Quality Reads Research Articles

Characterization and expression analysis of g- and c-type lysozymes in Dabry's sturgeon (Acipenser dabryanus)

Dabry's sturgeon (Acipenser dabryanus) is mainly distributed in the upper Yangtze River. Although extensively farmed, little information is available on its innate immune system. In this study, we conducted de novo transcriptome assembly of the head kidney to create a comprehensive dataset for A. dabryanus. A total of 51,324,686 high quality reads were obtained from head kidney cDNA library by the Illumina sequencing platform and 131,261 unigenes were determined to contain complete ORFs. The complete coding sequences of g- and c-type lysozymes were identified from unigenes, and designated as ADLysG and ADLysC. Aeromonas hydrophila infection of Dabry's sturgeon caused a significant increase (P < 0.05) in blood for both lysozyme types, confirming their active defensive role against bacterial infections. This research provides the first characterization of these enzymes in an ancestral chondrostean. These data suggest that ADLysG and ADLysC have the potential for immune defense system against bacterial infection.

Improved circRNA Identification by Combining Prediction Algorithms.

Non-coding RNA is an interesting class of gene regulators with diverse functionalities. One large subgroup of non-coding RNAs is the recently discovered class of circular RNAs (circRNAs). CircRNAs are conserved and expressed in a tissue and developmental specific manner, although for the vast majority, the functional relevance remains unclear. To identify and quantify circRNAs expression, several bioinformatic pipelines have been developed to assess the catalog of circRNAs in any given total RNA sequencing dataset. We recently compared five different algorithms for circRNA detection, but here this analysis is extended to 11 algorithms. By comparing the number of circRNAs discovered and their respective sensitivity to RNaseR digestion, the sensitivity and specificity of each algorithm are evaluated. Moreover, the ability to predict de novo circRNA, i.e., circRNAs not derived from annotated splice sites, is also determined as well as the effect of eliminating low quality and adaptor-containing reads prior to circRNA prediction. Finally, and most importantly, all possible pair-wise combinations of algorithms are tested and guidelines for algorithm complementarity are provided. Conclusively, the algorithms mostly agree on highly expressed circRNAs, however, in many cases, algorithm-specific false positives with high read counts are predicted, which is resolved by using the shared output from two (or more) algorithms.

Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk.

Circulating small RNAs, including miRNAs but also isomiRs and other RNA species, have the potential to be used as non-invasive biomarkers for communicable and non-communicable diseases. This study aims to characterize and compare small RNA profiles in human biofluids. For this purpose, RNA was extracted from plasma and breast milk samples from 15 healthy postpartum mothers. Small RNA libraries were prepared with the NEBNext® small RNA library preparation kit and sequenced in an Illumina HiSeq2000 platform. miRNAs, isomiRs and clusters of small RNAs were annotated using seqBuster/seqCluster framework in 5 plasma and 10 milk samples that passed the initial quality control. The RNA yield was 81 ng/mL [standard deviation (SD): 41] and 3985 ng/mL (SD: 3767) for plasma and breast milk, respectively. Mean number of good quality reads was 4.04 million (M) (40.01% of the reads) in plasma and 12.5M (89.6%) in breast milk. One thousand one hundred eighty two miRNAs, 12,084 isomiRs and 1,053 small RNA clusters that included piwi-interfering RNAs (piRNAs), tRNAs, small nucleolar RNAs (snoRNA) and small nuclear RNAs (snRNAs) were detected. Samples grouped by biofluid, with 308 miRNAs, 1,790 isomiRs and 778 small RNA clusters differentially detected. In summary, plasma and milk showed a different small RNA profile. In both, miRNAs, piRNAs, tRNAs, snRNAs, and snoRNAs were identified, confirming the presence of non-miRNA species in plasma, and describing them for the first time in milk.

Water Bacterial and Fungal Community Compositions Associated with Urban Lakes, Xi'an, China.

