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1.
Food Res Int ; 182: 114140, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38519172

RESUMO

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.


Assuntos
Código de Barras de DNA Taxonômico , DNA , Animais , Código de Barras de DNA Taxonômico/métodos , DNA/genética , Produtos Pesqueiros/análise , Primers do DNA , Peixes/genética
2.
ACS Appl Mater Interfaces ; 16(11): 14133-14143, 2024 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-38447141

RESUMO

The unique structural sensitivity of photonic crystals (PCs) endows them with stretchable or elastic tunability for light propagation and spontaneous emission modulation. Hydrogel PCs have been demonstrated to have biocompatibility and flexibility for potential human health detection and environmental security monitoring. However, current elastic PCs still possess a fixed elastic modulus and uncontrollable structural colors based on a tunable elastic modulus, posing considerable challenges for in situ detection, particularly in wearable or portable sensing devices. In this work, we introduced a novel chemo-mechanical transduction mechanism embedded within a photonic crystal nanomatrix, leading to the creation of structural colors and giving rise to a visual gustation sensing experience. By utilizing the captivating structural colors generated by the hydrogel PC, we employ abundant optical information to identify various analytes. The finite element analysis proved the electric field distribution in the PC matrix during stretch operations. The elastic-optical behaviors with various chemical cosolvents, including cations, anions, saccharides, or organic acids, were investigated. The mechanism of the Hofmeister effect regulating the elasticity of hydrogels was demonstrated with the network nanostructure of the hydrogels. The hydrogel PC matrix demonstrates remarkable capability in efficiently distinguishing a wide range of cations, anions, saccharides, and organic acids across various concentrations, mixtures, and even real food samples, such as tastes and soups. Through comprehensive research, a precise relationship between the structural colors and the elastic modulus of hydrogel PCs has been established, contributing to the biomatching elastic-optics platform for wearable devices, a dynamic environment, and clinical or health monitoring auxiliary.


Assuntos
Hidrogéis , Paladar , Humanos , Módulo de Elasticidade , Ânions , Cátions
3.
BMC Genomics ; 25(1): 194, 2024 Feb 19.
Artigo em Inglês | MEDLINE | ID: mdl-38373886

RESUMO

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.


Assuntos
Proteínas Morfogenéticas Ósseas , Cipriniformes , Animais , Filogenia , Proteínas Morfogenéticas Ósseas/genética , Proteínas Morfogenéticas Ósseas/metabolismo , Cipriniformes/genética , Fator de Crescimento Transformador beta/genética , Transcriptoma
4.
PeerJ ; 12: e16632, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38259668

RESUMO

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.


Assuntos
Cyprinidae , Cipriniformes , Genoma Mitocondrial , Animais , Filogenia , Genoma Mitocondrial/genética , Teorema de Bayes , Cyprinidae/genética , Nucleotídeos , RNA de Transferência/genética
5.
Anal Chem ; 96(3): 1205-1213, 2024 01 23.
Artigo em Inglês | MEDLINE | ID: mdl-38191284

RESUMO

Sweat has emerged as a compelling analyte for noninvasive biosensing technology because it contains a wealth of important biomarkers in hormones, organic biomacromolecules, and various ionic mixtures. These components offer valuable insights and can reflect an individual's physiological conditions. Here, we introduced an explainable deep learning (DL)-assisted wearable self-calibrating colorimetric biosensing analysis platform to efficiently and precisely detect the biomarker's concentration in sweat. Specifically, we have integrated the advantages of the colorimetric sensing method, adsorbing-swelling hydrogel, and explainable DL algorithms to develop an enzyme/indicator-immobilized colorimetric patch, which has reliable colorimetric sensing ability and excellent adsorbing-swelling function. A total of 5625 colorimetric images were collected as the analysis data set and assessed two DL algorithms and seven machine learning (ML) algorithms. Zn2+, glucose, and Ca2+ in human sweats could be facilely classified and quantified with 100% accuracy via the convolutional neural network (CNN) model, and the testing results of actual sweats via the DL-assisted colorimetric approach are 91.7-97.2% matching with the classical UV-vis spectrum. Class activation mapping (CAM) was utilized to visualize the inner working mechanism of CNN operation, which contributes to verify and explicate the design rationality of the noninvasive biosensing technology. An "end-to-end" model was established to ascertain the black box of the DL algorithm, promoted software design or principium optimization, and contributed facile indicators for health monitoring, disease prevention, and clinical diagnosis.


