Carrier-free chemo-phototherapeutic nanomedicines with endo/lysosomal escape function enhance the therapeutic effect of drug molecules in tumors.

Carrier-free nanomedicines offer advantages of extremely high drug loading capacity (>80%), minimal non-drug constituent burden, and facile preparation processes. Numerous studies have proved that multimodal cancer therapy can enhance chemotherapy efficiency and mitigate multi-drug resistance (MDR) through synergistic therapeutic effects. Upon penetration into the tumor matrix, nanoparticles (NPs) are anticipated to be uptaken by cancer cells, primarily through clathrin-meditated endocytosis pathways, leading to their accumulation in endosomes/lysosomes within cells. However, endo/lysosomes exhibit a highly degradative environment for organic NPs and drug molecules, often resulting in treatment failure. Hence, this study designed a lysosomal escape mechanism with carrier-free nanomedicine, combining the chemotherapeutic drug, curcumin (Cur), and the photothermal/photodynamic therapeutic drug, indocyanine green (ICG), for synergistic cancer treatment (ICG-Cur NPs) via a facile preparation process. To facilitate endo/lysosomal escape, ICG-Cur NPs were modified with metal-phenolic networks (MPNs) of different thickness. The results indicate that a thick MPN coating promotes rapid endo/lysosomal escape of ICG-Cur NPs within 4 h and enhances the photothermal conversion efficiency of ICG-Cur NPs by 55.8%, significantly improving anticancer efficacy in both chemo- and photo-therapies within 3D solid tumor models. This finding underscores the critical role of endo/lysosomal escape capacity in carrier-free drug NPs for therapeutic outcomes and offers a facile solution to achieve it.

Expansion of learning capacity elicited by interspecific hybridization.

Learned behavior, a fundamental adaptive trait in fluctuating environments, is shaped by species-specific constraints. This phenomenon is evident in songbirds, which acquire their species-specific songs through vocal learning. To explore the neurogenetic mechanisms underlying species-specific song learning, we generated F1 hybrid songbirds by crossing Taeniopygia guttata with Aidemosyne modesta. These F1 hybrids demonstrate expanded learning capacities, adeptly mimicking songs from both parental species and other heterospecific songs more extensively than their parental counterparts. Despite the conserved size of brain regions and neuron numbers in the neural circuits for song learning and production, single-cell transcriptomics reveals distinctive transcriptional characteristics in the F1 hybrids, especially in vocal-motor projection neurons. These neurons exhibit enrichment for nonadditively expressed genes, particularly those related to ion channel activity and cell adhesion, which are associated with the degree of song learning among F1 individuals. Our findings provide insights into the emergence of altered learning capabilities through hybridization, linked to cell type-specific transcriptional changes.

A predisposed motor bias shapes individuality in vocal learning.

The development of individuality during learned behavior is a common trait observed across animal species; however, the underlying biological mechanisms remain understood. Similar to human speech, songbirds develop individually unique songs with species-specific traits through vocal learning. In this study, we investigate the developmental and molecular mechanisms underlying individuality in vocal learning by utilizing F1 hybrid songbirds (Taeniopygia guttata cross with Taeniopygia bichenovii), taking an integrating approach combining experimentally controlled systematic song tutoring, unbiased discriminant analysis of song features, and single-cell transcriptomics. When tutoring with songs from both parental species, F1 hybrid individuals exhibit evident diversity in their acquired songs. Approximately 30% of F1 hybrids selectively learn either song of the two parental species, while others develop merged songs that combine traits from both species. Vocal acoustic biases during vocal babbling initially appear as individual differences in songs among F1 juveniles and are maintained through the sensitive period of song vocal learning. These vocal acoustic biases emerge independently of the initial auditory experience of hearing the biological father's and passive tutored songs. We identify individual differences in transcriptional signatures in a subset of cell types, including the glutamatergic neurons projecting from the cortical vocal output nucleus to the hypoglossal nuclei, which are associated with variations of vocal acoustic features. These findings suggest that a genetically predisposed vocal motor bias serves as the initial origin of individual variation in vocal learning, influencing learning constraints and preferences.

Music cues impact the emotionality but not richness of episodic memory retrieval.

