. Our study has deciphered the biological roles of the slc4 genes in maintaining ionic and acid-base homeostasis in teleost fishes and provides a foundation for future exploration of the highly differentiated gene family in Triplophysa. CONCLUSIONS: The results are relevant for the breeding of alkali-tolerant varieties in saline-alkali areas for aquaculture. Our findings have important implications for the adaptation process of freshwater species to saline-alkali water.

Large-scale DNA barcoding of the subfamily Culterinae (Cypriniformes: Xenocyprididae) in East Asia unveils a geographical scale effect, taxonomic warnings and cryptic diversity.

Geographical scale might be expected to impact significantly the efficiency of DNA barcoding as spatially comprehensive sampling provides opportunities to uncover intricate relationships among closely related species and to detect cryptic diversity for widespread taxa. Here, we present a DNA barcoding study on a Xencyprididae subfamily (Culterinae) involving the production of 998 newly generated DNA barcodes from East Asian drainages (80 localities). Together with 513 barcodes mined from BOLD and GenBank, a reference library consisting of 1511 DNA barcodes (116 localities) for 42 species was assembled, accounting for 66% of known Culterinae species. Intraspecific genetic distances are positively correlated to geographical scale, while a negative correlation is detected between interspecific genetic distances and geographical scale. The present study demonstrates that geographical scale influences the efficiency of DNA barcoding by narrowing the width of the barcoding gap. DNA-based species delimitation analyses delimited 44 molecular operational taxonomic units (MOTUs). Rampant cryptic diversity is detected within eight species with multiple MOTUs, whereas 25 species present mismatch between morphological and molecular delimitations. A total of 18 species are lumped into nine MOTUs due to low interspecific divergence and/or mixed lineages. Several MOTU divergences are hypothesized to relate to known biogeographical barriers and geological events during the Pliocene and Pleistocene. This study provides new insights into the taxonomy and phylogeography of the subfamily Culterinae.

Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene.

Freshwater shrimp are a rich species group, with a long and problematic taxonomic history attributed to their wide distribution and similar morphological characteristics. Shrimp diversity and species identification are important cornerstones for fisheries management. However, identification based on morphological characteristics is a difficult task for a nonspecialist. Abundant freshwater shrimp species are distributed in the waters of Henan Province, but investigations of freshwater shrimp are limited in this region, especially concerning molecular features. Here, we combined morphology and DNA barcodes to reveal the species diversity of freshwater shrimp in Henan province. A total of 1,200 freshwater shrimp samples were collected from 46 sampling sites, and 222 samples were chosen for further microscopic examination and molecular delimitation. We used tree-based methods (NJ, ML, and bPTP) and distance-based methods (estimation of the paired genetic distances and ABGD) to delimit species. The results showed that there were nine morphospecies based on morphological characteristics; all could effectively be defined by molecular methods, among which bPTP and ABGD defined 13 and 8 MOTUs, respectively. The estimation of the paired genetic distances of K2P and the p-distances had similar results. Mean K2P distances and p-distances within species were both equal to 1.2%. The maximum intraspecific genetic distances of all species were less than 2%, with the exception of Palaemon modestus and M. maculatum. Various analyses have shown that P. modestus and M. maculatum have a large genetic differentiation, which may indicate the existence of cryptic species. By contrast, DNA barcoding could unambiguously discriminate 13 species and detect cryptic diversity. Our results demonstrate the high efficiency of DNA barcoding to delimit freshwater shrimp diversity and detect the presence of cryptic species.

The Chromosome-Level Genome of Triplophysa dalaica (Cypriniformes: Cobitidae) Provides Insights into Its Survival in Extremely Alkaline Environment.

