Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscus waleckii) in an Extremely Alkaline Environment

Mussel-Inspired Molecular Strategies for Fabricating Functional Materials With Underwater Adhesion and Self-Healing Properties

The exceptional underwater adhesion and self-healing capabilities of mussels have fascinated researchers for over two decades. Extensive studies have shown that these remarkable properties arise from a series of reversible and dynamic molecular interactions involving mussel foot proteins. Inspired by these molecular interaction strategies, numerous functional materials exhibiting strong underwater adhesion and self-healing performance have been successfully developed. This review systematically explores the nanomechanical mechanisms of mussel-inspired molecular interactions, mainly revealed by direct force measurement techniques such as surface forces apparatus and atomic force microscopy. The development of functional materials, including coacervates, coatings, and hydrogels, with underwater adhesion and self-healing properties, is then summarized. Furthermore, the macroscopic material performances are correlated with the underlying molecular mechanisms, providing valuable insights for the rational design of next-generation mussel-inspired functional materials with enhanced underwater adhesion and self-healing properties.

Transcriptomic and Metabolomic Analyses Reveal Response Mechanisms of Sinonovacula Constricta to Saline-Alkalinity Stresses

The razor clam (Sinonovacula constricta) is a key species in marine aquaculture, known for its wide salinity adaptation, and potential for cultivation in saline-alkaline water. Understanding its response mechanisms is crucial for expanding its farming into these regions. This study reveals the response mechanisms of S. constricta in response to low-salinity alkaline stress through a combined analysis of transcriptomics and metabolomics. After 24 h of salt-alkali stress (SA group), 1378 differentially expressed genes (DEGs) were identified, with enriched pathways including glycerophospholipid metabolism, serine, taurine, and hypotaurine metabolism. Additionally, 341 significantly different metabolites (SDMs) were found, primarily involved in taurine and hypotaurine metabolism, purine metabolism, and the FoxO signaling pathway, etc. Both DEGs and SDMs were notably enriched in hypotaurine metabolism, glycerophospholipid metabolism, and the mTOR signaling pathway, showing significant upregulation in the SA group. Correlation analysis found that the integrated regulatory network was involved in the synthesis of taurine, glycerophospholipids, and L-glutamic acid, and the metabolism of 3-mercaptopropionic acid. These results suggest that low salinity and alkalinity induce stress responses in S. constricta by regulating osmotic balance, phospholipid synthesis, and lipid metabolism. This study offers insights into the molecular mechanisms of salt-alkali response in S. constricta.

Chromosome-level genome assembly of a critically endangered species Leuciscus chuanchicus

Leuciscus chuanchicus, a critically endangered cyprinid endemic in the Yellow River, represents an evolutionary significant lineage within Leuciscinae. However, conservation efforts for this species have been hindered by the lack of genetic and genomic resources. Here we reported a high-quality chromosome-level genome of L. chuanchicus by combining Illumina reads, PacBio HiFi long reads and Hi-C data. The assembled genome size was 1.16 Gb, with a contig N50 size of 31,116,631 bp and a scaffold N50 size of 43,855,677 bp. The resulting 130 scaffolds were further clustered and ordered into 25 chromosomes based on the Hi-C data, representing 97.84% of the assembled sequences. The genome contained 60.36% repetitive sequences and 35,014 noncoding RNAs. A total of 31,196 protein-coding genes were predicted, of which 28,323 (90.79%) were functionally annotated. The BUSCO and OMArk revealed 97.6% and 91.28% completion rates, respectively. This study assembled a high-quality genome of L. chuanchicus, and provided fundamental genomic resources for investigating the molecular mechanism and evolution of the Leuciscinae.

Transcriptomics and proteomics provide insights into the adaptative strategies of Tibetan naked carps (Gymnocypris przewalskii) to saline-alkaline variations

Gymnocypris przewalskii is an exclusively cyprinid fish that inhabits Lake Qinghai, which is characterized by high salinity and alkalinity. To elucidate the molecular basis of the adaptation of G. przewalskii to a wide range of salinity‒alkalinity conditions, we performed morphological, biochemical, transcriptomic and proteomic analyses of the major osmoregulatory organs of the gills and kidney. Morphological examination revealed that mitochondria-rich cells were replaced by mucus cells in the gills during the transition of G. przewalskii from freshwater to lake water. In the kidney, the tight junction formed dense structure in the renal tubules under lake water condition compared with the loose structure in freshwater. The results of the biochemical assays revealed an increased content of total amino acids, indicating their potential roles as osmolytes and energy supplies in freshwater. The decreased urea concentration suggested that urea synthesis might not be involved in the detoxicity of ammonia. The transcriptomic and proteomic data revealed that genes involved in ion absorption and ammonia excretion were activated in freshwater and that genes involved in cell junction and glutamine synthesis were induced in lake water, which was consistent with the morphological and biochemical observations. Together with the higher levels of glutamine and glutamate, we proposed that G. przewalskii alleviated the toxic effect of ammonia direct excretion through gills under freshwater and the activation of the conversion of glutamate to glutamine under high saline-alkaline condition. Our results revealed different expression profiles of genes involved in metabolic pathways, including the upregulation of genes involved in energy production in freshwater and the induction of genes involved in the synthesis of acetylneuramic acid and sphingolipid in soda lake water. In conclusion, the appearance of mitochondria-rich cells and increased energy production might contribute to ion absorption in G. przewalskii to maintain ion and solute homeostasis in freshwater. The existence of mucus cells and dense junctions, which are associated with increased gene expression, might be related to the adaptation of G. przewalskii to high salinity-alkalinity.

Convergent Gene Duplication in Arctic and Antarctic Teleost Fishes

Teleost fishes have independently colonized polar regions multiple times, facing many physiological and biochemical challenges due to frigid temperatures. Although increased gene copy numbers can contribute to adaptive evolution in extreme environments, it remains unclear which categories of genes exhibit increased copy numbers associated with polar colonization. Using 104 species of ray-finned fishes, we systematically identified genes with a significant correlation between copy number and polar colonization after phylogenetic correction. Several genes encoding extracellular glycoproteins, including zona pellucida (ZP) proteins, which increase their copy number in Antarctic notothenioid fishes, exhibited elevated copy numbers across multiple polar fish lineages. Additionally, some genes reported to be highly expressed under cold stress, such as cold-inducible RNA-binding protein (CIRBP), had significantly increased copy numbers in polar fishes. Further analysis will provide a fundamental basis for understanding the role of gene duplication in polar adaptations.

Dynamic Outlier Slicing Allows Broader Exploration of Adaptive Divergence: A Comparison of Individual Genome and Pool-Seq Data Linked to Humic Adaptation in Perch

How genetic variation contributes to adaptation at different environments is a central focus in evolutionary biology. However, most free-living species still lack a comprehensive understanding of the primary molecular mechanisms of adaptation. Here, we characterised the targets of selection associated with drastically different aquatic environments-humic and clear water-in the common freshwater fish, Eurasian perch (Perca fluviatilis). By using whole-genome sequencing (WGS) on a large population dataset (n = 42 populations) and analysing 873,788 SNPs, our primary aim was to uncover novel and confirm known footprints of selection. We compared individual and pooled WGS, and developed a novel approach, termed dynamic outlier slicing, to assess how the choice of outlier-calling stringency influences functional and Gene Ontology (GO) enrichment. By integrating genome-environment association (GEA) analysis with allele frequency-based approaches, we estimated composite selection signals (CSS) and identified 2679 outlier SNPs distributed across 324 genomic regions, involving 468 genes. Dynamic outlier slicing identified robust enrichment signals in five annotation categories (upstream, downstream, synonymous, 5'UTR and 3'UTR) highlighting the crucial role of regulatory elements in adaptive evolution. Furthermore, GO analyses revealed strong enrichment of molecular functions associated with gated channel activity, transmembrane transporter activity and ion channel activity, emphasising the importance of osmoregulation and ion balance maintenance. Our findings demonstrate that despite substantial random drift and divergence, WGS of high number of population pools enabled the identification of strong selection signals associated with adaptation to both humic and clear water environments, providing robust evidence of widespread adaptation. We anticipate that the dynamic outlier slicing method we developed will enable a more thorough exploration of adaptive divergence across a diverse range of species.

