The first chromosomal-level genome assembly and annotation of white suckerfish Remora albescens.

Remora albescens, also known as white suckerfish, recognized for its distinctive suction-cup attachment behavior and medicinal significance. In this study, we produced a high-quality chromosome-level genome assembly of R. albescens through the integration of 23.87 Gb PacBio long reads, 64.54 Gb T7 short reads, and 88.63 Gb Hi-C data. Initially, we constructed a contig-level genome assembly totaling 605.30 Mb with a contig N50 of 23.12 Mb. Subsequently, employing Hi-C technology, approximately 99.68% (603.38 Mb) of the contig-level genome was successfully assigned to 23 pseudo-chromosomes. Through the integration of homologous-based predictions, ab initio predictions, and RNA-sequencing methods, we successfully identified a comprehensive set of 22,445 protein-coding genes. Notably, 96.36% (21,629 genes) of these were effectively annotated with functional information. The genome assembly achieved an estimated completeness of 98.1% according to BUSCO analysis. This work promotes the applicability of the R. albescens genome, laying a solid foundation for future investigations into genomics, biology, and medicinal importance within this species.

The feedback of greening on local hydrothermal conditions in Northern China.

Northern China has experienced a significant increase in vegetation cover over the past few decades. It lacks a comprehensive understanding of how greening impacts local hydrothermal conditions. To address this issue, in our study, the RegCM-CLM45 model was used to conduct a thorough assessment of the impacts of greening on temperature, vapor pressure deficit (VPD), precipitation, and soil moisture. The findings revealed that the local climatic effects of greening varied across different drought gradients based on the aridity index (AI). In drier regions with AI<0.3, the increased energy induced by greening tended to dissipate as sensible heat, exacerbating both warming and drought conditions. Conversely, in wetter regions with AI>0.3, a greater proportion of energy was lost through evapotranspiration, attenuating warming. Additionally, greening enhanced precipitation and soil moisture in drier regions and moderated their decline in wetter regions. Significantly, our research emphasized the effectiveness of grassland expansion and conservation as prime strategies for ecological restoration, particularly in drylands, where they could effectively alleviate soil drought. Given the diverse responses of different land cover transformations to local hydrothermal conditions in drylands, there is an urgent need to address potential adverse effects arising from inappropriate ecological restoration strategies and to develop an optimal restoration framework for the future.

Imbalance in lake variability but not embodying driving factors on the Qinghai-Tibetan Plateau calls on heterogeneous lake management.

Comprehensive regional remote analysis tends to neglect lakes in exorheic basins on the Qinghai-Tibetan Plateau (QTP), and a concurrent lack of discussions on whether there exist imbalanced explanations for the driving forces of both internal and external lakes is also present. We integrate multisourced lake datasets, high-resolution information, and available altimetry datasets to establish multiple mathematical models to meta-simulate lake volume changes, extend current lake variation datasets, and quantify the imbalance of variations and factors driving the water mass budget. The results showed that the primary cause of lake variations in QTP is net precipitation (57.75 ± 31.46%), followed by glacier runoff (33.53 ± 31.42%), and permafrost (8.34 ± 7.87%). Even though glacier runoff is currently considered as a weak factor of lake variation, heterogeneous results call for remaining attention in glacier-induced lake basins. Imbalance embodying in lake variability but not in contributions of driving factors, which calls for special lake management ways in different watersheds.

The Role of Introgression During the Radiation of Endemic Fishes Adapted to Living at Extreme Altitudes in the Tibetan Plateau.