Previous studies have found that music evokes more vivid and emotional memories of autobiographical events than various other retrieval cues. However, it is possible such findings can be explained by pre-existing differences between disparate events that are retrieved in response to each cue type. To test whether music exhibits differential effects to other cues even when memory encoding is controlled, we compared music and environmental sounds as cues for memories of the same set of dynamic visual scenes. Following incidental encoding of 14 scenes (7 with music, 7 with sounds), the music and sounds were presented to participants (N = 56), who were asked to describe the scenes associated with these cues, and rate various memory properties. Music elicited fewer correct memories and more effortful retrieval than sound cues, and no difference was found in memory detail/vividness between cue types. However, music-evoked memories were rated as more positive and less arousing. These findings provide important critical insights that only partially support the common notion that music differs from other cue types in its effects on episodic memory retrieval.

Development of a Method for Fast Assessment of Protein Solubility Based on Ultrasonic Dispersion and Differential Centrifugation Technology.

Protein solubility is very important for protein crystallization, bioprocess development, and protein application. In this study, a method based on the stability of a protein dispersion system is proposed for fast assessment of protein solubility, which mainly involves ultrasonic dispersion, differential centrifugation, and spectral measurement (UDDCS) and curvature estimation. The appropriate ultrasonic time and centrifugal time were experimentally determined at first. The results show that the relationship between the standard deviation and the protein concentrations originally added accords with the modified exponential equation, and the corresponding concentration of the maximum curvature point is defined as the solubility of the protein. Lysozyme solubility data in NaCl aqueous solutions and zein solubility data in ethanol aqueous solutions are selected to verify the UDDCS method by comparing the data obtained by the UDDCS method and the results from references, and the results indicate that the UDDCS method is reliable, universal, and time-saving. Finally, measurements of zein solubility in NaOH solution and casein solubility in urea aqueous solution were conducted as test cases by the UDDCS method.

Effects of Surfactants on Zein Cast Films for Simultaneous Delivery of Two Hydrophilic Active Components.

In order to prepare edible films with outstanding antimicrobials and antioxidants utilized in applications of food and pharmaceutics, in this study, effects of surfactants on zein cast films for simultaneous delivery of lysozyme (LY) and ascorbic acid (AA) were investigated, where sodium alginate (SA), soy lecithin (SL), and Pluronic f-68 (PF-68) were selected as surfactants. FT-IR tests indicated that SL or PF-68 dramatically changed secondary structure of zein composite films, which heightened the irregularity of the composite film and inhibited LY crystallization. Mechanical tests showed that highly flexible films exhibiting elongations between 129% and 157% were obtained when adding PF-68. Compared with the film without emulsifier, zein film containing SL and PF-68 showed approximately 7.51 and 0.55 times lower initial release rates for LY and AA respectively, which significantly improved the controlled release and heightened the anti-microbial and anti-oxidant activities of the film. Finally, emulsified mechanisms of the surfactants in zein films were proposed.

Potential low-calorie model that inhibits free fatty acid release and helps curcumin deliver in vitro: Ca2+-induced emulsion gels from low methyl-esterified pectin with the presence of erythritol.

Our previous study showed that pectin de-esterified by high hydrostatic pressure assisted enzymatic method (HHP-pectin) had better Ca2+-induced gel performance and more stable emulsion than those from conventional enzymatic and alkaline methods. In this study, Ca2+-induced emulsion gels were further prepared by HHP-pectin in the presence of erythritol, and their texture properties, moisture distribution, the release of free fatty acids (FFAs) and curcumin were investigated. Results showed that gel strength, gel elasticity, and water cut-off capacity of the prepared emulsion gels significantly increased with Ca2+ concentration increasing. Compared with emulsions, HHP-pectin emulsion gels can significantly decrease FFAs and curcumin release in vitro digestion, especially for samples with better texture properties (higher Ca2+ concentration). This study indicated that Ca2+-induced HHP-pectin emulsion gels prepared with erythritol may provide a new choice for low-calorie foods preparing, and may become a potential alternative model that inhibiting FFAs release and helping fat-soluble nutrients (curcumin) deliver.

Transcriptional regulatory divergence underpinning species-specific learned vocalization in songbirds.