Urban lakes play a vital role in the sustainable development of urbanized areas. In this freshwater ecosystem, massive microbial communities can drive the recycling of nutrients and regulate the water quality. However, water bacterial and fungal communities in the urban lakes are not well understood. In the present work, scanning electron microscopy (SEM) was combined with community level physiological profiles (CLPPs) and Illumina Miseq sequence techniques to determine the diversity and composition of the water bacterial and fungal community in three urban lakes, namely Xingqing lake (LX), Geming lake (LG) and Lianhu lake (LL), located in Xi’an City (Shaanxi Province, China). The results showed that these three lakes were eutrophic water bodies. The highest total nitrogen (TN) was observed in LL, with a value of 12.1 mg/L, which is 2 times higher than that of LG. The permanganate index (CODMn) concentrations were 21.6 mg/L, 35.4 mg/L and 28.8 mg/L in LG, LL and LX, respectively (p < 0.01). Based on the CLPPs test, the results demonstrated that water bacterial communities in the LL and LX urban lakes had higher carbon source utilization ability. A total of 62,742 and 55,346 high quality reads were grouped into 894 and 305 operational taxonomic units (OTUs) for bacterial and fungal communities, respectively. Water bacterial and fungal community was distributed across 14 and 6 phyla. The most common phyla were Proteobacteriaand Cyanobacteria. Cryptomycota was particularly dominant in LL, while Chytridiomycota and Entomophthormycota were the most abundant fungal phyla, accounting for 95% of the population in the LL and 56% in the LG. Heat map and redundancy analysis (RDA) highlighted the dramatic differences of water bacterial communities among three urban lakes. Meanwhile, the profiles of fungal communities were significantly correlated with the water quality parameters (e.g., CODMn and total nitrogen, TN). Several microbes (Legionella sp. and Streptococcus sp.) related to human diseases, such as infectious diseases, were also found. The results from this study provides useful information related to the water quality and microbial community compositions harbored in the aquatic ecosystems of urban lakes.

BRANDING SERIAL KKPK: TINJAUAN PADA MINAT LITERASI ANAK-ANAK

Based on the results of a survey of literacy index published by Central Connecticut State of the University (CCSU) in March 2016 showed from 61 countries surveyed, Indonesia's literacy rankings are in the 60th sequence. The research also assessed the reading assessment score for children under the age of 18 , as quoted from page CCSU.edu (accessed 4/6/2017) shows that the ability of Indonesian children to understand the reading is also very low.Children's literacy skills can be very high. That means, the family and the form of early childhood education have a very big influence on the high-low literacy ability of a child.The publisher of Mizan through KKPK / Kecil-Kecil Punya Karya, is a pioneer of quality reading books written by Indonesian children. In KKPK's book, the writings published are children's writing from 7-12 years old, which also corresponds to a focused market share. Based on the point of view, the purpose of this study is to examine the branding of KPPK in the perspective of increasing the interest of children literacy. From the study of literature research methods conducted by the author, it is concluded that Dar Mizan Publisher through KKPK book has made a strong branding as a pioneer of book publishers that provides a container for children to publish their writing visually. The opportunity to write visual works is support for one's literacy skills, especially children. In this case, Dar Mizan Publisher, through KKPK book has increased interest and literacy ability of children. KKPK has become a medium to improve the literacy ability of children with earlier.

Hypothalamus and pituitary transcriptome profiling of male and female Hong Kong grouper (Epinephelus akaara)

Hong Kong grouper (Epinephelus akaara) is an important commercially cultured marine fish in Asia, and a protogynous hermaphrodite with the “diandry” pattern. In order to explore the gene expression patterns of hypothalamus and pituitary between male and female Hong Kong grouper, we used RNA-seq technology to investigate transcriptomes of both tissues in immature and mature male and female adults. This produced 227,227,148 and 215,858,948 high quality reads from hypothalamus and pituitary, which were jointly assembled into 199,203 unigenes. Among them, 30,786 unigenes were mapped to known genes. Differential expression analysis revealed 275 unigenes that were differentially expressed between immature male and female adults and 561 between mature male and female adults. According to annotation and KEGG information, these differentially expressed genes (DEGs) were involved in development, metabolism, and regulation of transcription. One DEG, amino-terminal enhancer of split (AES), a member of the Groucho/transducin-like enhancer of split family of transcriptional regulators that played important roles in neurogenesis, segmentation, and sex determination, was significantly upregulated in male individuals in both immature and mature adult comparisons, indicating it may be involved in male reproductive function during development. Our report, for the first time, uses RNA-seq technology to investigate transcriptomes of both hypothalamus and pituitary in teleost fish, and provides a basis for further studies of molecular mechanism of sex determination and development in Hong Kong grouper.

Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system

BackgroundCurrent technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopolymer-containing regions, since the repeating identical bases are going to incorporate during the same synthesis cycle, which leads to uncertainty in base calling. The aim of this study was to evaluate the analytical performance of a pyrosequencing-based next-generation sequencing system in detecting homopolymer sequences using homopolymer-preintegrated plasmid constructs and human DNA samples originating from patients with cystic fibrosis.ResultsIn the plasmid system average correct genotyping was 95.8% in 4-mers, 87.4% in 5-mers and 72.1% in 6-mers. Despite the experienced low genotyping accuracy in 5- and 6-mers, it was possible to generate amplicons with more than a 90% adequate detection rate in every homopolymer tract. When homopolymers in the CFTR gene were sequenced average accuracy was 89.3%, but varied in a wide range (52.2 – 99.1%). In all but one case, an optimal amplicon-sequencing primer combination could be identified. In that single case (7A tract in exon 14 (c.2046_2052)), none of the tested primer sets produced the required analytical performance.ConclusionsOur results show that pyrosequencing is the most reliable in case of 4-mers and as homopolymer length gradually increases, accuracy deteriorates. With careful primer selection, the NGS system was able to correctly genotype all but one of the homopolymers in the CFTR gene. In conclusion, we configured a plasmid test system that can be used to assess genotyping accuracy of NGS devices and developed an accurate NGS assay for the molecular diagnosis of CF using self-designed primers for amplification and sequencing.

