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

Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei

Penaeusvannamei is the most important economic shrimp in the world. Many selective breeding programs are carried out to improve its production and performance traits. Although significant differences in the reproductive ability of female P. vannamei under artificial breeding conditions have been reported, the genome-wide adaption of the reproductive ability of domesticated female P. vannamei is less investigated. In this study, whole-genome analysis was performed along with pooled DNA sequencing on two fecundity separated bulks, high fecundity bulk (HB), and low fecundity bulk (LB). Each bulk contained 30 individuals from 3 commercial populations. A sequencing depth of >30× was achieved for each bulk, leading to the identification of 625,181 and 629,748 single nucleotide polymorphisms (SNPs) in HB and LB, respectively. Fixation index (Fst) combined with p ratio allowed for the identification of 145 selective sweep regions, with a sequence length of 14.5 Mb, accounting for 0.59% of the genome. Among the 145 selective sweep regions, a total of 64,046 SNPs were identified, and further verification was performed by genotyping 50 candidate SNPs on 60 samples from the offspring of the three populations. Furthermore, 121 genes were screened from the sweep regions. GO annotation and KEGG enrichment analyses showed that partial genes were essential for fecundity regulation. This study provides important information for in-depth investigation of genomic characteristics for long-term selective breeding on the fecundity of female P. vannamei and will also be important for genome-assisted breeding of P. vannamei in the future.

The use of molecular markers in the verification of fish and seafood authenticity and the detection of adulteration

The verification of authenticity and detection of food mislabeling are elements that have been of high importance for centuries. During the last few decades there has been an increasing consumer demand for the verification of food identity and the implementation of stricter controls around these matters. Fish and seafood are among the most easily adulterated foodstuffs mainly due to the significant alterations of the species' morphological characteristics that occur during the different types of processing, which render the visual identification of the animals impossible. Even simple processes, such as filleting remove very important morphological elements and suffice to prevent the visual identification of species in marketed products. Novel techniques have therefore been developed that allow identification of species, the differentiation between species and also the differentiation of individuals that belong to the same species but grow in different populations and regions. Molecular markers have been used during the last few decades to fulfill this purpose and several improvements have been implemented rendering their use applicable to a commercial scale. The reliability, accuracy, reproducibility, and time-and cost-effectiveness of these techniques allowed them to be established as routine methods in the industry and research institutes. This review article aims at presenting the most important molecular markers used for the authentication of fish and seafood. The most important techniques are described, and the results of numerous studies are outlined and discussed, allowing interested parties to easily access and compare information about several techniques and fish/seafood species.

The important role of phagocytosis and interleukins for nile tilapia (Oreochromis niloticus) to defense infection of Aeromonas hydrophila based on transcriptome analysis

Tilapia is an important economic fish worldwide. It is vital to understand the mechanism of immune response for the prevention and treatment the infection of Aeromonas hydrophila. Based on high-throughput sequencing of Illumina HiSeq™, we found differentially expressed genes in the immune-related pathway were classified into phagosome, cytokine-cytokine receptor interaction and toll-like receptor signaling pathway. Gene Ontology terms were divided into three categories of transporting function, DNA replication activity and energy supply activity. The first one was related to phagocytosis and the process or transporting of antigen driven by tubulins; the second one was to differentiation and proliferation of lymphocyte activated by cytokines; and the former two both needed energy provided by the third one. According to colchicine assay, cross-immune assay, ELISA of interleukins and classical phagocytosis assay, phagocytosis and interleukins were verified to be most important to defense the infection of A. hydrophila.