Genetic Basis and Identification of Candidate Genes for Alkalinity Tolerance Trait in Spotted Sea Bass (Lateolabrax maculatus) by Genome-Wide Association Study (GWAS)

Given the challenges of overcrowded coastal aquaculture spaces and insufficient production, utilizing saline-alkaline water areas represents a vital strategy to alleviate these bottlenecks. Spotted sea bass (Lateolabrax maculatus), with its formidable osmoregulatory capabilities, is an ideal candidate to develop a saline-alkaline tolerant strain. In our study, genotypic and phenotypic data from 287 L. maculatus individuals exposed to carbonate alkaline conditions were collected, and a genome-wide association study (GWAS) conducted to elucidate genetic basis related to carbonate alkalinity tolerance trait. Results showed that 14 SNPs and 8 InDels were markedly related to carbonate alkalinity tolerance trait, and 404 candidate genes were pinpointed within a ± 300-kb region surrounding these variants. Notably, the most significant SNP (SNP_05_17240108), along with two adjacent SNPs (SNP_05_17240102 and SNP_05_17240340) and two InDels (InDel_05_17240228 and InDel_05_17240231), was situated in the intron region of trio gene that could play vital roles in cell remodeling, and cell junction and activity of aquaporins to deal with carbonate alkalinity stress. Furthermore, candidate genes were significantly involved in pathways associated with carbohydrate metabolism, cell remodeling, ion transport, and RNA degradation, which were consistent with RNA-Seq analysis results of gills and kidneys in response to alkalinity stress. Our study will contribute to elucidate the genetic basis of alkalinity tolerance and the identified SNPs and InDels could be used for marker-assisted selection (MAS) and genomic selection (GS) for alkalinity tolerance trait in the breeding programs of spotted sea bass.

Study on the physiological responses and tolerance mechanisms to subchronic carbonate alkalinity exposure in the gills of Paramisgurnus dabryanus

Given the reduction of freshwater resources, saline-alkaline aquaculture has emerged as an effective approach to expand the fishery's accessible space. High carbonate alkalinity (CA) is a major stressor for aquatic organisms in saline-alkaline environments. Paramisgurnus dabryanus is a potential species for culture in saline-alkaline water, making it an ideal model for investigating the physiological responses and tolerance mechanisms to CA exposure in freshwater fishes. In the current study, P. dabryanus were exposed to 15 and 30 mmol/L NaHCO3, combining blood biochemical, gill histological, transcriptomic, and metabolomic methods for conjoint analysis of response mechanisms. After 28-d exposure, the gill ventilation frequency of P. dabryanus decreased significantly, gill lamellae twisted and atrophied, and gill filament epithelial cells proliferated, potentially limiting gas exchange, whereas the accessory air-breathing frequency increased significantly, possibly for greater oxygen uptake. Serum osmolality and blood pH remained relatively steady, while serum ammonia levels rose significantly. A total of 3718 differentially expressed genes (DEGs) and 205 differential metabolites (DMs) were identified between the control group and 30 mmol/L NaHCO3 group, involved in ion transport (Na+/K+-ATPase, V-type ATPase, carbonic anhydrase, and ABC transporters), ammonia transport (Rh glycoproteins and Aquaporins), amino acid metabolism, carbohydrate metabolism, and fatty acid metabolism. Furthermore, DEGs were significantly associated with cell-cell/ extracellular matrix interaction and protein synthesis. An integrated multi-omics analysis revealed the activation of carbon metabolism and TCA cycle. These results indicate that in response to CA exposure, P. dabryanus may facilitate carrier-mediated ion and ammonia transport to maintain the internal osmotic equilibrium and lessen the deleterious effects of blocked ammonia excretion. Meanwhile, amino acid metabolism and protein synthesis are disturbed, P. dabryanus can modulate carbohydrate catabolism to maintain energy homeostasis. The above findings provide novel insights into saline-alkaline adaptation in freshwater fishes, paving the way for future research and development of saline-alkaline-tolerant Cobitidae strains.

Exome-wide comparative analyses revealed differentiating genomic regions for performance traits in Indian native buffaloes

In India, 20 breeds of buffalo have been identified and registered, yet limited studies have been conducted to explore the performance potential of these breeds, especially in the Indian native breeds. This study is a maiden attempt to delineate the important variants and unique genes through exome sequencing for milk yield, milk composition, fertility, and adaptation traits in Indian local breeds of buffalo. In the present study, whole exome sequencing was performed on Chhattisgarhi (n = 3), Chilika (n = 4), Gojri (n = 3), and Murrah (n = 4) buffalo breeds and after stringent quality control, 4333, 6829, 4130, and 4854 InDels were revealed, respectively. Exome-wide FST along 100-kb sliding windows detected 27, 98, 38, and 35 outlier windows in Chhattisgarhi, Chilika, Gojri, and Murrah, respectively. The comparative exome analysis of InDels and subsequent gene ontology revealed unique breed specific genes for milk yield (CAMSAP3), milk composition (CLCN1, NUDT3), fertility (PTGER3) and adaptation (KCNA3, TH) traits. Study provides insight into mechanism of how these breeds have evolved under natural selection, the impact of these events on their respective genomes, and their importance in maintaining purity of these breeds for the traits under study. Additionally, this result will underwrite to the genetic acquaintance of these breeds for breeding application, and in understanding of evolution of these Indian local breeds.

The Identification of Proteomic Signatures Associated with Alkaline Tolerance in the Skin Mucus of Crucian Carp (Carassius auratus)

The skin is covered by a protective mucus layer, which is essential to the innate defense mechanism of fish. Investigating the response of skin mucus to various toxic stresses is crucial for enhancing its ability to tackle environmental challenges and developing strategies to mitigate toxic effects. Alkalinity stress assays (50 mmol/L NaHCO3) were conducted on crucian carp (Carassius auratus) from Lake Dali Nur (pH = 9.6) and Ping Xiang red crucian carp from freshwater (pH = 7) over 7 days. The expression of skin mucous proteins was analyzed using the liquid chromatography (LC)-spectrometry (MS)/MS Analysis-Data-independent acquisition (DIA) mode. A total of 12,537 proteins were identified across 20 samples from four groups, with 12,025 quantified. In the alkaline water population, high alkali stress resulted in the up-regulation of 139 proteins and the down-regulation of 500 proteins. In contrast, the freshwater population showed an increase in 112 proteins and a decrease in 120; both populations had a total of 23 genes up-regulated and 21 down-regulated. The protein regulatory network for the alkaline water group included 3146 pairwise interactions among 464 nodes, with only 20 being differentially expressed proteins. Conversely, the freshwater group's network comprised just 1027 specific interactions across 337 nodes, with 6 corresponding to differentially expressed proteins. A common protein regulatory network responding to high alkali stress was extracted and visualized for both populations. Based on their regulatory relationships and expression levels, these proteins are hypothesized to play similar roles under high alkali stress. Notably, the alpha-globin fragment and keratin type I cytoskeletal 13-like proteins showed markedly up-regulated expression, with the alpha-globin fragment increasing nearly a thousandfold from an extremely low level. This suggests it could serve as a potential biomarker for alkali tolerance, warranting further investigation.