Learning of most motor skills is constrained in a species-specific manner. However, the proximate mechanisms underlying species-specific learned behaviors remain poorly understood. Songbirds acquire species-specific songs through learning, which is hypothesized to depend on species-specific patterns of gene expression in functionally specialized brain regions for vocal learning and production, called song nuclei. Here, we leveraged two closely related songbird species, zebra finch, owl finch, and their interspecific first-generation (F1) hybrids, to relate transcriptional regulatory divergence between species with the production of species-specific songs. We quantified genome-wide gene expression in both species and compared this with allele-specific expression in F1 hybrids to identify genes whose expression in song nuclei is regulated by species divergence in either cis- or trans-regulation. We found that divergence in transcriptional regulation altered the expression of approximately 10% of total transcribed genes and was linked to differential gene expression between the two species. Furthermore, trans-regulatory changes were more prevalent than cis-regulatory and were associated with synaptic formation and transmission in song nucleus RA, the avian analog of the mammalian laryngeal motor cortex. We identified brain-derived neurotrophic factor (BDNF) as an upstream mediator of trans-regulated genes in RA, with a significant correlation between individual variation in BDNF expression level and species-specific song phenotypes in F1 hybrids. This was supported by the fact that the pharmacological overactivation of BDNF receptors altered the expression of its trans-regulated genes in the RA, thus disrupting the learned song structures of adult zebra finch songs at the acoustic and sequence levels. These results demonstrate functional neurogenetic associations between divergence in region-specific transcriptional regulation and species-specific learned behaviors.

Vocal practice regulates singing activity-dependent genes underlying age-independent vocal learning in songbirds.

The development of highly complex vocal skill, like human language and bird songs, is underlain by learning. Vocal learning, even when occurring in adulthood, is thought to largely depend on a sensitive/critical period during postnatal development, and learned vocal patterns emerge gradually as the long-term consequence of vocal practice during this critical period. In this scenario, it is presumed that the effect of vocal practice is thus mainly limited by the intrinsic timing of age-dependent maturation factors that close the critical period and reduce neural plasticity. However, an alternative, as-yet untested hypothesis is that vocal practice itself, independently of age, regulates vocal learning plasticity. Here, we explicitly discriminate between the influences of age and vocal practice using a songbird model system. We prevented zebra finches from singing during the critical period of sensorimotor learning by reversible postural manipulation. This enabled to us to separate lifelong vocal experience from the effects of age. The singing-prevented birds produced juvenile-like immature song and retained sufficient ability to acquire a tutored song even at adulthood when allowed to sing freely. Genome-wide gene expression network analysis revealed that this adult vocal plasticity was accompanied by an intense induction of singing activity-dependent genes, similar to that observed in juvenile birds, rather than of age-dependent genes. The transcriptional changes of activity-dependent genes occurred in the vocal motor robust nucleus of the arcopallium (RA) projection neurons that play a critical role in the production of song phonology. These gene expression changes were accompanied by neuroanatomical changes: dendritic spine pruning in RA projection neurons. These results show that self-motivated practice itself changes the expression dynamics of activity-dependent genes associated with vocal learning plasticity and that this process is not tightly linked to age-dependent maturational factors.

Facile encapsulation of hydroxycamptothecin nanocrystals into zein-based nanocomplexes for active targeting in drug delivery and cell imaging.

Nano-drug delivery systems that integrate inorganic and organic or even bioactive components into a single nanoscale platform are playing a hugely important role in cancer treatment. In this article, the fabrication of a versatile nanocarrier based on self-assembled structures of gold nanoparticles (AuNPs)-zein is reported, which displays high drug-loading efficiency for needle-shaped hydroxycamptothecin (HCPT) nanocrystals. The surface modification with folate-conjugated polydopamine (PFA) renders them stable and also facilitates their selective cellular internalization and enhancement of endocytosis. The release of payloads from nanocomplexes (NCs) was shown to be limited at physiological pH (17.1±2.8%) but significantly elevated at endosomal/lysosomal pH (58.4±3.0%) and at enzymatic environment (81.4±4.2%). Compared to free HCPT and its non-targeting equivalent, HCPT@AuNPs-Zein-PFA exerted a superior tumor suppression capacity as well as low side effects due to its active and passive targeting delivery both in vitro and in vivo. These results suggest that the NCs with well-defined core@shell nanostructures encapsulated with HCPT nanocrystals hold great promise to improve cancer therapy with high efficiency in the clinic. STATEMENT OF SIGNIFICANCE: A novel nanocomplex with HCPT nanocrystals encapsulated was designed to achieve selective cellular uptake by endocytosis, acid responsive release in the tumor microenvironment and excellent tumor suppression without toxicity. This nanocomplex with conjugation of folate was stable in the bloodstream, with minimal drug release in extracellular conditions, leading to prolonged blood circulation and high accumulation in tumor tissues. The entrapment of a nanocrystal drug into nanomaterials might be capable of delivering drugs in a predictable and controllable manner.

Transcriptome analysis of tube foot and large scale marker discovery in sea cucumber, Apostichopus japonicus.