Liver transcriptome analysis of the Sparus macrocephlus in response to Vibrio parahaemolyticus infection

The black seabream (Sparus macrocephlus) is an economically pivotal aquaculture species cultured in China and Southeast Asian countries. To understand the molecular immune mechanisms underlying the response to Vibrio parahaemolyticus, a comparative gene transcription analysis were performed with utilized fresh livers of V. parahaemolyticus-immunized Sparus macrocephlus with a control group through RNA-Seq technology. A total of 256663 contigs were obtained after excluded the low-quality sequences and assembly. The average length of contigs collected from this research is 1066.93 bp. Furthermore, blast analysis indicates 30747 contigs were annotated based on homology with matches in the NT, NR, gene, and string databases. A gene ontology analysis was employed to classify 21598 genes according to three major functional categories: molecular function, cellular component, and biological process. A total of 14470 genes were discovered in 303 KEGG pathways. RSEM and EdgeR were introduced to estimate 3841 genes significantly different expressed (False Discovery Rate<0.001) which includes 4072 up-regulated genes and 3771 down-regulated genes. A significant enrichment analysis of these differentially expressed genes and isogenes were conducted to reveal the major immune-related pathways which refer to the toll-like receptor, complement, coagulation cascades, and chemokine signaling pathways. In addition, 92175 potential simple sequence repeats (SSRs) and 121912 candidate single nucleotide polymorphisms (SNPs) were detected and identified sequencely in the Sparus macrocephlus liver transcriptome. This research characterized a gene expression pattern for normal and the V. parahaemolyticus -immunized Sparus macrocephlus for the first time and not only sheds new light on the molecular mechanisms underlying the host-V. parahaemolyticus interaction but contribute to facilitate future studies on Sparus macrocephlus gene expression and functional genomics.

Immune-Related Functional Differential Gene Expression in Koi Carp (Cyprinus carpio) after Challenge with Aeromonas sobria

In order to understand the molecular basis underlying the host immune response of koi carp (Cyprinus carpio), Illumina HiSeq^TM 2000 is used to analyze the muscle and spleen transcriptome of koi carp infected with Aeromonas sobria (A. sobria). De novo assembly of paired-end reads yielded 69,480 unigenes, of which the total length, average length, N50, and GC content are 70,120,028 bp, 1037 bp, 1793 bp, and 45.77%, respectively. Annotation is performed by comparison against various databases, yielding 42,229 (non-redundant protein sequence (NR): 60.78%), 59,255 (non-redundant nucleotide (NT): 85.28%), 35,900 (Swiss-Prot: 51.67%), 11,772 (clusters of orthologous groups (COG): 16.94%), 33,057 (Kyoto Encyclopedia of Genes and Genomes (KEGG): 47.58%), 18,764 (Gene Ontology (GO): 27.01%), and 32,085 (Interpro: 46.18%) unigenes. Comparative analysis of the expression profiles between bacterial challenge fish and control fish identifies 7749 differentially expressed genes (DEGs) from the muscle and 7846 DEGs from the spleen. These DEGs are further categorized with KEGG. Enrichment analysis of the DEGs and unigenes reveals major immune-related functions, including up-regulation of genes related with Toll-like receptor signaling, complement and coagulation cascades, and antigen processing and presentation. The results from RNA-Seq data are also validated and confirmed the consistency of the expression levels of seven immune-related genes after 24 h post infection with qPCR. Microsatellites (11,534), including di-to hexa nucleotide repeat motifs, are also identified. Altogether, this work provides valuable insights into the underlying immune mechanisms elicited during bacterial infection in koi carp that may aid in the future development of disease control measures in protection against A. sobria.

Identification of SNPs potentially related to immune responses and growth performance in Litopenaeus vannamei by RNA-seq analyses