Decoding the fish genome opens a new era in important trait research and molecular breeding in China

Aquaculture represents the fastest-growing global food production sector, as it has become an essential component of the global food supply. China has the world's largest aquaculture industry in terms of production volume. However, the sustainable development of fish culture is hindered by several concerns, including germplasm degradation and disease outbreaks. The practice of genomic breeding, which relies heavily on genome information and genotypephenotype relationships, has significant potential for increasing the efficiency of aquaculture production. In 2014, the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in China. Since then, domestic researchers have made dramatic progress in functional genomic studies. To date, the genomes of more than 60 species of fish in China have been assembled and annotated. Based on these reference genomes, evolutionary, comparative, and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes, including growth and development, sex determination, disease resistance, metamorphosis, and pigmentation. Furthermore, genomic tools and breeding techniques such as SNP arrays, genomic selection, and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding activities. This review aims to summarize the current status, advances, and perspectives of the genome resources, genomic study of important traits, and genomic breeding techniques of fish in China. The review will provide aquaculture researchers, fish breeders, and farmers with updated information concerning fish genomic research and breeding technology. The summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.

Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life

From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.

Fine Mapping of QTLs for Alkaline Tolerance in Crucian Carp (Carassius auratus) Using Genome-Wide SNP Markers

Crucian carp (Carassius auratus) is widely distributed in the world and has become an economically freshwater fish. The population in Lake Dali Nur can tolerate the extreme alkaline environment with alkalinity over 50 mmol/L (pH 9.6), thus providing a special model for exploring alkali-tolerant molecular markers in an extremely alkaline environment. In this study, we constructed a high-density and high-resolution linkage map with 16,224 SNP markers based on genotyping-by-sequencing (GBS) consisting of 152 progenies and conducted QTL studies for alkali-tolerant traits. The total length of the linkage map was 3918.893 cM, with an average distance of 0.241 cM. Two QTLs for the ammonia-N-tolerant trait were detected on LG27 and LG45. A QTL for the urea-N-tolerant trait was detected on LG27. Interestingly, mapping the two QTLs on LG27 revealed that the mapped genes were both located in the intron of CDC42. GO functional annotation and KEGG enrichment analysis results indicated that the biological functions might be involved in the cell cycle, cellular senescence, MAPK, and Ras signaling pathways. These findings suggest that CDC42 may play an important role in the process of dealing with extremely alkaline environments.

Rh proteins and H+ transporters involved in ammonia excretion in Amur Ide (Leuciscus waleckii) under high alkali exposure

High alkaline environment can lead to respiratory alkalosis and ammonia toxification to freshwater fish. However, the Amur ide (Leuciscus waleckii), which inhabits an extremely alkaline lake in China with titratable alkalinity up to 53.57 mM (pH 9.6) has developed special physiological and molecular mechanisms to adapt to such an environment. Nevertheless, how the Amur ide can maintain acid-base balance and perform ammonia detoxification effectively remains unclear. Therefore, this study was designed to study the ammonia excretion rate (Tamm), total nitrogen accumulation in blood and tissues, including identification, expression, and localization of ammonia-related transporters in gills of both the alkali and freshwater forms of the Amur ide. The results showed that the freshwater form Amur ide does not have a perfect ammonia excretion mechanism exposed to high-alkaline condition. Nevertheless, the alkali form of Amur ide was able to excrete ammonia better than freshwater from Amur ide, which was facilitated by the ionocytes transporters (Rhbg, Rhcg1, Na+/H+ exchanger 2 (NHE2), and V-type H+ ATPase (VHA)) in the gills. Converting ammonia into urea served as an ammonia detoxication strategy to reduced endogenous ammonia accumulation under high-alkaline environment.

Population structure and adaptability analysis of Schizothorax o'connori based on whole-genome resequencing

BACKGROUND

Schizothorax o'connori is an endemic fish distributed in the upper and lower reaches of the Yarlung Zangbo River in China. It has experienced a fourth round of whole gene replication events and is a good model for exploring the genetic differentiation and environmental adaptability of fish in the Qinghai-Tibet Plateau. The uplift of the Qinghai-Tibet Plateau has led to changes in the river system, thereby affecting gene exchange and population differentiation between fish populations. With the release of fish whole genome data, whole genome resequencing has been widely used in genetic evolutionary analysis and screening of selected genes in fish, which can better elucidate the genetic basis and molecular environmental adaptation mechanisms of fish. Therefore, our purpose of this study was to understand the population structure and adaptive characteristics of S. o'connori using the whole-genome resequencing method.

RESULTS

The results showed that 23,602,746 SNPs were identified from seven populations, mostly distributed on chromosomes 2 and 23. There was no significant genetic differentiation between the populations, and the genetic diversity was relatively low. However, the Zangga population could be separated from the Bomi, Linzhi, and Milin populations in the cluster analysis. Based on historical dynamics analysis of the population, the size of the ancestral population of S. o'connori was affected by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Glacial Age. The selected sites were mostly enriched in pathways related to DNA repair and energy metabolism.

CONCLUSION

Overall, the whole-genome resequencing analysis provides valuable insights into the population structure and adaptive characteristics of S. o'connori. There was no obvious genetic differentiation at the genome level between the S. o'connori populations upstream and downstream of the Yarlung Zangbo River. The current distribution pattern and genetic diversity are influenced by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Ice Age. The selected sites of S. o'connori are enriched in the energy metabolism and DNA repair pathways to adapt to the low temperature and strong ultraviolet radiation environment at high altitude.

Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep

Understanding the genetic makeup of local sheep breeds is essential for their scientific conservation and sustainable utilization. The Liangshan semi-fine-wool sheep (LSS), a Chinese semi-fine-wool breed renowned for its soft wool, was analyzed using whole-genome sequencing data including 35 LSS, 84 sheep from other domestic breeds, and 20 Asiatic mouflons. We investigated the genetic composition of LSS by conducting analyses of the population structure, runs of homozygosity, genomic inbreeding coefficients, and selection signature. Our findings indicated that LSS shares greater genetic similarity with Border Leicester and Romney sheep than with Tibetan (TIB), Yunnan (YNS), and Chinese Merino sheep. Genomic analysis indicated low to moderate inbreeding coefficients, ranging from 0.014 to 0.154. In identifying selection signals across the LSS genome, we pinpointed 195 candidate regions housing 74 annotated genes (e.g., IRF2BP2, BVES, and ALOX5). We also found the overlaps between the candidate regions and several known quantitative trait loci related to wool traits, such as the wool staple length and wool fiber diameter. A selective sweep region, marked by the highest value of cross-population extended haplotype homozygosity, encompassed IRF2BP2-an influential candidate gene affecting fleece fiber traits. Furthermore, notable differences in genotype frequency at a mutation site (c.1051 + 46T > C, Chr25: 6,784,190 bp) within IRF2BP2 were observed between LSS and TIB and YNS sheep (Fisher's exact test, p < 2.2 × 10-16). Taken together, these findings offer insights crucial for the conservation and breeding enhancement of LSS.

Population genomics analysis to identify ion and water transporter genes involved in the adaptation of Tibetan naked carps to brackish water

Understanding how evolutionary processes shape the genetic variations and influence the response of species to environmental alterations is critical for biodiversity conservation and molecular breeding. Gymnocypris przewalskii przewalskii is the only known cyprinid fish that dwells in the brackish water of Lake Qinghai on the Qinghai-Tibetan Plateau. To reveal the genetic basis of its adaptation to high salinity and alkalinity, whole-genome sequencing was performed in G. p. przewalskii and its freshwater relatives Gymnocypris eckloni and Gymnocypris przewalskii ganzihonensis. Compared with freshwater species, lower genetic diversity and higher linkage disequilibrium were observed in G. p. przewalskii. Selective sweep analysis identified 424 core-selective genes enriched in transport activities. Transfection analysis showed that genetic changes in the positively selected gene aquaporin 3 (AQP3) improved cell viability after salt treatment, suggesting its involvement in brackish water adaptation. Our analysis indicates that ion and water transporter genes experienced intensive selection, which might have contributed to the maintenance of high osmolality and ion content in G. p. przewalskii. The current study identified key molecules involved in the adaptation of fish to brackish water, providing valuable genomic resources for the molecular breeding of salt-tolerant fish.