Tube foot as one of the ambulacral appendages types in Aspidochirote holothurioids, is known for their functions in locomotion, feeding, chemoreception, light sensitivity and respiration. In this study, we explored the characteristic of transcriptome in the tube foot of sea cucumber (Apostichopus japonicus). Our results showed that among 390 unigenes which specifically expressed in the tube foot, 190 of them were annotated. Based on the assembly transcriptome, we found 219,860 SNPs from 34,749 unigenes, 97,683, 53,624, 27,767 and 40,786 were located in CDSs, 5'-UTRs, 3'-UTRs and non-CDS separately. Furthermore, 12,114 SSRs were detected from 7394 unigenes. Target genes of four specifically expressed miRNAs (miR-29a, miR-29b, miR-278-3p and miR-2005) in tube foot were also predicted based on the transcriptome, which contain immune-related factors (MBL, VLRA, AjC3, MyD88, CFB), skin pigmentation (MITF), candidate regeneration factor (TRP) and holothurians autolysis-related factor (CL). These results develop a relatively large number of molecular markers and transcriptome resources, and will provide a foundation for further analyses on the function and molecular mechanisms underlying A. japonicas tube foot.

A quantitative method for analyzing species-specific vocal sequence pattern and its developmental dynamics.

BACKGROUND: Songbirds are a preeminent animal model for understanding the neural basis underlying the development and evolution of a complex learned behavior, bird song. However, only a few quantitative methods exist to analyze these species-specific sequential behaviors in multiple species using the same calculation method. NEW METHOD: We report a method of analysis that focuses on calculating the frequency of characteristic syllable transitions in songs. This method comprises two steps: The first step involves forming correlation matrices of syllable similarity scores, named syllable similarity matrices (SSMs); these are obtained by calculating the round-robin comparison of all the syllables in two songs, while maintaining the sequential order of syllables in the songs. In the second step, each occurrence rate of three patterns of binarized "2 rows×2 columns" cells in the SSMs is calculated to extract information on the characteristic syllable transitions. RESULTS: The SSM analysis method allowed obtaining species-specific features of song patterns and intraspecies individual variability simultaneously. Furthermore, it enabled quantitative tracking of the developmental trajectory of the syllable sequence patterns. COMPARISON WITH EXISTING METHOD: This method enables us to extract the species-specific song patterns and dissect the regulation of song syntax development without human-biased procedures for syllable identification. This method can be adapted to study the acoustic communication systems in several animal species, such as insects and mammals. CONCLUSIONS: This present method provides a comprehensive qualitative approach for understanding the regulation of species specificity and its development in vocal learning.

Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus.

Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origin, but they are morphologically and functionally very different. In the present study, we performed comparative transcriptome analysis of the papilla and skin from the sea cucumber (Apostichopus japonicus) in order to identify and characterize gene expression profiles by using RNA-Seq technology. We generated 30.6 and 36.4 million clean reads from the papilla and skin and de novo assembled in 156,501 transcripts. The Gene Ontology (GO) analysis indicated that cell part, metabolic process and catalytic activity were the most abundant GO category in cell component, biological process and molecular funcation, respectively. Comparative transcriptome analysis between the papilla and skin allowed the identification of 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at higher levels in skin. In addition, 236 differentially expressed unigenes were not annotated with any database, 160 of which were apparently expressed at higher levels in papilla, 76 were expressed at higher levels in skin. We identified a total of 288 papilla-specific genes, 171 skin-specific genes and 600 co-expressed genes. Also, 40 genes in papilla-specific were not annotated with any database, 2 in skin-specific. Development-related genes were also enriched, such as fibroblast growth factor, transforming growth factor-ß, collagen-α2 and Integrin-α2, which may be related to the formation of the papilla and skin in sea cucumber. Further pathway analysis identified ten KEGG pathways that were differently enriched between the papilla and skin. The findings on expression profiles between two key organs of the sea cucumber should be valuable to reveal molecular mechanisms involved in the development of organs that are related but with morphological differences in the sea cucumber.

In vitro and in vivo anti-tumor efficacy of 10-hydroxycamptothecin polymorphic nanoparticle dispersions: shape- and polymorph-dependent cytotoxicity and delivery of 10-hydroxycamptothecin to cancer cells.