Recent genomic analyses of evolutionary radiations suggest that ancient introgression may facilitate rapid diversification and adaptive radiation. The loach genus Triplophysa, a genus with most species endemic to Tibetan Plateau, shows ecological diversity and rapid evolution and represents a potential example of adaptive radiation linked to the uplift of the Tibetan Plateau. Here, we interrogate the complex evolutionary history of Triplophysa fishes through the analysis of whole-genome sequences. By reconstructing the phylogeny of Triplophysa, quantifying introgression across this clade, and simulating speciation and migration processes, we confirm that extensive gene flow events occurred across disparate Triplophysa species. Our results suggest that introgression plays a more substantial role than incomplete lineage sorting in underpinning phylogenetic discordance in Triplophysa. The results also indicate that genomic regions affected by ancient gene flow exhibit characteristics of lower recombination rates and nucleotide diversity and may associate with selection. Simulation analysis of Triplophysa tibetana suggests that the species may have been affected by the Gonghe Movement in the third uplift of the Tibetan Plateau, resulting in founder effects and a subsequent reduction in Ne.

Biofilm-Based Biocatalysis for Galactooligosaccharides Production by the Surface Display of ß-Galactosidase in Pichia pastoris.

Galactooligosaccharides (GOS) are one of the most important functional oligosaccharide prebiotics. The surface display of enzymes was considered one of the most excellent strategies to obtain these products. However, a rough industrial environment would affect the biocatalytic process. The catalytic process could be efficiently improved using biofilm-based fermentation with high resistance and activity. Therefore, the combination of the surface display of ß-galactosidase and biofilm formation in Pichia pastoris was constructed. The results showed that the catalytic conversion rate of GOS was up to 50.3% with the maximum enzyme activity of 5125 U/g by screening the anchorin, and the number of the continuous catalysis batches was up to 23 times. Thus, surface display based on biofilm-immobilized fermentation integrated catalysis and growth was a co-culture system, such that a dynamic equilibrium in the consolidated integrative process was achieved. This study provides the basis for developing biofilm-based surface display methods in P. pastoris during biochemical production processes.

Fast Image Super-Resolution Using Particle Swarm Optimization-Based Convolutional Neural Networks.

Image super-resolution based on convolutional neural networks (CNN) is a hot topic in image processing. However, image super-resolution faces significant challenges in practical applications. Improving its performance on lightweight architectures is important for real-time super-resolution. In this paper, a joint algorithm consisting of modified particle swarm optimization (SMCPSO) and fast super-resolution convolutional neural networks (FSRCNN) is proposed. In addition, a mutation mechanism for particle swarm optimization (PSO) was obtained. Specifically, the SMCPSO algorithm was introduced to optimize the weights and bias of the CNNs, and the aggregation degree of the particles was adjusted adaptively by a mutation mechanism to ensure the global searching ability of the particles and the diversity of the population. The results showed that SMCPSO-FSRCNN achieved the most significant improvement, being about 4.84% better than the FSRCNN model, using the BSD100 data set at a scale factor of 2. In addition, a chest X-ray super-resolution images classification test experiment was conducted, and the experimental results demonstrated that the reconstruction ability of this model could improve the classification accuracy by 13.46%; in particular, the precision and recall rate of COVID-19 were improved by 45.3% and 6.92%, respectively.

Molecular cloning and tissue distribution of the leptin gene in gibel carp (Carassius auratus gibelio): Regulation by postprandial and long-term fasting treatment.

Leptin is a multifunctional hormone that serves as a feeding regulator in mammals. However, the effect of leptin on fish remains unclear. We sequenced the leptin gene from gibel carp (Carassius auratus gibelio) and designated it gLEP. The length of the gLEP cDNA sequence was 562 bp, including an open reading frame (ORF) of 516 bp. The ORF putatively encodes a peptide of 171 amino acids, including a signal peptide of 20 amino acids. gLEP shared low primary amino acid sequence homology with leptin genes in vertebrates, whereas three-dimensional (3D) structural modeling revealed strong identity with the structures in other vertebrates. gLEP mRNA was widely distributed in all of the tissue that we examined, with the highest levels of expression in the hepatopancreas. Hepatopancreas gLEP mRNA expression levels showed no changes following postprandial treatment. However, hepatopancreas gLEP mRNA expression levels greatly decreased (P < 0.05) after fasting but substantially increased (P < 0.05) after refeeding in the long-term fasting treatment. In summary, these results indicate that leptin expression could be influenced by the regulation of food intake. These results provide the initial step toward elucidating the appetite regulatory systems associated with leptin in gibel carp.