Histological, Physiological and Transcriptomic Analysis Reveal the Acute Alkalinity Stress of the Gill and Hepatopancreas of Litopenaeus vannamei

The pacific white shrimp (Litopenaeus vannamei) has gradually become a promising economic species in the development of saline-alkali water fishery. The study related to the stress reaction of pacific white shrimp under alkalinity stress is still limited, which is also a critical limiting factor for its saline-alkaline aquaculture. In this study, we aim to analyse the stress reaction of pacific white shrimp under acute alkalinity stress between control group (alkalinity:40 mg/L) and treatment group (alkalinity:350 mg/L) through histological observation, physiological determination and transcriptome. In the present study, during the process of acute alkalinity stress, the activities of Na+-K+-ATPase, carbonic anhydrase, sodium/hydrogen exchanger in gill related to homeostasis were significantly changed, the activities of superoxide dismutase and catalase related to antioxidant were decreased in both gill and hepatopancreas, and the activities of protease, lipase and amylase in hepatopancreas were decreased. At the same time, different degrees of histological damages were occured in the gill and hepatopancreas under acute alkalinity stress. There were 194 and 236 different expressed genes identified in gill and hepatopancreas respectively. Functional enrichment assessment indicated that the alkalinity stress-related genes in both gill and hepatopancreas were primarily involved in fatty acid metabolism, glycolysis/gluconeogenesis, glycerophospholipid metabolism. The results indicated that the functions of homeostasis regulation, antioxidation and digestion of pacific white shrimp were decreased under acute alkalinity stress, at the same time, the energy metabolism in gill and hepatopancreas were modified to cope with alkalinity stress. This work provides important clues for understanding the response mechanism of pacific white shrimp under acute alkalinity stress.

Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review

Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.

The complete mitochondrial genome of Leuciscus merzbacheri (Cypriniformes: Cyprinidae)

Leuciscus merzbacheri (Zugmayer, 1912) is a cyprinid fish endemic to China, with a distribution range limited to Xinjiang Province. As a landmark species in the Junggar Basin, L. merzbacheri is of considerable significance regarding our understanding of the adaptive evolution of salt and alkali tolerance. In this study, the complete mitochondrial sequence of L. merzbacheri was obtained for the first time by high-throughput sequencing. The circular mitogenome is 16,609 bp in length and contains the standard 37 genes, including 13 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes, which is similar to that of other fish. The mitogenome contents of A, T, C, and G were 27.9, 26.3, 27.1, and 18.7%, respectively. Phylogenetically, L. merzbacheri was located on a new branch near the base of the phylogenetic tree, thereby suggesting an early origin.

The genome-wide identification and adaptive evolution of slc9 genes in Leuciscus waleckii under extremely alkaline conditions

The solute carrier family 9 (slc9) genes, especially slc9a isoform coding proteins contribute to electroneutral countertransport of H⁺ for Na⁺ across the plasmalemmal and organellar membranes, intracellular pH and cellular volume regulation as well as the electrolyte, acid-base, and fluid volume homeostasis at the systemic level. These functional properties determine a potential basis for organisms to challenge stressful conditions. However, these well-done researches have been reported more in mammals. Thus, in this study, a total of eleven slc9 genes were identified from the latest version genome of L. waleckii, a cyprinid fish that could tolerate extremely alkaline environments (pH 9.6). The evolutionary footprint of slc9 genes was uncovered via the analysis of copy numbers, gene structure, motif composition, chromosome location and phylogenetic relationship. More importantly, there were two SNPs located on 5' UTR and three non-synonymous mutations in the coding region of the slc9a3.2 gene by comparing freshwater with alkaline water populations attached to resequencing technology. Slc9a3.2 gene was a statistically significant low expression in gill tissue with extremely alkaline pressure. Generally, slc9 gene family in L. waleckii was highly conserved. Several important SNPs with high Fst values were identified where non-synonymous mutations occurred between freshwater and alkaline water populations, and they may play an important role in specific functional differentiation. Slc9 genes had clear tissue expression preferences and were involved in abiotic stress response, indicating their roles in physiological function and strong self-regulating capacity. Our insight into the genetic variations that take place in the individual genes under extreme conditions could provide a feasible example for studying specific molecular mechanisms based on genomic data with increasing environmental stress.

Whole-genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch

Extreme environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, modern bony fishes have colonized various aquatic environments, including perpetually dark, hypoxic, hypersaline and toxic habitats. Eurasian perch (Perca fluviatilis) is among the few fish species of northern latitudes that is able to live in very acidic humic lakes. Such lakes represent almost "nocturnal" environments; they contain high levels of dissolved organic matter, which in addition to creating a challenging visual environment, also affects a large number of other habitat parameters and biotic interactions. To reveal the genomic targets of humic-associated selection, we performed whole-genome sequencing of perch originating from 16 humic and 16 clear-water lakes in northern Europe. We identified over 800,000 single nucleotide polymorphisms, of which >10,000 were identified as potential candidates under selection (associated with >3000 genes) using multiple outlier approaches. Our findings suggest that adaptation to the humic environment may involve hundreds of regions scattered across the genome. Putative signals of adaptation were detected in genes and gene families with diverse functions, including organism development and ion transportation. The observed excess of variants under selection in regulatory regions highlights the importance of adaptive evolution via regulatory elements, rather than via protein sequence modification. Our study demonstrates the power of whole-genome analysis to illuminate the multifaceted nature of humic adaptation and provides the foundation for further investigation of causal mutations underlying phenotypic traits of ecological and evolutionary importance.

Genomic investigations provide insights into the mechanisms of resilience to heterogeneous habitats of the Indian Ocean in a pelagic fish

The adaptive genetic variation in response to heterogeneous habitats of the Indian Ocean was investigated in the Indian oil sardine using ddRAD sequencing to understand the subpopulation structure, stock complexity, mechanisms of resilience, and vulnerability in the face of climate change. Samples were collected from different ecoregions of the Indian ocean and ddRAD sequencing was carried out. Population genetic analyses revealed that samples from the Gulf of Oman significantly diverged from other Indian Ocean samples. SNP allele-environment correlation revealed the presence of candidate loci correlated with the environmental variables like annual sea surface temperature, chlorophyll-a, and dissolved oxygen concentration which might represent genomic regions allegedly diverging as a result of local adaptation. Larval dispersal modelling along the southwest coast of India indicated a high dispersal rate. The two major subpopulations (Gulf of Oman and Indian) need to be managed regionally to ensure the preservation of genetic diversity, which is crucial for climatic resilience.

Effects of Bicarbonate Stress on Serum Ions and Gill Transporters in Alkali and Freshwater Forms of Amur Ide (Leuciscus waleckii)

The Amur ide (Leuciscus waleckii) is a fish in the Cyprinidae family. Compared with other Amur ide living in freshwater ecosystems, the Amur ide population in Lake Dali Nor of China is famous for its high tolerance to the alkaline conditions of 54 mM (pH 9.6). Yet, surprisingly, the ionoregulatory mechanism responsible for this remarkable alkaline adaptation remains unclear. Therefore, this study sought to investigate how bicarbonate affects the acid-base balancing and ionoregulatory responses of this animal. Here, using a comparative approach, the alkali form of Amur ide and its ancestral freshwater form living in other freshwater basins were each exposed to 50 mM (pH 9.59 ± 0.09), a level close to the alkalinity of Lake Dali Nor, and their physiological (AE1) adjustment of ions and acid-base regulation were investigated. This study highlighted differences in blood pH and serum ions (e.g., Na⁺, K⁺, Cl⁻, and Ca²⁺), Na⁺/K⁺ ATPase (NKA) activity and its mRNA level, and mRNA expression of gill transporters (Na⁺/H⁺ exchanger member 2 and/or 3, Na⁺/HCO3- cotransporter (NBC1), Cl⁻/HCO3- exchanger, Na⁺/Cl⁻ cotransporter (NCC), Na⁺/K⁺/2Cl⁻ (NKCC1), SLC26A5, and SLC26A6) for alkalinity adaptation between the two forms of Amur ide differing in alkalinity tolerance. Specifically, close relationships among the serum Na⁺ and mRNA levels of NCC, NKCC1, and NHE, and also NKA and NBC1, in addition to serum Cl⁻ and bicarbonate transporters (e.g., SLC26A5 and SLC26A6), characterized the alkali form of Amur ide. We propose that this ecotype can ensure its transepithelial Cl⁻ and Na⁺ uptake/base secretions are highly functional, by its basolateral NKA with NBC1 and apical ionic transporters, and especially NCC incorporated with other transporters (e.g., SLC26). This suggests an evolved strong ability to maintain an ion osmotic and acid-base balance for more effectively facilitating its adaptability to the high alkaline environment. This study provides new insights into the physiological responses of the alkaline form of the Amur ide fish for adapting to extreme alkaline conditions. This information could be used as a reference to cultivating alkaline-tolerant fish species in abandoned alkaline waters.