Lake Dali Nur, located in Inner Mongolia, North China, is alkaline, with Triplophysa dalaica one of the three fish species that not only survive, but thrive, in the lake. To investigate the presence of molecular mutations potentially responsible for this adaptation, the whole-genome sequence of the species was sequenced. A total of 126.5 and 106 Gb data, covering nearly 200× of the estimated genome, were generated using long-read sequencing and Hi-C technology, respectively. De novo assembly generated a genome totalled 607.91 Mb, with a contig N50 of 9.27 Mb. Nearly all whole-genome sequences were anchored and oriented onto 25 chromosomes, with telomeres for most chromosomes also being recovered. Repeats comprised approximately 35.01% of the whole genome. A total of 23,925 protein-coding genes were predicted, within which, 98.62% could be functionally annotated. Through comparisons of T. dalaica, T. tibetana, and T. siluroides gene models, a total of 898 genes were identified as likely being subjected to positive selection, with several of them potentially associated with alkaline adaptation, such as sodium bicarbonate cotransporter, SLC4A4. Demographic analyses suggested that the Dali population might have diverged from endemic freshwater Hai River populations, approximately 1 Ma. The high-quality T. dalaica genome, created in this study, not only aids in the analyses of alkaline adaptation, but may also assist in revealing the mysteries of the highly divergent genus Triplophysa in the future.

Homatula guanheensis sp. nov. (Teleostei: Nemacheilidae), a new species of loach from Henan Province, China.

BACKGROUND: The genus Homatula belongs to the order Cypriniformes and family Nemacheilidae. Nichols (1925) set up the genus as a subgenus of Barbatula by the type species of Nemacheilus potanini. Currently, it is recognised as a valid genus. Nineteen valid species have been already reported in the drainage of the Yellow, Yangtze, Pearl, Lancang, Red and Nujiang Rivers. H. variegata, H. longidorsalis, H. berezowskii and H. potanini are distributed in the Yangtze River drainage in China. H. laxiclathra is mainly distributed in the Weihe River, a tributary of the Yellow River. The remaining species are mainly distributed in the rivers of Yunnan Province. NEW INFORMATION: Homatula guanheensis sp. nov., a new species, is described from the Guanhe River of the HanJiang River drainage (a tributary of the Yangtze River), Xixia County, Henan Province, China. It can be distinguished from its congeners by a combination of the following characters: the vertical brown bars on the body are wider than their interspaces, numbering 19-22; predorsal body partially scaled; the lateral line complete; adipose crest on caudal peduncle not reaching forward; the position of the anal-fin origin and the intestinal form. The new species displays distinct molecular divergence in the Cytochrome oxidase I (COI) and Cytochrome b (Cyt b) genes.

Application of DNA barcoding in fish identification of supermarkets in Henan province, China: More and longer COI gene sequences were obtained by designing new primers.

In recent years, DNA barcode technology has been widely used in food identification, especially in the identification of fish. In China, there are few studies on the authenticity of fish products in Henan province of China. In this study, 179 fish samples were collected from supermarkets in Zhengzhou city and Xinxiang city in Henan province, China. COI gene sequences were obtained with PCR technology by designing specific primers and universal primers. COI gene sequences of all samples were obtained to identify species, which is used to investigate species substitution and mislabeling of the fish sold in the two regional markets. The molecular identification results showed that 28.49% (51/179) fish samples were not consistent with the labels. Substitution of high-price fish by low-price fish was prevalent. For example, halibut (Pleuronectiformes) and cod (Gadus) are replaced by striped catfish (Pangasianodon hypophthalmus), and some merchants label bighead carp (Hypophthalmichthys nobilis) as cod (Gadus), there are also accidental labeling errors (such as labels for greenfin horse-faced filefish (Thamnaconus septentrionalis) have been identified as grass carp (Ctenopharyngodon idella) and Wuchang bream (Megalobrama amblycephala) etc. Most of the samples labeled correctly are the fish of low economic value and the fresh fish. This study shows that almost all the commercial fish can be identified by COI DNA barcoding by newly designed primers. Finally, this study also gives a reference of real species of fish fillet in Henan province in China.

Taxonomy of the Hirtodrosophila melanderi species group (Diptera: Drosophilidae), with descriptions of four new species from southwestern China.