Nanotechnology associated with a crystal engineering approach was proposed for improving the solubility and efficacy of hydrophobic drugs in this study. 10-hydroxycamptothecin polymorphic nanoparticle dispersions (HCPT-PNDs) were prepared using the supercritical anti-solvent technique coupled with the high-pressure homogenization method. Shape- and polymorph-dependent tumor suppression was observed in both in vitro and in vivo models, where needle-shaped HCPT-PND exhibited dramatic improvement of antitumor efficacy. A benefit of controllable size and a large surface-to-volume ratio of needle-shaped nanoparticles is the improvement of dissolution properties, which facilitates enhancing pharmacokinetic and pharmaco-dynamic properties. The needle-shaped HCPT-PND, which with longer blood retention time and more effective cellular uptake, makes it possible to accumulate drug in tumor tissues and exhibit higher cytotoxicity. No severe systemic toxicity was observed due to sustained-dissolution and the low dose of drug in normal tissues. The results suggest that the needle-shaped HCPT-PND is an interesting nano-formulation of HCPT. FROM THE CLINICAL EDITOR: Nanotechnology has enabled the production of novel therapeutics drugs against cancer. Here, the authors investigated the use of a crystal engineering approach for the modification of camptothecin in order to improve its water solubility. Physicochemical and biological properties were studied. The results would suggest the applicability of this approach for nano-formulation.

New polymorphs of 9-nitro-camptothecin prepared using a supercritical anti-solvent process.

Recrystallization and micronization of 9-nitro-camptothecin (9-NC) has been investigated using the supercritical anti-solvent (SAS) technology in this study. Five operating factors, i.e., the type of organic solvent, the concentration of 9-NC in the solution, the flow rate of 9-NC solution, the precipitation pressure and the temperature, were optimized using a selected OA16 (4(5)) orthogonal array design and a series of characterizations were performed for all samples. The results showed that the processed 9-NC particles exhibited smaller particle size and narrower particle size distribution as compared with 9-NC raw material (Form I), and the optimum micronization conditions for preparing 9-NC with minimum particle size were determined by variance analysis, where the solvent plays the most important role in the formation and transformation of polymorphs. Three new polymorphic forms (Form II, III and IV) of 9-NC, which present different physicochemical properties, were generated after the SAS process. The predicted structures of the 9-NC crystals, which were consistent with the experiments, were performed from their experimental XRD data by the direct space approach using the Reflex module of Materials Studio. Meanwhile, the optimal sample (Form III) was proved to have higher cytotoxicity against the cancer cells, which suggested the therapeutic efficacy of 9-NC is polymorph-dependent.

Identification and Characterization of MicroRNAs from Longitudinal Muscle and Respiratory Tree in Sea Cucumber (Apostichopus japonicus) Using High-Throughput Sequencing.

MicroRNAs (miRNAs), as a family of non-coding small RNAs, play important roles in the post-transcriptional regulation of gene expression. Sea cucumber (Apostichopus japonicus) is an important economic species which is widely cultured in East Asia. The longitudinal muscle (LTM) and respiratory tree (RPT) are two important tissues in sea cucumber, playing important roles such as respiration and movement. In this study, we identified and characterized miRNAs in the LTM and RPT of sea cucumber (Apostichopus japonicus) using Illumina HiSeq 2000 platform. A total of 314 and 221 conserved miRNAs were identified in LTM and RPT, respectively. In addition, 27 and 34 novel miRNAs were identified in the LTM and RPT, respectively. A set of 58 miRNAs were identified to be differentially expressed between LTM and RPT. Among them, 9 miRNAs (miR-31a-3p, miR-738, miR-1692, let-7a, miR-72a, miR-100b-5p, miR-31b-5p, miR-429-3p, and miR-2008) in RPT and 7 miRNAs (miR-127, miR-340, miR-381, miR-3543, miR-434-5p, miR-136-3p, and miR-300-3p) in LTM were differentially expressed with foldchange value being greater than 10. A total of 14,207 and 12,174 target genes of these miRNAs were predicted, respectively. Functional analysis of these target genes of miRNAs were performed by GO analysis and pathway analysis. This result provided in this work will be useful for understanding biological characteristics of the LTM and RPT of sea cucumber and assisting molecular breeding of sea cucumber for aquaculture.

Characterization and expression analysis of microRNAs in the tube foot of sea cucumber Apostichopus japonicus.