Genome and population evolution and environmental adaptation of Glyptosternon maculatum on the Qinghai-Tibet Plateau.

Persistent uplift means the Qinghai-Tibet Plateau (QTP) is an ideal natural laboratory to investigate genome evolution and adaptation within highland environments. However, how paleogeographic and paleoclimatic events influence the genome and population of endemic fish species remains unclear. Glyptosternon maculatum is an ancient endemic fish found on the QTP and the only critically endangered species in the Sisoridae family. Here, we found that major transposons in the G. maculatum genome showed episodic bursts, consistent with contemporaneous geological and climatic events during the QTP formation. Notably, histone genes showed significant expansion in the G. maculatum genome, which may be mediated by long interspersed nuclear elements (LINE) repetitive element duplications. Population analysis showed that ancestral G. maculatum populations experienced two significant depressions 2.6 million years ago (Mya) and 10 000 years ago, exhibiting excellent synchronization with Quaternary glaciation and the Younger Dryas, respectively. Thus, we propose that paleogeography and paleoclimate were dominating driving forces for population dynamics in endemic fish on the QTP. Tectonic movements and temperature fluctuation likely destroyed the habitat and disrupted the drainage connectivity among populations. These factors may have caused severe bottlenecks and limited migration among ancestral G. maculatum populations, resulting in the low genetic diversity and endangered status of the species today.

3DPhenoFish: Application for two- and three-dimensional fish morphological phenotype extraction from point cloud analysis.

Fish morphological phenotypes are important resources in artificial breeding, functional gene mapping, and population-based studies in aquaculture and ecology. Traditional morphological measurement of phenotypes is rather expensive in terms of time and labor. More importantly, manual measurement is highly dependent on operational experience, which can lead to subjective phenotyping results. Here, we developed 3DPhenoFish software to extract fish morphological phenotypes from three-dimensional (3D) point cloud data. Algorithms for background elimination, coordinate normalization, image segmentation, key point recognition, and phenotype extraction were developed and integrated into an intuitive user interface. Furthermore, 18 key points and traditional 2D morphological traits, along with 3D phenotypes, including area and volume, can be automatically obtained in a visualized manner. Intuitive fine-tuning of key points and customized definitions of phenotypes are also allowed in the software. Using 3DPhenoFish, we performed high-throughput phenotyping for four endemic Schizothoracinae species, including Schizopygopsis younghusbandi, Oxygymnocypris stewartii, Ptychobarbus dipogon, and Schizothorax oconnori. Results indicated that the morphological phenotypes from 3DPhenoFish exhibited high linear correlation (>0.94) with manual measurements and offered informative traits to discriminate samples of different species and even for different populations of the same species. In summary, we developed an efficient, accurate, and customizable tool, 3DPhenoFish, to extract morphological phenotypes from point cloud data, which should help overcome traditional challenges in manual measurements. 3DPhenoFish can be used for research on morphological phenotypes in fish, including functional gene mapping, artificial selection, and conservation studies. 3DPhenoFish is an open-source software and can be downloaded for free at https://github.com/lyh24k/3DPhenoFish/tree/master.

Chromosome-level genome assembly of the Chinese longsnout catfish Leiocassis longirostris.

The Chinese longsnout catfish ( Leiocassis longirostris Günther) is one of the most economically important freshwater fish in China. As wild populations have declined sharply in recent years, it is also a valuable model for research on sexual dimorphism, comparative biology, and conservation. However, the current lack of high-quality chromosome-level genome information for the species hinders the advancement of comparative genomic analysis and evolutionary studies. Therefore, we constructed the first high-quality chromosome-level reference genome for L. longirostris. The total genome was 703.19 Mb, with 389 contigs and contig N50 length of 4.29 Mb. Using high-throughput chromosome conformation capture (Hi-C) data, the genome sequences (685.53 Mb) were scaffolded into 26 chromosomes ranging from 17.36 to 43.97 Mb, resulting in a chromosomal anchoring rate for the genome of 97.44%. In total, 23 708 protein-coding genes were identified in the genome. Phylogenetic analysis indicated that L. longirostris and its closest related species P. fulvidraco diverged approximately 26.6 million years ago. This high-quality reference genome of L. longirostris should pave the way for future genomic comparisons and evolutionary research.