The CC and CXC chemokine receptors in turbot (Scophthalmus maximus L.) and their response to Aeromonas salmonicida infection

Chemokines are crucial regulators of cell mobilization for development, homeostasis, and immunity. Chemokines signal through binding to chemokine receptors, a superfamily of seven-transmembrane domain G-coupled receptors. In the present study, eleven CC chemokine receptors (CCRs) and seven CXC chemokine receptors (CXCRs) were identified from turbot genome. Phylogenetic and syntenic analyses were performed to annotate these genes, indicating the closest relationship between the turbot chemokine receptors and their counterparts of Japanese flounders (Paralichthys olivaceus). Evolutionary analyses revealed that the tandem duplications of CCR8 and CXCR3, the whole genome duplications of CCR6, CCR9, CCR12, and CXCR4, and the teleost-specific CCR12 led to the expansion of turbot chemokine receptors. In addition, turbot chemokine receptors were ubiquitously expressed in nine examined healthy tissues, with high expression levels observed in spleen, gill, and head kidney. Moreover, most turbot chemokine receptors were significantly differentially expressed in spleen and gill after Aeromonas salmonicida infection, and exhibited general down-regulations at early time points and then gradually up-regulated. Finally, protein-protein interaction network (PPI) analyses indicated that chemokine receptors interacted with a few immune-related genes such as interleukins, Grk genes, CD genes, etc. These results should be valuable for comparative immunological studies and provide insights for further functional characterization of chemokine receptors in turbots.

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.

Protein-mediated bioadhesion in marine organisms: A review

Protein-mediated bioadhesion is one of the crucial physiological processes in marine organisms, by which they can firmly adhere to underwater substrates. Most marine adhesive organisms are biofoulers, causing negative effects on marine ecosystems and huge economic losses to aquaculture and maritime industries. Furthermore, adhesive proteins in these organisms are promising bionic candidates for high-performance artificial materials with great application value. In-depth understanding of the bioadhesion in marine ecosystems is of dual significance for resolving biofouling issue and developing marine bionic products. Here, we review the research progress of protein-mediated bioadhesion in marine organisms. The adhesion processes such as protein biosynthesis and secretion are similar among organisms, but the detailed features such as compositions, structures, and molecular functions of adhesive proteins are distinct. Hydroxylation, glycosylation, and phosphorylation are important post-translational modifications during the processes of adhesion. The contents of some amino acids such as glycine, tyrosine and cysteine involved in underwater adhesion are significantly higher, which is a sequence feature of barnacle cement and mussel foot proteins. The amyloid structures and conserved domains/motifs such as EGF and vWFA distributed in adhesive proteins are involved in the underwater adhesion. In addition, the oxidative cross-linking also plays an important role in marine bioadhesion. Overall, the unique and common features identified for the protein-mediated bioadhesion in diverse marine organisms here provide background information and essential reference for characterizing marine adhesive proteins and associated functional domains, formulating antifouling strategies, and developing novel biomimetic adhesives.

Identification and Analysis of Long Non-coding RNAs in Leuciscus waleckii Adapted to Highly Alkaline Conditions

Leuciscus waleckii is a freshwater fish that is known to inhabit the Dali Nor Lake, Inner Mongolia, China. The water in this lake has an HCO3 -/CO3 2- concentration of 54 mM (pH 9.6) and a salinity of 0.6‰. The physiological mechanisms that allow this fish to tolerate these saline/alkaline conditions have yet to be elucidated. Transcriptional component analysis has shown that the expression levels of a large number of genes involved in the pathways responsible for osmo-ionoregulation and arachidonic acid metabolism pathway expression change significantly (p < 0.05) during the regulation of acid-base balance under high alkaline stress. In this study, we investigated the role of long non-coding RNAs (lncRNAs) during adaptation to high alkaline conditions. Fish were challenged to an NaHCO3-adjusted alkalinity of 0 mM, 30 mM (pH 9.44 ± 0.08), and 50 mM (pH 9.55 ± 0.06) for 20 days in the laboratory. Gill and kidney tissues were then collected for high-throughput sequencing assays. A total of 159 million clean reads were obtained by high-throughput sequencing, and 41,248 lncRNA transcripts were identified. Of these, the mean number of exons and the mean length of the lncRNA transcripts were 4.8 and 2,079 bp, respectively. Based on the analysis of differential lncRNA transcript expression, a total of 5,244 and 6,571 lncRNA transcripts were found to be differentially expressed in the gills and kidneys, respectively. Results derived from Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the coding genes were correlated with the lncRNA expression profiles. GO analysis showed that many lncRNAs were enriched in the following processes: "transporter activity," "response to stimulus," and "binding." KEGG analysis further revealed that metabolic pathways were significantly enriched. A random selection of 16 lncRNA transcripts was tested by RT-qPCR; these results were consistent with our sequencing results. We found that a large number of genes, with the same expression profiles as those with differentially expressed lncRNAs, were associated with the regulation of acid-base balance, ion transport, and the excretion of ammonia and nitrogen. Collectively, our data indicate that lncRNA-regulated gene expression plays an important role in the process of adaptation to high alkaline conditions in L. waleckii.

High-throughput sequencing reveals differential expression of miRNAs in yak and cattleyak epididymis

Cattleyaks (CY) are interspecific hybrids between cattle (Bos taurus) and yak (Bos gruniens, YK) exhibiting the same prominent adaptability and higher performances than YK. MiRNAs have played an important role in the acquisition and maintenance of male fertility in reproduction, where deletion of Dicer in mice germ cells results in infertility. According to a body of evidence, the function of miRNA in the male reproductive system extends from the testis into the epididymis and, as such, regulates gene expression and contributes to regional gene expression variations. Using RNA sequencing on biological replicates, we described differentially expressed miRNAs profiles for tissue from epididymis of YK and CY. In the present study, High-throughput sequencing analysis showed that 55 differentially expressed (DE) miRNAs were identified in the epididymis of YK and CY. Among these, 43 DE miRNAs were upregulated while the remaining 12 DE miRNAs were downregulated between epididymis of YK and CY. Our results showed that the top most important DE miRNAs, bta-miR-449c, bta-miR-539, bta-miR-136, bta-miR-504, bta-miR-31 and bta-miR-222 were found to be involved in the reproductive system of CY. In addition, some targeted genes, Clusterins (CLU), Retinoic Acid Receptor a (RARa) and Hydroxy acyl glutathione Hydrolase (HAGH) and HSPH1 targeted by bta-miR-2411-3p and bta-miR-1298 were involved in the sperm motility, sperm morphology and post-testicular sperm maturation. Furthermore, GO and KEGG analyses were performed to classify the functions of target genes for DE miRNAs. In addition, RT-qPCR validation of the DE miRNAs and its targeted genes revealed that putative miRNAs are involved in the male CY infertility by altering the gene expression. Present findings may not only increase our understanding of the molecular mechanisms regulated by the miRNAs in epididymis, but also provide a valuable information to understand the male infertility mechanism of CY.