Litopenaeus vannamei is one of the most important shrimp species for worldwide aquaculture. Despite this, little genomic information is available for this penaeid and other closely related taxonomic crustaceans. Consequently, genes, proteins and their respective polymorphisms are poorly known for these species. In this work, we used the RNA sequencing technology (RNA-seq) in L. vannamei shrimp evaluated for growth performance, and exposed to the White Spot Syndrome Virus (WSSV), in order to investigate the presence of Single Nucleotide Polymorphisms (SNPs) within genes related to innate immunity and growth, both features of great interest for aquaculture activity. We analyzed individuals with higher and lower growth rates; and infected (unhealthy) and non-infected (healthy), after exposure to WSSV. Approximately 7,000 SNPs were detected in the samples evaluated for growth, being 3,186 and 3,978 exclusive for individuals with higher and lower growth rates, respectively. In the animals exposed to WSSV we found about 16,300 unique SNPs, in which 9,338 were specific to non-infected shrimp, and 7,008 were exclusive to individuals infected with WSSV and symptomatic. In total, we describe 4,312 unigenes containing SNPs. About 60% of these unigenes returned GO blastX hits for Biological Process, Molecular Function and Cellular Component ontologies. We identified 512 KEGG unique KOs distributed among 275 pathways, elucidating the majority of metabolism roles related to high protein metabolism, growth and immunity. These polymorphisms are all located in coding regions, and certainly can be applied in further studies involving phenotype expression of complex traits, such as growth and immunity. Overall, the set of variants raised herein enriches the genomic databases available for shrimp, given that SNPs originated from nextgen are still rare for this relevant crustacean group, despite their huge potential of use in genomic selection approaches.

Omics in fish mucosal immunity

The mucosal immune system of fish is a complex network of immune cells and molecules that are constantly surveilling the environment and protecting the host from infection. A number of "omics" tools are now available and utilized to understand the complexity of mucosal immune systems in non-traditional animal models. This review summarizes recent advances in the implementation of "omics" tools pertaining to the four mucosa-associated lymphoid tissues in teleosts. Genomics, transcriptomics, proteomics, and "omics" in microbiome research require interdisciplinary collaboration and careful experimental design. The data-rich datasets generated are proving really useful at discovering new innate immune players in fish mucosal secretions, identifying novel markers of specific mucosal immune responses, unraveling the diversity of the B and T cell repertoires and characterizing the diversity of the microbial communities present in teleost mucosal surfaces. Bioinformatics, data analysis and storage platforms should be developed to facilitate rapid processing of large datasets, especially when mammalian tools such as bioinformatics analysis software are not available in fishes.

iTRAQ-based proteomic analysis of myofibrillar contents and relevant synthesis and proteolytic proteins in soleus muscle of hibernating Daurian ground squirrels (Spermophilus dauricus)

BACKGROUND

Daurian ground squirrels (Spermophilus dauricus) deviate from significant increase of protein catabolism and loss of myofibrillar contents during long period of hibernation inactivity.

METHODS

Here we use iTRAQ based quantitative analysis to examine proteomic changes in the soleus of squirrels in pre-hibernation, hibernation and post-hibernation states. The total proteolysis rate of soleus was measured by the release of the essential amino acid tyrosine from isolated muscles. Immunofluorescent analysis was used to determine muscle fiber cross-sectional area. Western blot was used for the validation of the quantitative proteomic analysis.

RESULTS

The proteomic responses to hibernation had a 0.4- to 0.8-fold decrease in the myofibrillar contractile protein levels of myosin-3, myosin-13 and actin, but a 2.1-fold increase in myosin-2 compared to pre-hibernation group. Regulatory proteins such as troponin C and tropomodulin-1 were 1.4-fold up-regulated and 0.7-fold down-regulated, respectively, in hibernation compared to pre-hibernation group. Moreover, 10 proteins with proteolytic function in hibernation, which was less than 14 proteins in the post-hibernation group, were up-regulated relative to the pre-hibernation group. The total proteolysis rates of soleus in hibernation and post-hibernation groups were significantly inhibited as compared with pre-hibernation group.

CONCLUSION

These findings suggest that the myofibrillar remodeling and partial suppression of myofibrillar proteolysis were likely responsible for preventing skeletal muscle atrophy during prolonged disuse in hibernation. This is the first study where the myofibrillar contents and relevant synthesis and proteolytic proteins in slow soleus was discussed based on proteomic investigation performed on wild Daurian ground squirrels. Our results lay the foundation for further research in preventing disuse-induced skeletal muscle atrophy in mammals.