Assuntos
Aprendizado Profundo , Humanos , Suor , Colorimetria , Redes Neurais de Computação , Algoritmos
6.
ACS Nano ; 17(5): 5129-5139, 2023 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-36876910

RESUMO

A particular sense, touchable gustation, was achieved. We proposed a chemical-mechanical interface strategy with an iontronic sensor device. A conductive hydrogel, amino trimethylene phosphonic acid (ATMP) assisted poly(vinyl alcohol) (PVA), was employed as the dielectric layer of the gel iontronic sensor. The Hofmeister effect of the ATMP-PVA hydrogel was well investigated to establish the quantitative description of the gel elasticity modulus to chemical cosolvents. The mechanical properties of hydrogels can be transduced extensively and reversibly by regulating the aggregation state of polymer chains with hydrated ions or cosolvents. Scanning electron microscopy (SEM) images of ATMP-PVA hydrogel microstructures stained with different soaked cosolvents present different networks. The information on different chemical components will be stored in the ATMP-PVA gels. The flexible gel iontronic sensor with a hierarchical pyramid structure performed high linear sensitivity of 3224.2 kPa-1 and wide pressure response in the range of 0-100 kPa. The finite element analysis proved the pressure distribution at the gel interface of the gel iontronic sensor and the capacitation-stress response relation. Various cations, anions, amino acids, and saccharides can be discriminated, classified, and quantified with the gel iontronic sensor. The Hofmeister effect regulated chemical-mechanical interface performs the response and conversion of biological/chemical signals into electrical output in real time. The particular function to tactile with gustation percept will contribute promising applications in the human-machine interaction, humanoid robot, clinic treatment, or athletic training optimization.

7.
Anal Chem ; 95(6): 3309-3316, 2023 02 14.
Artigo em Inglês | MEDLINE | ID: mdl-36716054

RESUMO

Photochromic sensors have the advantages of diverse isomers for multi-analysis, providing more sensing information and possessing more recognition units and more sensitivity to external stimulations, but they present enormous complexity with various stimulations as well. Deep learning (DL) algorithms contribute a huge advantage at analyzing nonlinear and multidimensional data, but they suffer from nontransparent inner networks, "black-boxes". In this work, we employed the explainable DL approach to process and explicate photochromic sensing. Spirooxazine metallic complexes were adopted to prepare a multi-state analysis array for ß-Lactams identification and quantitation. A dataset of 2520 unduplicated fluorescence intensity images was collected for convolutional neural network (CNN) operation. The method clearly discriminated six ß-Lactams with 97.98% prediction accuracy and allowed rapid quantification with a concentration range from 1 to 100 mg/L. The photochromic sensing mechanism was verified via molecular simulation and class activation mapping, which explicated how the CNN model assesses the importance of photochromic sensor states and makes a discrimination decision. The explainable DL-assisted analysis method establishes an end-to-end strategy to ascertain and verify the complicated sensing mechanism for device optimization and even new scientific discovery.


Assuntos
Aprendizado Profundo , Redes Neurais de Computação , Algoritmos , beta-Lactamas , Antibacterianos
8.
Biodivers Data J ; 11: e93947, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-38327321

RESUMO

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.

9.
BMC Genomics ; 23(1): 824, 2022 Dec 13.
Artigo em Inglês | MEDLINE | ID: mdl-36513970

RESUMO

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.


Assuntos
Cipriniformes , Salinidade , Animais , Filogenia , Cipriniformes/genética , Sódio/metabolismo , Álcalis , Mamíferos/metabolismo
10.
DNA Res ; 29(4)2022 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-35861387

RESUMO

Gymnocypris przewalskii, a cyprinid fish endemic to the Qinghai-Tibetan Plateau, has evolved unique morphological, physiological and genetic characteristics to adapt to the highland environment. Herein, we assembled a high-quality G. przewalskii tetraploid genome with a size of 2.03 Gb and scaffold N50 of 44.93 Mb, which was anchored onto 46 chromosomes. The comparative analysis suggested that gene families related to highland adaptation were significantly expanded in G. przewalskii. According to the G. przewalskii genome, we evaluated the phylogenetic relationship of 13 schizothoracine fishes, and inferred that the demographic history of G. przewalskii was strongly associated with geographic and eco-environmental alterations. We noticed that G. przewalskii experienced whole-genome duplication, and genes preserved post duplication were functionally associated with adaptation to high salinity and alkalinity. In conclusion, a chromosome-scale G. przewalskii genome provides an important genomic resource for teleost fish, and will particularly promote our understanding of the molecular evolution and speciation of fish in the highland environment.