Genomic Signature of Shifts in Selection and Alkaline Adaptation in Highland Fish

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.

Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments

Amur ide (Leuciscus waleckii), a Cyprinid species, is broadly distributed in Northeast Asia. Different from its freshwater counterparts, the population in Lake Dali Nor has a strong alkalinity tolerance and can adapt to extremely alkali-saline water with bicarbonate over 50 mmol/L. To uncover the genetic basis of its alkaline adaptation, three populations, including one alkali form from Lake Dali Nor (DL), one freshwater form from its adjacent sister Lake Ganggeng Nor (GG), and one freshwater form from its historical origin, namely, the Songhua River (SH), were analyzed using genome resequencing technology. A total of 679.82 Gb clean data and 38,091,163 high-quality single-nucleotide polymorphism (SNP) loci were detected in the three populations. Nucleotide diversity and population structure analysis revealed that the DL and GG populations have lower nucleotide diversities and different genetic structures than those of the SH population. Selective sweeping showed 21 genes involved in osmoregulatory regulation (DLG1, VIPR1, AKT1, and GNAI1), inflammation and immune responses (DLG1, BRINP1, CTSL, TRAF6, AKT1, STAT3, GNAI1, SEC22b, and PSME4b), and cardiorespiratory development (TRAF6, PSME4b, STAT3, AKT1, and COL9A1) to be associated with alkaline adaption of the DL population. Interestingly, selective pressure (CodeML, MEME, and FEL) methods identified two functional codon sites of VIPR1 to be under positive selection in the DL population. The subsequent 3D protein modeling confirmed that these selected sites will incur changes in protein structure and function in the DL population. In brief, this study provides molecular evidence of population divergence and alkaline adaptation, which will be very useful for revealing the genetic basis of alkaline adaptation in Amur ide.

Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast

The whole mitochondrial genome ofLateolabrax maculatus(Cuvier, 1828) was used to investigate the reasons for the observed patterns of genetic differentiation among 12 populations in northern and southern China. The haplotype diversity and nucleotide diversity ofL. maculatuswere 0.998 and 0.00169, respectively. Pairwise FSTvalues between populations ranged from 0.001 to 0.429, correlating positively with geographic distance. Genetic structure analysis and haplotype network analysis indicated that these populations were split into two groups, in agreement with geographic segregation and environment. Tajima’s D values, Fu’s Fs tests and Bayesian skyline plot (BSP) indicated that a demographic expansion event may have occurred in the history ofL. maculatus. Through selection pressure analysis, we found evidence of significant negative selection at the ATP6, ND3, Cytb, COX3, COX2 and COX1 genes. In our hypotheses, this study implied that demographic events and selection of local environmental conditions, including temperature, are responsible for population divergence. These findings are a step forward toward the understanding of the genetic basis of differentiation and adaptation, as well as conservation ofL. maculatus.

Genome-wide adaptive evolution to underground stresses in subterranean mammals: Hypoxia adaption, immunity promotion, and sensory specialization

Life underground has provided remarkable examples of adaptive evolution in subterranean mammals; however, genome-wide adaptive evolution to underground stresses still needs further research. There are approximately 250 species of subterranean mammals across three suborders and six families. These species not only inhabit hypoxic and dark burrows but also exhibit evolved adaptation to hypoxia, cancer resistance, and specialized sensory systems, making them an excellent model of evolution. The adaptive evolution of subterranean mammals has attracted great attention and needs further study. In the present study, phylogenetic analysis of 5,853 single-copy orthologous gene families of five subterranean mammals (Nannospalax galili, Heterocephalus glaber, Fukomys damarensis, Condylura cristata, and Chrysochloris asiatica) showed that they formed fou distinct clusters. This result is consistent with the traditional systematics of these species. Furthermore, comparison of the high-quality genomes of these five subterranean mammalian species led to the identification of the genomic signatures of adaptive evolution. Our results show that the five subterranean mammalian did not share positively selected genes but had similar functional enrichment categories, including hypoxia tolerance, immunity promotion, and sensory specialization, which adapted to the environment of underground stresses. Moreover, variations in soil hardness, climate, and lifestyles have resulted in different molecular mechanisms of adaptation to the hypoxic environment and different degrees of visual degradation. These results provide insights into the genome-wide adaptive evolution to underground stresses in subterranean mammals, with special focus on the characteristics of hypoxia adaption, immunity promotion, and sensory specialization response to the life underground.

Mitogenomic Perspectives on the Adaptation to Extreme Alkaline Environment of Amur ide (Leuciscus waleckii)

Amur ide (Leuciscus waleckii, Family Cyprinidae) is widely distributed in Northeast Asia. L. waleckii usually inhabits freshwater environments but can also survive in the Lake Dali Nur, one of the most extreme aquatic environments on the earth, with an alkalinity up to 50 mmol/L (pH 9.6). To investigate mechanisms of mitogenomic evolution underlying adaptation to extreme environments, we determined 30 complete mitogenomes that included Lake Dali Nur (alkaline environment, AL) population and Amur basin (freshwater environment, FW) population. Through phylogenetic and divergence time analysis, we found that AL and FW populations forming distinct two groups which were consistent with geographic divergence (the formation of Lake Dali Nur). In addition, we found that almost of the windows exhibited higher nucleotide diversity in FW population (avg 0.0046) than AL population (avg 0.0012). This result indicated that severe environment selection had remarkably reduced the genetic diversity of mitogenome in AL population and suggested that severe environment selection had remarkably reduced the genetic diversity of mitogenome in the AL population. Compared with the FW population (ω = 0.064), the AL population (ω = 0.092) had a larger mean ω (dN/dS ratios) value for the 13 concatenated mitochondrial protein-coding genes, indicating that the high alkaline tolerated group had accumulated more nonsynonymous mutations. These nonsynonymous mutations had resulted in slightly beneficial amino acid changes that allowed adaption to the severe conditions. This study provides an additional view to decipher the adaptive mitogenome evolution of L. waleckii of the high alkaline environment.

Fine-Scale Population Genetic Structure and Parapatric Cryptic Species of Kuruma Shrimp (Marsupenaeus japonicus), Along the Northwestern Pacific Coast of China

The kuruma shrimp (Marsupenaeus japonicus) includes two cryptic species, which are distributed mostly allopatrically but co-occur in the northern South China Sea (from Huilai to Beihai). To obtain a better understanding of the fine-scale genetic structure and parapatric diversification of these two varieties in the northwestern Pacific region, we used a genotyping-by-sequencing (GBS) and comparative transcriptomics approach to establish their phylogenetic relationships. Using the GBS technique, we genotyped 28891 SNPs in 160 individuals in the Northwest Pacific. The results supported two highly diverged evolutionary lineages of kuruma shrimp (var. I and II). The ND and XM populations showed complex genetic patterns, which might be affected by the complex environment of the Taiwan Strait. In addition, the migration rates and inbreeding coefficients of XM and BH were much lower than those of the other populations, which might be related to the land-sea changes and complex ocean currents in the Taiwan Strait and Qiongzhou Strait. Based on the synonymous substitution rates (ds) of 2,491 candidate orthologs, we estimated that the divergence time between the two varieties was 0.26~0.69 Mya. Choice and no-choice interbreeding experiments provided support for the biological species concept, by showing the existence of reproductive isolation or incompatibility. In view of these differences between the two Marsupenaeus species, we believe that it is essential and urgent to establish a genetic database for each and reevaluate their ecological suitable conditions in order to improve species-specific culturing techniques. Moreover, this research can serve as a case study for future research on speciation and hybridization.