Characterization and evaluation of the tissue distribution of CRH, apelin, and GnRH2 reveal responses to feeding states in Schizothorax davidi.

Schizothorax davidi is a rare fish in Southwest China and is considered a promising species for aquaculture. Compared with other teleosts, little is known about the endocrine regulation of feeding in this species. In this study, we identified the CRH, apelin, and GnRH2 genes in S. davidi and assessed the effects of different energy statuses on CRH, apelin, and GnRH2 expression. Our results showed that the full-length cDNA sequences of CRH, apelin, and GnRH2 of S. davidi were 995, 905, and 669 bp long, respectively. Furthermore, CRH was mainly expressed in the hypothalamus, telencephalon, and myelencephalon; apelin was highly expressed in the spleen and heart; and GnRH2 mRNA was widely distributed in all examined tissues, with the highest level in the hypothalamus. Notably, the levels of CRH and GnRH2 increased in the hypothalamus at 1 h and 3 h post-feeding, while hypothalamic apelin levels decreased. Conversely, CRH and GnRH2 expression in the hypothalamus significantly decreased after fasting for 7 days and returned to the control levels after re-feeding for 3 or 5 days. In contrast, fasting increased apelin levels in the hypothalamus. Overall, this study suggests that CRH, apelin, and GnRH2 play critical roles in appetite regulation in S. davidi. These results provide an essential groundwork to elucidate the appetite regulatory systems in S. davidi as well as in other teleosts.

Genome of Tetraploid Fish Schizothorax o'connori Provides Insights into Early Re-diploidization and High-Altitude Adaptation.

Whole-genome duplications (WGDs) of Schizothoracinae are believed to have played a significant role in speciation and environmental adaptation on the Qinghai-Tibet Plateau (QTP). Here, we present a genome for Schizothorax o'connori, a QTP endemic fish and showed the species as a young tetraploid with a recent WGD later than ∼1.23 mya. We exhibited that massive insertions between duplicated genomes caused by transposon bursts could induce mutagenesis in adjacent sequences and alter the expression of neighboring genes, representing an early re-diploidization process in a polyploid genome after WGD. Meanwhile, we found that many genes involved in DNA repair and folate transport/metabolism experienced natural selection and might contribute to the environmental adaptation of this species. Therefore, the S. o'connori genome could serve as a young tetraploid model for investigations of early re-diploidization in polyploid genomes and offers an invaluable genetic resource for environmental adaptation studies of the endemic fish of the QTP.

Full-length transcript sequencing accelerates the transcriptome research of Gymnocypris namensis, an iconic fish of the Tibetan Plateau.

Gymnocypris namensis, the only commercial fish in Namtso Lake of Tibet in China, is rated as nearly threatened species in the Red List of China's Vertebrates. As one of the highest-altitude schizothorax fish in China, G. namensis has strong adaptability to the plateau harsh environment. Although being an indigenous economic fish with high value in research, the biological characterization, genetic diversity, and plateau adaptability of G. namensis are still unclear. Here, we used Pacific Biosciences single molecular real time long read sequencing technology to generate full-length transcripts of G. namensis. Sequences clustering analysis and error correction with Illumina-produced short reads to obtain 319,044 polished isoforms. After removing redundant reads, 125,396 non-redundant isoforms were obtained. Among all transcripts, 103,286 were annotated to public databases. Natural selection has acted on 42 genes for G. namensis, which were enriched on the functions of mismatch repair and Glutathione metabolism. Total 89,736 open reading frames, 95,947 microsatellites, and 21,360 long non-coding RNAs were identified across all transcripts. This is the first study of transcriptome in G. namensis by using PacBio Iso-seq. The acquisition of full-length transcript isoforms might accelerate the transcriptome research of G. namensis and provide basis for further research.