The Hirtodrosophila melanderi species group contains nine known species recorded from either the Old or the New World. All these species were thought to be strict fungivorous drosophilids. In the present study, we give supplementary descriptions for three of these known species, all recorded from Yunnan, southwestern China, H. furcapenis, H. furcapenisoides, and H. longifurcapenis, by examining respective type specimen(s). We then describe four new species of the same group, H. seticlasper Katoh Gao, sp. nov., H. spinicerca Katoh Gao, sp. nov., H. serratifurcapenis Katoh Gao, sp. nov., and H. truncifurca Katoh Gao, sp. nov., all discovered recently from high altitudes (ca. 3,500 to 3,800 m a.s.l.) in Tibet (Xizang), southwestern China. The delimitation of these new species is firstly performed in light of morphology and further with the aid of DNA sequences of the mitochondrial COI (cytochrome c oxydase, subunits I) gene. In addition, a key to all the species of the species group is provided.

Label-free proteomic analysis of intestinal mucosa proteins in common carp (Cyprinus carpio) infected with Aeromonas hydrophila.

Outbreaks of infectious diseases in common carp Cyprinus carpio, a major cultured fish in northern regions of China, constantly result in significant economic losses. Until now, information proteomic on immune defence remains limited. In the present study, a profile of intestinal mucosa immune response in Cyprinus carpio was investigated after 0, 12, 36 and 84 h after challenging tissues with Aeromonas hydrophila at a concentration of 1.4 × 108 CFU/mL. Proteomic profiles in different samples were compared using label-free quantitative proteomic approach. Based on MASCOT database search, 1149 proteins were identified in samples after normalisation of proteins. Treated groups 1 (T1) and 2 (T2) were first clustered together and then clustered with control (C group). The distance between C and treated group 3 (T3) represented the maxima according to hierarchical cluster analysis. Therefore, comparative analysis between C and T3 was selected in the following analysis. A total of 115 proteins with differential abundance were detected to show conspicuous expressing variances. A total of 52 up-regulated proteins and 63 down-regulated proteins were detected in T3. Gene ontology analysis showed that identified up-regulated differentially expressed proteins in T3 were mainly localised in the hemoglobin complex, and down-regulated proteins in T3 were mainly localised in the major histocompatibility complex II protein complex. Forty-six proteins of differential abundance (40% of 115) were involved in immune response, with 17 up-regulated and 29 down-regulated proteins detected in T3. This study is the first to report proteome response of carp intestinal mucosa against A. hydrophila infection; information obtained contribute to understanding defence mechanisms of carp intestinal mucosa.

Complete mitochondrial genome of Danio myersi (Teleostei: Cypriniformes: Cyprinidae).

The complete mitochondrial genome (mitogenome) of Danio myersi (Teleostei: Cypriniformes: Cyprinidae) has been sequenced, and it is a circular molecule of 16,565 bp in length and contains the typical complement of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 12 non-coding regions. The order and orientation of the genes are identical to the typical arrangement in vertebrates, and most of the genes were encoded on the H-strand except for ND6 and eight tRNA genes. The AT content of the overall base composition of H-strand is 63.4% (T, 26.8%; C, 25.3%; A, 31.6%; G, 16.4%) and the length of control region is 925 bp with 65.5% AT content. The mitogenome sequenced in the present study will be an important step forward in completely resolving phylogenetic relationships of the subfamily Danioninae in the future.

The complete mitogenome of Acrossocheilus kreyenbergii (Cypriniformes; Cyprinidae).

Acrossocheilus kreyenbergii is a small fish and widely distributed in China, for example, Guangxi, Jiangxi, Zhejiang, Anhui, and also found in Henan province. The complete mitochondrial genome sequence of Acrossocheilus kreyenbergii has been obtained with PCR by using the conservative fragment primers of its closely relative species. Just like most of fishes, the gene composition and arrangement of mitochondrial genome sequence of this species are similar to most of other vertebrates', which including 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and a non-coding control region with total length of 16,849 bp. There is a 270 bp non-coding fragment (from 15,768 to 16,037) in its control region compared with other fish of genus Acrossocheilus. Most of genes are encoded on Heavy-Strand (H-strand), exclude eight tRNA and ND6 genes, which are encoded on Light-Strand (L-strand). The complete mitochondrial genome sequence of Acrossocheilus kreyenbergii would contribute to better understand population genetics, conservation, and diversity of genus Acrossocheilus.

The complete mitogenome of natural triploid Carassius auratus in Qihe River.