De Novo Transcriptome Analysis of Differential Functional Gene Expression in Largemouth Bass (Micropterus salmoides) after Challenge with Nocardia seriolae

Largemouth bass (Micropterus salmoides) are common hosts of an epizootic bacterial infection by Nocardia seriolae. We conducted transcriptome profiling of M. salmoides to understand the host immune response to N. seriolae infection, using the Illumina sequencing platform. De novo assembly of paired-end reads yielded 47,881 unigenes, the total length, average length, N50, and GC content of which were 49,734,288, 1038, 1983 bp, and 45.94%, respectively. Annotation was performed by comparison against non-redundant protein sequence (NR), non-redundant nucleotide (NT), Swiss-Prot, Clusters of Orthologous Groups (COG), Kyoto Encyclopaedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Interpro databases, yielding 28,964 (NR: 60.49%), 36,686 (NT: 76.62%), 24,830 (Swissprot: 51.86%), 8913 (COG: 18.61%), 20,329 (KEGG: 42.46%), 835 (GO: 1.74%), and 22,194 (Interpro: 46.35%) unigenes. Additionally, 8913 unigenes were classified into 25 Clusters of Orthologous Groups (KOGs) categories, and 20,329 unigenes were assigned to 244 specific signalling pathways. RNA-Seq by Expectation Maximization (RSEM) and PossionDis were used to determine significantly differentially expressed genes (False Discovery Rate (FDR) < 0.05) and we found that 1384 were upregulated genes and 1542 were downregulated genes, and further confirmed their regulations using reverse transcription quantitative PCR (RT-qPCR). Altogether, these results provide information on immune mechanisms induced during bacterial infection in largemouth bass, which may facilitate the prevention of nocardiosis.

Transcriptome profiling analysis of rare minnow (Gobiocypris rarus) gills after waterborne cadmium exposure

Rare minnow (Gobiocypris rarus) is a widely used experimental fish in risk assessments of aquatic pollutants in China. Cadmium (Cd) is one of the most toxic heavy metals in the world; however, few studies have used fish gills, a multi-functional organ. In this study, we characterized the differential expression of adult female rare minnow gills after sub-chronic waterborne Cd (75μg/L CdCl2) exposure for 35d. A total of 452 genes (209 up-regulated and 243 down-regulated) were identified by gene expression profiling using RNA-Seq before and after treatment. Of these differentially expressed genes, 75, 21, and 54 differentially expressed genes are related to ion transport, oxidation-reduction processes, and the immune response, respectively. The results of GO and KEGG enrichment analyses, together with the altered transcript levels of major histocompatibility complex (MHC) class I and class II molecules and the significant increases in the levels of serum tumor necrosis factor α (TNF-α), interleukin 1β (IL1β) and nuclear factor-κB (NF-κB), indicated a disruption of the immune system, particularly the induction of inflammation and autoimmunity. The significant down-regulation of coagulation factor XIII A1 polypeptide (F13A1), tripartite motif-containing protein 21 (TRIM21), and Golgi-associated plant pathogenesis-related protein (GAPr) during both acute (≤96h) and sub-chronic (35d) waterborne Cd exposure, as well as their dosage dependence, suggested that these three genes could be used as sensitive biomarkers for aquatic Cd risk assessment.

Transcriptome analysis of the Larimichthys crocea liver in response to Cryptocaryon irritans

The large yellow croaker (Larimichthys crocea) is an economically important marine fish cultured in China and East Asian countries and is facing a serious threat from Cryptocaryon irritans, which is a protozoan ectoparasite that infects most reared marine fish species. To understand the molecular immune mechanisms underlying the response to C. irritans, we first performed a comparative gene transcription analysis using livers from C. irritans-immunized L. croceas and from a control group through RNA-Seq technology. After the removal of low-quality sequences and assembly, 51360 contigs were obtained, with an average length of 1066.93 bp. Further, a blast analysis indicates that 30747 contigs can be annotated based on homology with matches in the NT, NR, gene, and string databases. A gene ontology analysis was used to classify 21598 genes according to three major functional categories: molecular function, cellular component, and biological process. Moreover, 14470 genes were found in 303 KEGG pathways. We used RSEM and EdgeR to determine that 3841 genes were significantly differentially expressed (FDR < 0.001), including 2129 up-regulated genes and 1712 down-regulated genes. A significant enrichment analysis of these differentially expressed genes and isogenes revealed major immune-related pathways, including the toll-like receptor, complement and coagulation cascades, and chemokine signaling pathways. In addition, 28748 potential simple sequence repeats (SSRs) were detected from 12776 transcripts, and 62992 candidate single nucleotide polymorphisms (SNPs) were identified in the L. croceas liver transcriptome. This study characterized a gene expression pattern for normal and C. irritans-immunized L. croceas for the first time and not only sheds new light on the molecular mechanisms underlying the host-C. irritans interaction but also facilitates future studies on L. croceas gene expression and functional genomics.