The Regional Impact of Ecological Restoration in the Arid Steppe on Dust Reduction over the Metropolitan Area in Northeastern China.

A massive ecological restoration program has been implemented in northern China with the aim of protecting the Beijing-Tianjin-Hebei metropolitan area of eastern China from dust events. However, some current studies have cast doubt on the efficacy of such ecological restoration projects, partly due to the constraint of available water in northern China, leading to poor survival rates of planted trees in semiarid regions (15%). In this study, using a logical framework combining statistical analysis, partial least-squares path model analysis, and a regional climate model (RegCM) simulation with multisource dust indicators, we found that there was a reduction of dust in northern China that was synchronous with the increase in vegetation growth after ecological restoration. In contrast to previous reports of a decrease in wind speed due to ecological restoration, this study found that the increase in vegetation had an insignificant impact on local wind speed (p = 0.30). Instead, ecological restoration mainly reduced the sand emission in steppe area by improving the soil conditions of the underlying surface, and hence contributed 15% of the reduction of dust events in the Beijing-Tianjin-Hebei metropolitan area through dust transmission (p = 0.002). The effect of ecological restoration in the northern steppe on dust reduction over the northeastern metropolitan area of China should not be overstated.

Effects of feeding status on nucb1 and nucb2A mRNA expression in the hypothalamus of Schizothorax davidi.

NUCB1 and NUCB2, two novel nucleobindins, have attracted extensive attention for their role in the appetite regulation in mammals. However, little is known about the appetite regulation of NUCB1 and NUCB2 in fish species. Therefore, we investigated the role of these peptides in the regulation of feeding in Schizothorax davidi (S. davidi). In this study, full-length cDNA sequences of nucb1 and nucb2A of S. davidi were obtained for the first time. Additionally, the tissue distribution and the effects of different energy status on nucb1 and nucb2A mRNAs abundance were assessed, showing that nucb1 and nucb2A are widely distributed in 18 detected tissues, with the highest expression in the cerebellum. The abundances of nucb1 and nucb2A increased in the hypothalamus at 1 h and 3 h post-feeding. Furthermore, fasting and re-feeding experiments showed that the expressions of nucb1 and nucb2A in hypothalamus significantly decreased after fasting for 7 days, and returned to the control level after re-feeding for 3 or 5 days. In conclusion, the present study suggests that both NUCB1 and NUCB2A are involved in the short-term and long-term appetite regulation, as an anorexigenic factor, in S. davidi. These results can provide a basis for further investigation into the appetite regulatory role of NUCB family in teleost.

Genome Sequence of Novoherbaspirillum sp. UKPF54, a Plant Growth-Promoting Rhizobacterial Strain with N2O-Mitigating Abilities, Isolated from Paddy Soil.

Novoherbaspirillum sp. strain UKPF54, a plant growth-promoting rhizobacterium with the ability to mitigate nitrous oxide emission from agriculture soils, has been successfully isolated from paddy soil in Kumamoto, Japan. Here, we report the whole-genome sequence of this strain.

Comprehensive transcriptome data for endemic Schizothoracinae fish in the Tibetan Plateau.

The Schizothoracinae fishes, endemic species in the Tibetan Plateau, are considered as ideal models for highland adaptation and speciation investigation. Despite several transcriptome studies for highland fishes have been reported before, the transcriptome information of Schizothoracinae is still lacking. To obtain comprehensive transcriptome data for Schizothoracinae, the transcriptome of a total of 183 samples from 14 representative Schizothoracinae species, were sequenced and de novo assembled. As a result, about 1,363 Gb transcriptome clean data was obtained. After the assembly, we obtain 76,602-154,860 unigenes for each species with sequence N50 length of 1,564-2,143 bp. More than half of the unigenes were functionally annotated by public databases. The Schizothoracinae fishes in this work exhibited diversified ecological distributions, phenotype characters and feeding habits; therefore, the comprehensive transcriptome data of those species provided valuable information for the environmental adaptation and speciation of Schizothoracinae in the Tibetan Plateau.