Assuntos
Carpas , Cyprinidae , Adaptação Fisiológica/genética , Animais , Carpas/genética , Cromossomos/genética , Cyprinidae/genética , Filogenia , Tibet
11.
Anal Chem ; 94(22): 7936-7943, 2022 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-35608073

RESUMO

Drug abuse is seriously endangering human health and jeopardizing society. There is an urgent need for rapid, sensitive, portable, and easy-to-operate methods for the daily detection of drugs in biological matrices. However, current drug detection methods based on chromatography, spectroscopy, immunosorbent assays, etc. are limited by the requirements of high logistical instruments and laboratory. Herein, we proposed a wearable electrochemical aptasensor with high sensitivity and specificity for the direct capture and rapid detection of multiple drugs in sweat. The single aptamer and dual aptamers with different base compositions were designed to compose the aptasensor array. Molecular docking simulations demonstrated different binding affinities between bioamines and aptamers. The developed aptasensor array is shown to be sufficient to generate distinct electrochemical fingerprints for different psychoactive drugs and interfering substances by extracting variable features from electrochemical signals. Sixteen analytes in the same concentration or gradient concentrations were identified with 100% accuracy. In addition, the wearable sensor platform was demonstrated to discriminate various drugs with similar chemical structures in artificial sweat and human sweat samples. The sensor array not only provided a new rapid method for the detection of drugs but also served as a reference for developing wearable sensors for onsite and daily testing of human biochemical information.


Assuntos
Aptâmeros de Nucleotídeos , Técnicas Biossensoriais , Aptâmeros de Nucleotídeos/química , Bioensaio , Técnicas Biossensoriais/métodos , Técnicas Eletroquímicas/métodos , Humanos , Limite de Detecção , Simulação de Acoplamento Molecular , Suor/química
12.
Natl Sci Rev ; 9(12): nwac291, 2022 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-36778108

RESUMO

Apparent cases of sympatric speciation may actually be due to micro-allopatric or micro-parapatric speciation. One way to distinguish between these models is to examine the existence and nature of genomic islands of divergence, wherein divergent DNA segments are interspersed with low-divergence segments. Such islands should be rare or absent under micro-allopatric speciation but common in cases of speciation with gene flow. Sympatric divergence of endemic fishes is known from isolated saline, crater, postglacial, and ancient lakes. Two morphologically distinct cyprinid fishes, Gymnocypris eckloni scoliostomus (GS) and G. eckloni eckloni (GE), in a small glacial lake on the Qinghai-Tibet Plateau, Lake Sunmcuo, match the biogeographic criteria of sympatric speciation. In this study, we examined genome-wide variation in 46 individuals from these two groups. The divergence time between the GS and GE lineages was estimated to be 20-60 Kya. We identified 54 large genomic islands (≥100 kb) of speciation, which accounted for 89.4% of the total length of all genomic islands. These islands harboured divergent genes related to olfactory receptors and olfaction signals that may play important roles in food selection and assortative mating in fishes. Although the genomic islands clearly indicated speciation with gene flow and rejected micro-allopatric speciation, they were too large to support the hypothesis of sympatric speciation. Theoretical and recent empirical studies suggested that continual gene flow in sympatry should give rise to many small genomic islands (as small as a few kilobases in size). Thus, the observed pattern is consistent with the extensive evidence on parapatric speciation, in which adjacent habitats facilitate divergent selection but also permit gene flow during speciation. We suggest that many, if not most, of the reported cases of sympatric speciation are likely to be micro-parapatric speciation.

13.
ACS Appl Mater Interfaces ; 13(50): 60689-60696, 2021 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-34902964

RESUMO

Inspired by the spider's slit organ embedded in the leg joint exoskeleton and its ultrasensitive stress perception, we propose to fix the conflict between the stress concentration requirement for bright mechanoluminescence (ML) and the stress dispersion effect of soft material via integrating slit microstructures into flexible films. The designed slits focus weak stresses onto the corner to achieve high sensitivity, leading to 10-30 times ML intensity improvement at weak strain (<10% stretch) application. Slit morphology and various patterns were well investigated to address the stress distribution regularity. The slit-based ML film offers a facile light-luminescent artificial skin for visualizable stress presentations or detections without electricity power source. It is a practical endeavor of photonic skin for visible vocalization and a significant contribution to dysaudia auxiliary or luminescence augmented expressions for human social interactions, similar to jellyfish or squids.