Qihe Carassius auratus is the territorial Carassius auratus, which is known as for its limited distribute in Qihe River (mainly distributed in Henan province, China), this species is natural triploid in China. In this study, the complete mitochondrial genome sequence of Carassius auratus in Qihe River has been obtained with PCR. The gene composition and arrangement of mitochondrial genome sequence of this species are similar to most of other vertebrates', which contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes, and a non-coding control region with total length of 16,580 bp. Most of genes are encoded on Heavy-Strand (H-strand), exclude eight tRNA and ND6 genes, which are encoded on Light-Strand (L-strand). The bias of G and C has been found in different regions/genes and different statistic results. The complete mitochondrial genome sequence of this species would contribute to better understand population genetics, conservation, and the evolution of natural triploid.

The complete mitochondrial genome sequence of Schizothorax dolichonema (Cypriniformes: Cyprinidae).

The complete mitochondrial genome sequence of Schizothorax dolichonema has been sequenced, which contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and 2 non-coding regions: origin of light-strand replication and control region, with the total length of 16,583 bp. The gene order and composition are similar to most of other vertebrates. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The mitogenome sequence of S. dolichonema would contribute for better understanding of biogeography and evolution of Schizothoracine fishes.

Biogeographic history and high-elevation adaptations inferred from the mitochondrial genome of Glyptosternoid fishes (Sisoridae, Siluriformes) from the southeastern Tibetan Plateau.

BACKGROUND: The distribution of the Chinese Glyptosternoid catfish is limited to the rivers of the Tibetan Plateau and peripheral regions, especially the drainage areas of southeastern Tibet. Therefore, Glyptosternoid fishes are ideal for reconstructing the geological history of the southeastern Tibet drainage patterns and mitochondrial genetic adaptions to high elevations. RESULTS: Our phylogenetic results support the monophyly of the Sisoridae and the Glyptosternoid fishes. The reconstructed ancestral geographical distribution suggests that the ancestral Glyptosternoids was widely distributed throughout the Brahmaputra drainage in the eastern Himalayas and Tibetan area during the Late Miocene (c. 5.5 Ma). We found that the Glyptosternoid fishes lineage had a higher ratio of nonsynonymous to synonymous substitutions than those found in non-Glyptosternoids. In addition, ωpss was estimated to be 10.73, which is significantly higher than 1 (p-value 0.0002), in COX1, which indicates positive selection in the common ancestral branch of Glyptosternoid fishes in China. We also found other signatures of positive selection in the branch of specialized species. These results imply mitochondrial genetic adaptation to high elevations in the Glyptosternoids. CONCLUSIONS: We reconstructed a possible scenario for the southeastern Tibetan drainage patterns based on the adaptive geographical distribution of the Chinese Glyptosternoids in this drainage. The Glyptosternoids may have experienced accelerated evolutionary rates in mitochondrial genes that were driven by positive selection to better adapt to the high-elevation environment of the Tibetan Plateau.

Expression patterns of Toll-like receptors in natural triploid Carassius auratus after infection with Aeromonas hydrophila.

Toll-like receptors (TLRs) play the important roles in the innate immune system. In the present study, we have cloned fragments of 13 members of TLR family in natural triploid Qihe crucian carp (C. auratus) and investigated the expression profiles of these TLRs in spleen and head kidney at different time points after A. hydrophila infection. The results showed that the expressions of certain TLRs including TLR4, TLR5, and TLR22 were significantly up-regulated after infection, and the expression levels of TLR5 and TLR22 were the highest in spleen with 52.56-fold and 28.14-fold increase, respectively, whereas the other TLRs were down-regulated or no significant changes were observed compared with the control at most time points. These findings suggested that three TLRs (TLR4, TLR5, and TLR22) may play important roles in the immune responses of C. auratus to A. hydrophila infection. Additionally, the expression of most TLRs was significantly up-regulated at 6h post infection, which implied that the immune response of C. auratus reached the highest level at this time point. This work will facilitate our comprehensive understanding for the functions of TLRs in the process of bacterial infection in C. auratus and provide new insights for developing preventive and therapeutic measures against A. hydrophila infection.