Cloning, expression profiling, and effects of fasting status on neuropeptide Y in Schizothorax davidi.

To better comprehend the mechanism that neuropeptide Y (npy) regulates feeding in Schizothorax davidi, we cloned and identified the full-length cDNA sequence of the npy gene in this species using RACE technology. Subsequently, we explored the npy mRNA distribution in 18 tissues and investigated the expression of npy mRNA at postprandial and fasting stages. We found that the npy full-length cDNA sequence is 803 bp. Moreover, npy mRNAs extensively expressed in all detected tissues, with the highest expression in hypothalamus. In postprandial study, the expression of npy mRNA in the hypothalamus was significantly decreased after eating (p < 0.01). In addition, the expression of the npy gene was significantly increased on the fifth day after fasting (p < 0.05). However, after refeeding, the expression of the npy gene was decreased significantly on days 9, 11, and 14 (p < 0.01). Our research suggest that npy may have an orexigenic role in S. davidi. PRACTICAL APPLICATIONS: S. davidi, a coldwater fish native to China, has high economic value, and it has gained great popularity. To date, there is still no large-scale breeding of S. davidi in China. How to strengthen the production performance of S. davidi is a hot research area. Neuropeptide Y (NPY), a 36-amino-acid single-chain polypeptide, is one of the main appetite regulation factors. However, to date, no studies have reported on the biological function of npy in the feeding of S. davidi. In our study, we revealed that the trend of hypothalamic npy expression during the postprandial and fasting stages. The results suggested that npy might be an appetite-promoting factor in this species. Overall, we provide the theoretical basis for how to strengthen the production performance of S. davidi through appetite regulation.

Three forms of cocaine- and amphetamine-regulated transcript may be involved in food intake regulation in gibel carp (Carassius auratus gibelio).

In fish, as in mammals, several studies have demonstrated that the cocaine- and amphetamine-regulated transcript (CART) plays an important role in feeding. However, thus far, the function of CART in gibel carp (Carassius auratus gibelio) feeding regulation has not been reported. In our study, we first identified three forms of CART peptide precursors from gibel carp brain and named these CART-1, CART-2, and CART-3. The full-length cDNA sequences of CART-1, CART-2, and CART-3 were 616 bp, 705 bp, and 760 bp, respectively, encoding peptides of 118, 120, and 104 amino acid residues. We detected mRNA expression of CART-1, CART-2, and CART-3 in a wide range of peripheral and central tissues, with the highest expression detected in the brain. After a meal, mRNA expression of CART-1, CART-2, and CART-3 was significantly elevated, suggesting that CART-1, CART-2, and CART-3 may act as postprandial satiety signals. Moreover, mRNA expression of all three CART-1, CART-2, and CART-3 was significantly reduced during fasting and significantly elevated with refeeding. Our findings indicate that CART-1, CART-2, and CART-3 might function as a satiety factor in the gibel carp.

The sequence and de novo assembly of Oxygymnocypris stewartii genome.

Animal genomes in the Qinghai-Tibetan Plateau provide valuable resources for scientists to understand the molecular mechanism of environmental adaptation. Tibetan fish species play essential roles in the local ecology; however, the genomic information for native fishes was still insufficient. Oxygymnocypris stewartii, belonging to Oxygymnocypris genus, Schizothoracinae subfamily, is a native fish in the Tibetan plateau living within the elevation from roughly 3,000 m to 4,200 m. In this report, PacBio and Illumina sequencing platform were used to generate ~385.3 Gb genomic sequencing data. A genome of about 1,849.2 Mb was obtained with a contig N50 length of 257.1 kb. More than 44.5% of the genome were identified as repetitive elements, and 46,400 protein-coding genes were annotated in the genome. The assembled genome can be used as a reference for future population genetic studies of O. stewartii and will improve our understanding of high altitude adaptation of fishes in the Qinghai-Tibetan Plateau.