Assuntos
Materiais Biocompatíveis/química , Articulação do Joelho/química , Medições Luminescentes , Pele/química , Dispositivos Eletrônicos Vestíveis , Animais , Humanos , Perna (Membro) , Teste de Materiais , Aranhas , Estresse Mecânico
14.
Micromachines (Basel) ; 12(7)2021 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-34357199

RESUMO

Ionic hydrogels with intrinsic conductivity and stretchability show great potential in flexible electronics. However, it remains a great challenge to achieve hydrogels with mechanical stretchability, ionic conductivity, optical transparency, and a self-healing ability at the same time. In this paper, we developed a hydroxyethylidene diphosphonic acid (HEDP) assisted poly(vinyl alcohol) (PVA) composite hydrogel to achieve high-performance stretch-sensitive sensor. Through a facile freeze-thaw strategy, the hydrogel could achieve large stretchability (up to 950% strain), good conductivity (10.88 S/m), excellent linear sensitivity (GF = 2.72, within 100% strain), high transparency, and significant self-healing ability. The PVA-HEDP hydrogel-based strain sensor is capable of monitoring various human movements from small scale (e.g., laryngeal vibration while speaking) to large scale (e.g., knee joint movement). Moreover, the multisite sensor array is capable of detecting the subtle differences between the pulse wave features from Cun, Guan and Chi positions, mimicking the three-finger palpation in Traditional Chinese Medicine. This work demonstrates that the composite hydrogel-based flexible sensor provides a promising solution for multifunctional human activities and health monitoring.

15.
Ecol Evol ; 11(15): 10502-10514, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34367592

RESUMO

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.

16.
Genome Biol Evol ; 13(8)2021 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-34185063

RESUMO

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.


Assuntos
Cipriniformes , Adaptação Fisiológica/genética , Animais , Cromossomos , Cipriniformes/genética , Genoma , Filogenia
17.
Biodivers Data J ; 9: e65130, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34177310

RESUMO

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.

18.
Genome Biol Evol ; 13(5)2021 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-33892511

RESUMO

Understanding how organisms adapt to aquatic life at high altitude is fundamental in evolutionary biology. This objective has been addressed primarily related to hypoxia adaptation by recent comparative studies, whereas highland fish has also long suffered extreme alkaline environment, insight into the genomic basis of alkaline adaptation has rarely been provided. Here, we compared the genomes or transcriptomes of 15 fish species, including two alkaline tolerant highland fish species and their six alkaline intolerant relatives, three alkaline tolerant lowland fish species, and four alkaline intolerant species. We found putatively consistent patterns of molecular evolution in alkaline tolerant species in a large number of shared orthologs within highland and lowland fish taxa. Remarkably, we identified consistent signatures of accelerated evolution and positive selection in a set of shared genes associated with ion transport, apoptosis, immune response, and energy metabolisms in alkaline tolerant species within both highland and lowland fish taxa. This is one of the first comparative studies that began to elucidate the consistent genomic signature of alkaline adaptation shared by highland and lowland fish. This finding also highlights the adaptive molecular evolution changes that support fish adapting to extreme environments at high altitude.


Assuntos
Cyprinidae/genética , Adaptação Fisiológica , Álcalis/metabolismo , Altitude , Animais , Cyprinidae/classificação , Cyprinidae/fisiologia , Evolução Molecular , Feminino , Masculino , Filogenia , Salinidade , Seleção Genética , Tibet
19.
Food Res Int ; 136: 109516, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32846590

RESUMO

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.


Assuntos
Código de Barras de DNA Taxonômico , Supermercados , Animais , China , Produtos Pesqueiros/análise , Peixes/genética , Cavalos
20.
Zool Res ; 41(4): 465-470, 2020 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-32543793

RESUMO

A new species of Tibetan loach, Triplophysa weiheensis sp. nov., is described from the Weihe River in Gansu Province, China, based on morphological and molecular analyses. The new species can be distinguished from all known congeners by a unique combination of the following characters: scaleless; snout abruptly sloping downward, anterior to anterior nostril; lower jaw crescentic, not sharp; body without obvious mottling; lateral line interrupted on posterior trunk at pelvic-fin distal extremity; caudal-peduncle length 2.0-2.7 times its depth; branched rays of pectoral fin 10-11; branched rays of pelvic fin 5-6; inner gill rakers on 1 st gill arch 14-16; vertebrae 4+34-36; intestine with 6-7 loops, length ca. 1.8 times SL ( n=3); bony capsule of air bladder small and thin; posterior chamber of air bladder absent.


Assuntos
Cipriniformes/classificação , Animais , China , Cipriniformes/anatomia & histologia , Cipriniformes/genética , Citocromos b/análise , Feminino , Proteínas de Peixes/análise , Masculino , Filogenia , Rios , Análise de Sequência de DNA/veterinária
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