Comparative Genomics Identifies Putative Signatures of Sociality in Spiders

Comparative genomics has begun to elucidate the genomic basis of social life in insects, but insight into the genomic basis of spider sociality has lagged behind. To begin, to characterize genomic signatures associated with the evolution of social life in spiders, we performed one of the first spider comparative genomics studies including five solitary species and two social species, representing two independent origins of sociality in the genus Stegodyphus. We found that the two social spider species had a large expansion of gene families associated with transport and metabolic processes and an elevated genome-wide rate of molecular evolution compared with the five solitary spider species. Genes that were rapidly evolving in the two social species relative to the five solitary species were enriched for transport, behavior, and immune functions, whereas genes that were rapidly evolving in the solitary species were enriched for energy metabolism processes. Most rapidly evolving genes in the social species Stegodyphus dumicola were broadly expressed across four tissues and enriched for transport functions, but 12 rapidly evolving genes showed brain-specific expression and were enriched for social behavioral processes. Altogether, our study identifies putative genomic signatures and potential candidate genes associated with spider sociality. These results indicate that future spider comparative genomic studies, including broader sampling and additional independent origins of sociality, can further clarify the genomic causes and consequences of social life.

Comparative transcriptome analysis of Triplophysa yarkandensis in response to salinity and alkalinity stress

Triplophysa yarkandensis, a fish belonging to the family Nemacheilidae, is distributed in the Tarim River, China, immediately north of the Qinghai-Tibet Plateau. Due to increasing salinity and alkalinity in the Tarim River, the habitats of T. yarkandensis have been seriously altered. To identify the genes and pathways that are important for responding to salinity and alkalinity stress, the gill transcriptomes of fish living under different salinity and alkalinity conditions were obtained using RNA sequencing. A total of 1,123,448,964 clean reads were obtained and assembled into 177,271 unigenes, with an average length of 1703 bp. Around 13,526 unigenes showed differential expression when comparing different salinity concentrations with the controls, 6967 of which were upregulated and 6559 were downregulated. When comparing different alkalinity concentrations with the controls, there were 17,475 unigenes that showed differential expression, of which 10,457 were upregulated and 7018 were downregulated. Only 146 unigenes were both differentially expressed in salinity and alkalinity groups compared to the control. The results of KEGG enrichment showed that there were five upregulated and 12 downregulated pathways in fish subject to salinity treatment. For fish exposed to alkalinity treatment, 15 pathways were upregulated and 13 downregulated. There were four upregulated and four downregulated pathways that were shared by fish subject to salinity and alkalinity treatments. To our knowledge, this is the first study on the T. yarkandensis transcriptome; the information presented here will provide further understanding of the fish's response to salinity and alkalinity stress, as well as further insight into the T. yarkandensis genome.

The sequence and de novo assembly of Takifugu bimaculatus genome using PacBio and Hi-C technologies

Takifugu bimaculatus is a native teleost species of the southeast coast of China where it has been cultivated as an important edible fish in the last decade. Genetic breeding programs, which have been recently initiated for improving the aquaculture performance of T. bimaculatus, urgently require a high-quality reference genome to facilitate genome selection and related genetic studies. To address this need, we produced a chromosome-level reference genome of T. bimaculatus using the PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The genome was assembled into 2,193 contigs with a total length of 404.21 Mb and a contig N50 length of 1.31 Mb. After chromosome-level scaffolding, 22 chromosomes with a total length of 371.68 Mb were constructed. Moreover, a total of 21,117 protein-coding genes and 3,471 ncRNAs were annotated in the reference genome. The highly accurate, chromosome-level reference genome of T. bimaculatus provides an essential genome resource for not only the genome-scale selective breeding of T. bimaculatus but also the exploration of the evolutionary basis of the speciation and local adaptation of the Takifugu genus.

Patterns of Geographical and Potential Adaptive Divergence in the Genome of the Common Carp (Cyprinus carpio)

The common carp, Cyprinus carpio, is a cyprinid fish species cultured in Europe and Asia. It accounts for >70% of freshwater aquaculture production worldwide. We conducted a population genomics analysis on C. carpio using high-throughput SNP genotyping of 2,198 individuals from 14 populations worldwide to determine the genetic architecture of common carp populations and the genetic bases for environmental adaptation. Structure analyses including phylogeny and principal component analysis were also conducted, showing distinct geographical patterns in European and Asian populations. The linkage disequilibrium block average lengths of the 14 populations ranged from 3.94 kb to 36.67 kb. Genes within selective sweep regions were identified by genome scanning among the different populations, including gdf6a, bmpr1b, and opsin5. Gene Ontology and KEGG enrichment analyses revealed potential trait-related loci and genes associated with body shape, scaling patterns, and skin color. This population genomics analysis may provide valuable clues for future genome-assisted breeding of C. carpio.

De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication

For over a thousand years, the common goldfish (Carassius auratus) was raised throughout Asia for food and as an ornamental pet. As a very close relative of the common carp (Cyprinus carpio), goldfish share the recent genome duplication that occurred approximately 14 million years ago in their common ancestor. The combination of centuries of breeding and a wide array of interesting body morphologies provides an exciting opportunity to link genotype to phenotype and to understand the dynamics of genome evolution and speciation. We generated a high-quality draft sequence and gene annotations of a "Wakin" goldfish using 71X PacBio long reads. The two subgenomes in goldfish retained extensive synteny and collinearity between goldfish and zebrafish. However, genes were lost quickly after the carp whole-genome duplication, and the expression of 30% of the retained duplicated gene diverged substantially across seven tissues sampled. Loss of sequence identity and/or exons determined the divergence of the expression levels across all tissues, while loss of conserved noncoding elements determined expression variance between different tissues. This assembly provides an important resource for comparative genomics and understanding the causes of goldfish variants.

Divergence, evolution and adaptation in ray-finned fish genomes

With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications.

Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation

Background

Walking catfish (Clarias batrachus) is a freshwater fish capable of air-breathing and locomotion on land. It usually inhabits various low-oxygen habitats, burrows inside the mudflat, and sometimes “walks” to search for suitable environments during summer. It has evolved accessory air-breathing organs for respiring air and corresponding mechanisms to survive in such challenging environments. Thereby, it serves as a great model for understanding adaptations to terrestrial life.

Results

Comparative genomics with channel catfish (Ictalurus punctatus) revealed specific adaptations of C. batrachus in DNA repair, enzyme activator activity, and small GTPase regulator activity. Comparative analysis with 11 non-air-breathing fish species suggested adaptive evolution in gene expression and nitrogenous waste metabolic processes. Further, myoglobin, olfactory receptor related to class A G protein-coupled receptor 1, and sulfotransferase 6b1 genes were found to be expanded in the air-breathing walking catfish genome, with 15, 15, and 12 copies, respectively, compared to non-air-breathing fishes that possess only 1–2 copies of these genes. Additionally, we sequenced and compared the transcriptomes of the gill and the air-breathing organ to characterize the mechanism of aerial respiration involved in elastic fiber formation, oxygen binding and transport, angiogenesis, ion homeostasis and acid-base balance. The hemoglobin genes were expressed dramatically higher in the air-breathing organ than in the gill of walking catfish.

Conclusions

This study provides an important genomic resource for understanding the adaptive mechanisms of walking catfish to terrestrial environments. It is possible that the coupling of enhanced abilities for oxygen storage and oxygen transport through genomic expansion of myoglobin genes and transcriptomic up-regulation of hemoglobin and angiogenesis-related genes are important components of the molecular basis for adaptation of this aquatic species to terrestrial life.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5355-9) contains supplementary material, which is available to authorized users.