MicroRNAs (miRNAs) are a class of endogenous non-coding small RNA with average length of 22 nucleotides, participating in the post-transcriptional regulation of gene expression. In this study, we report the identification and characterization of miRNAs in the tube foot of sea cucumber (Apostichopus japonicus) by next generation sequencing with Illumina HiSeq 2000 platform. Through the bioinformatic analysis, we identified 260 conserved miRNAs and six novel miRNAs from the tube foot small RNA transcriptome. Quantitative realtime PCR (qRT-PCR) was performed to characterize the specific expression in the tube foot. The results indicated that four miRNAs, including miR-29a, miR-29b, miR-2005 and miR-278-3p, were significantly up-regulated in the tube foot. The target genes of the four specifically expressed miRNAs were predicted in silico and validated by performing qRT-PCR. Gene ontology (GO) and KEGG pathway analyses with the target genes of these four miRNAs were conducted to further understand the regulatory function in the tube foot. This is the first study to profile the miRNA transcriptome of the tube foot in sea cucumber. This work will provide valuable genomic resources to understand the mechanisms of gene regulation in the tube foot, and will be useful to assist the molecular breeding in sea cucumber.

Identification of two SNPs in myostatin (MSTN) gene of Takifugu rubripes and their association with growth traits.

The myostatin (MSTN) is a member of transforming growth factor-ß superfamily which inhibits muscle growth. In this study, the genomic DNA sequence of MSTN gene was cloned from Takifugu rubripes (T. rubripes). Two polymorphisms of the MSTN gene were detected by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing methods in 296 T. rubripes. One A748G locates in exon 2 and the other, C1197T, in intron 2. Analysis showed that the A748G mutation caused an amino acid change from Thr to Ala (Ala166Glu). These two SNPs showed a low degree of linkage disequilibrium and four haplotypes were identified. The most frequent haplotype was AC, which occurred at a frequency of 44.3%. Association analyses between these two SNPs and growth traits showed that the individuals with genotype CT and TT of the mutation C1197T had significantly higher body mass, body length and body height than those with genotype CC (P < 0.05). These results show that MSTN gene can be utilized as a candidate gene for molecular marker-assisted breeding of T. rubripes.

Transcriptome analysis of the gill of Takifugu rubripes using Illumina sequencing for discovery of SNPs.

Single nucleotide polymorphisms (SNPs) have become the marker of choice for genome-wide association studies in many species. High-throughput sequencing of RNA was developed primarily to analyze global gene expression, while it is an efficient way to discover SNPs from the expressed genes. In this study, we conducted transcriptome sequencing of the gill samples of Takifugu rubripes analyzed by using Illumina HiSeq 2000 platform to identify gene-associated SNPs from the transcriptome of T. rubripes gill. A total of 27,085,235 unique-mapped-reads from 55,061,524 raw data reads were generated. A total of 56,972 putative SNPs were discovered, which were located in 11,327 genes. 35,839 SNPs were transitions (Ts), 21,074 SNPs were transversions (Tv) and 88.1% of 56,972 SNPs were assigned to the 22 chromosomes. The average minor allele frequency (MAF) of the SNPs was 0.26. GO and KEGG pathway analyses were conducted to analyze the genes containing SNPs. Validation of selected SNPs revealed that 63.4% of SNPs (34/52) were true SNPs. RNA-Seq is a cost-effective way to discover gene-associated SNPs. In this study, a large number of SNPs were identified and these data will be useful resources for population genetic study, evolution analysis, resource assessment, genetic linkage analysis and genome-wide association studies. The results of our study can also offer some useful information as molecular makers to help select and cultivate T. rubripes.

SNP discovery from transcriptome of the swimbladder of Takifugu rubripes.

Single nucleotide polymorphisms (SNPs) have become the marker of choice for genome-wide association studies in many species. High-throughput sequencing of RNA was developed primarily to analyze global gene expression, while it is an efficient way to discover SNPs from the expressed genes. In this study, we conducted transcriptome sequencing of the swimbladder of Takifugu rubripes using Illumina HiSeq2000 platform to identify gene-associated SNPs in the swimbladder. A total of 30,312,181 unique-mapped-reads were obtained from 44,736,850 raw reads. A total of 62,270 putative SNPs were discovered, which were located in 11,306 expressed genes and 2,246 scaffolds. The average minor allele frequency (MAF) of the SNPs was 0.26. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Validation of selected SNPs revealed that 54% of SNPs (26/48) were true SNPs. The results suggest that RNA-Seq is an efficient and cost-effective approach to discover gene-associated SNPs. In this study, a large number of SNPs were identified and these data will be useful resources for population genetic study, evolution analysis, resource assessment, genetic linkage analysis and genome-wide association studies.