De novo assembly and characterization of tissue-specific transcriptome in the endangered golden mahseer, Tor putitora

The golden mahseer (Tor putitora) graces most of the Himalayan Rivers of India and neighboring South Asian countries. Despite its several importance as a research model, as food, and in sport fishing, knowledge on transcriptome database is nil. Therefore, it was targeted to develop reference transcriptome databases of the species using next-generation sequencing. In the present study, 100,540,130 high-quality paired-end reads were obtained from six cDNA libraries of spleen, liver, gill, kidney, muscle, and brain with 28.4 GB data using Illumina paired-end sequencing technology. Tissue-specific transcriptomes as well as complete transcriptome assembly were analyzed for concise representation of the study. In brief, the de novo assembly of individual tissue resulted in an average of 31,829 (18,512–46,348) contigs per sample, while combined transcriptome comprised 77,907 unique transcript fragments (unigenes) assembled from reads of six tissues. Approximately 75,407 (96.8%) unigenes could be annotated according to their homology matches in the nr, SwisseProt, GO, or KEGG databases. Comparative analysis showed that 84% of the unigenes have significant similarity to zebra fish RefSeq proteins. Tissue-specific-dominated genes were also identified to hypothesize their localization and expression in individual tissue. In addition, 2485 simple sequence repeats (SSRs) were detected from 77,907 transcripts in the combined transcriptome of the golden mahseer. This study has generated organ-specific transcriptome profiles, which will be helpful to understand the local adaptation, genome evolution, and also future functional studies on immune system of the golden mahseer.

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Organ specific and concatenated transcriptome of 6 organs of golden mahseer was generated using illumina sequencing.

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A total of 100,540,130 high-quality paired-ends reads with 28.4 GB data that assembled into 77,907 contigs were obtained.

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Contigs were annotated using GO and KEGG pathway and organ-specific few genes were identified.

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Thirty four usable SSR markers were extracted from 2485 identified.

Transcriptional Profiling Reveals Differential Gene Expression of Amur Ide (Leuciscus waleckii) during Spawning Migration

Amur ide (Leuciscus waleckii), an important aquaculture species, inhabits neutral freshwater but can tolerate high salinity or alkalinity. As an extreme example, the population in Dali Nor lake inhabits alkalized soda water permanently, and migrates from alkaline water to neutral freshwater to spawn. In this study, we performed comparative transcriptome profiling study on the livers of Amur ide to interrogate the expression differences between the population that permanently inhabit freshwater in Ganggeng Nor lake (FW) and the spawning population that recently migrated from alkaline water into freshwater (SM). A total of 637,234,880 reads were generated, resulting in 53,440 assembled contigs that were used as reference sequences. Comparisons of these transcriptome files revealed 444 unigenes with significant differential expression (p-value ≤ 0.01, fold-change ≥ 2), including 246 genes that were up-regulated in SM and 198 genes that were up-regulated in FW. The gene ontology (GO) enrichment analysis and KEGG pathway analysis indicated that the mTOR signaling pathway, Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway, and oxidative phosphorylation were highly likely to affect physiological changes during spawning migration. Overall, this study demonstrates that transcriptome changes played a role in Amur ide spawning migration. These results provide a foundation for further analyses on the physiological and molecular mechanisms underlying Amur ide spawning migration.