Transcriptional differences provide insight into environmental acclimatization in wild amur ide (Leuciscus waleckii) during spawning migration from alkalized lake to freshwater river

Amur ide (Leuciscus waleckii) inhabits alkaline water in Lake Dali Nur and migrates to fresh water river for spawning every year. To investigate the potential genetic mechanisms underlying their alkaline acclimation, adaptation, and spawning migration, we performed differential gene expression analysis using high-throughput RNA-Seq data from liver of Amur ide samples collected before and after spawning migration. First, the short RNA-Seq reads were de novo assembled into 44,318 contigs, and provided the transcriptome reference sequences. Differential gene expression analysis identified 2575 genes with significant differential expression (p-value ≤.01, log2-fold-change ≥2). GO enrichment and KEGG pathway analyses were subsequently performed to determine gene functions and regulation. The results indicated that there were numerous differentially expressed genes involved in acid-base regulation, nitrogenous waste excretion, sexual maturation and reproduction, and stress response. These results provide fundamental information for further analyses of the physiological and molecular mechanisms underlying Amur ide alkaline acclimation, adaptation, and spawning migration.

Phenotypic and molecular consequences of stepwise temperature increase across generations in a coral reef fish

Global warming will have far-reaching consequences for marine species over coming decades, yet the magnitude of these effects may depend on the rate of warming across generations. Recent experiments show coral reef fishes can compensate the metabolic challenges of elevated temperature when warm conditions are maintained across generations. However, the effects of a gradual temperature increase across generations remain unknown. In the present study, we analysed metabolic and molecular traits in the damselfish Acanthochromis polyacanthus that were exposed to +1.5°C in the first generation and +3.0°C in the second (Step +3.0°C). This treatment of stepwise warming was compared to fish reared at current-day temperatures (Control), second-generation fish of control parents reared at +3.0°C (Developmental +3.0°C) and fish exposed to elevated temperatures for two generations (Transgenerational +1.5°C and Transgenerational +3.0°C). Hepatosomatic index, oxygen consumption and liver gene expression were compared in second-generation fish of the multiple treatments. Hepatosomatic index increased in fish that developed at +3.0°C, regardless of the parental temperature. Routine oxygen consumption of Step +3.0°C fish was significantly higher than Control; however, their aerobic scope recovered to the same level as Control fish. Step +3.0°C fish exhibited significant upregulation of genes related to mitochondrial activity and energy production, which could be associated with their increased metabolic rates. These results indicate that restoration of aerobic scope is possible when fish experience gradual thermal increase across multiple generations, but the metabolic and molecular responses are different from fish reared at the same elevated thermal conditions in successive generations.

Bioinformatic analyses of zona pellucida genes in vertebrates and their expression in Nile tilapia

Zona pellucida (ZP) genes encode ZP glycoproteins which constitute the coat surrounding oocytes and early embryos. Genome-wide identification of ZP genes is still lacking in vertebrates, especially in fish species. Herein, we conducted bioinformatic analyses of the ZP genes of the Nile tilapia and other vertebrates. Totally 16, 9, 17, 27, 21, 20, 26, 19, 14,11, 24, 17, 9, 18, 8, 11, 9, 8, 5, and 4 ZP genes belonging to 5 subfamilies (ZPA, ZPB, ZPC, ZPD, and ZPAX) were found in the sea lamprey, elephant shark, coelacanth, spotted gar, zebrafish, medaka, stickleback, Nile tilapia, Amazon molly, platyfish, seahorse, Northern snakehead, cavefish, tetraodon, clawed frog, turtle, chicken, platypus, kangaroo rat, and human genomes, respectively. The expansion of ZP genes in basal vertebrates was mainly achieved by gene duplication of ZPB, ZPC, and ZPAX subfamilies, while the shrink of ZP gene number in viviparous mammals was achieved by keeping only one copy of the ZP genes in each subfamily or even secondary loss of some subfamilies. The number of ZP gene is related to the environment where the eggs are fertilized and the embryos develop in vertebrates. Transcriptomic analysis showed that 14 ZP genes were expressed in the ovary of Nile tilapia, while two (ZPB2b and ZPC2) were highly expressed in the liver. On the other hand, ZPB1a and ZPB2c were not found to be expressed in any tissue or at any developmental stage of the gonads examined. In the ovary, the expression of ZP genes started from 30 dah (days after hatching), significantly upregulated at 90 dah and maintained this level at 180 dah. The expression of ZPC2 in the liver and ZPC5-2 and ZPAX1 in the ovary was confirmed by in situ hybridization. The ovary- and liver-expressed ZP genes are expressed coordinately with oocyte growth in tilapia.

Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (Lateolabrax maculatus)

The marine species usually show high dispersal capabilities accompanied by high levels of gene flow. On the other hand, many physical barriers distribute along the continental marginal seas and may prevent dispersals and increase population divergence. These complexities along the continental margin generate serious challenges to population genetic studies of marine species. Chinese sea bass Lateolabrax maculatus distributes broad latitudinal gradient spanning from the tropical to the mid-temperate zones in the continental margin seas of the Northwest Pacific Ocean. Using the double digest restriction-site-associated DNA tag sequencing (ddRAD) approach, we genotyped 10,297 SNPs for 219 Chinese seabass individuals of 12 populations along the Chinese coast in the Northwest Pacific region. Genetic divergence among these populations was evaluated, and population structure was established. The results suggested that geographically distant populations in the Bohai Gulf and the Beibu Gulf retain significant genetic divergence, which are connected by a series of intermediate populations in between. The results also suggested that Leizhou Peninsula, Hainan Island, and Shandong Peninsula are major physical barriers and substantially block gene flow and genetic admixture of L. maculatus. We also investigated the potential genetic basis of local adaptation correlating with population differentiation of L. maculatus. The sea surface temperature is a significantly differentiated environmental factor for the distribution of L. maculatus. The correlation of water temperature and genetic variations in extensively distributed populations was investigated with Bayesian-based approaches. The candidate genes underlying the local selection in geographically divergent populations were identified and annotated, providing clues to understand the potential mechanisms of adaptive evolution. Overall, our genome scale population genetic analysis provided insight into population divergence and local adaptation of Chinese sea bass in the continental marginal seas along Chinese coast.

Genomic signature of highland adaptation in fish: a case study in Tibetan Schizothoracinae species

Background

Genome-wide studies on highland adaptation mechanism in terrestrial animal have been widely reported with few available for aquatic animals. Tibetan Schizothoracinae species are ideal model systems to study speciation and adaptation of fish. The Schizothoracine fish, Gymnocypris przewalskii ganzihonensis had underwent the ecological niche shift from salt water to freshwater, and also experienced a recent split from Gymnocypris przewalskii przewalskii. In addition, G. p. ganzihonensis inhabited harsh aquatic environment including low temperature and hypoxia as well as other Schizothoracinae species, its genetic mechanism of highland adaptation have yet to be determined.

Results

Our study used comparative genomic analysis based on the transcriptomic data of G. p. ganzihonensis and other four fish genome datasets to investigate the genetic basis of highland adaptation in Schizothoracine fish. We found that Schizothoracine fish lineage on the terminal branch had an elevated dN/dS ratio than its ancestral branch. A total of 202 gene ontology (GO) categories involved into transport, energy metabolism and immune response had accelerated evolutionary rates than zebrafish. Interestingly, we also identified 162 genes showing signature of positive selection (PSG) involved into energy metabolism, transport and immune response in G. p. ganzihonesis. While, we failed to find any PSG related to hypoxia response as previous studies.

Conclusions

Comparative genomic analysis based on G. p. ganzihonensis transcriptome data revealed significant genomic signature of accelerated evolution ongoing within Tibetan Schizothoracinae species lineage. Molecular evolution analysis suggested that genes involved in energy metabolism, transport and immune response functions in Schizothoracine fish underwent positive selection, especially in innate immunity including toll-like receptor signaling pathway genes. Taken together, our result as a case study in Schizothoracinae species provides novel insights in understanding the aquatic animal adaptation to extreme environment on the Tibetan Plateau, and also provides valuable genomic resource for further functional verification studies.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4352-8) contains supplementary material, which is available to authorized users.