Transcriptome analysis of genes involved in the response of a pollinator fig wasp to volatile organic compounds from its host figs

The mutualism of figs and their pollinating fig wasps is widely regarded as a model for coevolved mutualism. A high degree of host specificity is ensured by female wasps only being attracted by their specific fig tree species through the volatile organic compounds (VOCs) released by the figs when they are ready to be pollinated. However, very little is known about the molecular mechanisms underlying the production of VOCs and how pollinators respond to these VOCs. Here we present transcriptome sequencing data from VOC-treated fig wasps and control fig wasps. Using Illumina paired-end sequencing, approximately 6.47 Gbp and 6.48 Gbp high quality reads were generated for fig wasps that had been exposed or not to VOCs of their host fig. After read trimming, the de novo assembly of both types of reads produced 58,192 unigenes with an average length of 817 bp. Then functional annotation and GO enrichment analysis was performed by aligning all-unigenes with public protein databases including NR, SwissProt, and KEGG. Differentially expressed genes (DEGs) were investigated using the RPKM method. Overall, 16 up-regulated genes and 13 down-regulated genes were identified. We further performed GO enrichment and metabolic pathway enrichment analyses. One gene involved in the synoptic vesicle cycle and two genes coding for odorant binding proteins (OBP) are likely to have potential impacts on the response of fig wasps to the VOCs emitted by their host figs. This is the first transcriptome sequencing of a fig wasp in the presence of VOCs of its host figs using the next-generation sequencing technology. Our studies suggest that the expression of some genes in the olfactory neural system of the fig wasps is affected by the VOCs released from the figs. This suggests the presence of a dynamic molecular system of detection and hence response to host plant VOCs. As such our findings provide indications for further mechanistic studies on the fig-fig wasp interactions.

Characterization of microbial community structure and metabolic potential using Illumina MiSeq platform during the black garlic processing

Black garlic is a distinctive garlic deep-processed product made from fresh garlic at high temperature and controlled humidity. To explore microbial community structure, diversity and metabolic potential during the 12days of the black garlic processing, Illumina MiSeq sequencing technology was performed to sequence the 16S rRNA V3–V4 hypervariable region of bacteria. A total of 677,917 high quality reads were yielded with an average read length of 416bp. Operational taxonomic units (OTU) clustering analysis showed that the number of species OTUs ranged from 148 to 1974, with alpha diversity increasing remarkably, indicating the high microbial community abundance and diversity. Taxonomic analysis indicated that bacterial community was classified into 45 phyla and 1125 distinct genera, and the microbiome of black garlic samples based on phylogenetic analysis was dominated by distinct populations of four genera: Thermus, Corynebacterium, Streptococcus and Brevundimonas. The metabolic pathways were predicted for 16S rRNA marker gene sequences based on Kyoto Encyclopedia of Genes and Genomes (KEGG), indicating that amino acid metabolism, carbohydrate metabolism and membrane transport were important for the black garlic fermentation process. Overall, the study was the first to reveal microbial community structure and speculate the composition of functional genes in black garlic samples. The results contributed to further analysis of the interaction between microbial community and black garlic components at different stages, which was of great significance to study the formation mechanism and quality improvement of black garlic in the future.

Wireless Internet of Things-Based Air Quality Device for Smart Pollution Monitoring

Living in a healthy environment is a need for every human being whether indoor or outdoor. However, pollutions occur everywhere and most people are merely mindful of the importance of having clean outdoor air to breathe and are not concerned about the indoor air quality. Indoor air quality refers to the quality within the building, and relates to the health and comfort of the building occupants. Dangerous particles exist in the outside air, pollute the indoor environment and produce harmful conditions as the polluted air travels into the house or building through windows or doors. Therefore, a wireless Internet of Things-based air quality device is developed to monitor the air quality in the indoor environment. The proposed system integrates a low-cost air quality sensor, temperature and humidity sensors, a single-board computer (Raspberry Pi 2 microprocessor) and cloud storage. The system provides realtime air quality reading, transfers the data through a wireless network to the Internet and displays the data in dedicated webpage. Furthermore, it stores records in cloud storage and sends e-mail notification message to the user when unhealthy condition is met. The study has a significant impact on promoting affordable and portable smart pollution monitoring system as the development of the device utilizing low-cost and off-the-shelf components.

Comparative transcriptome analysis of purple-fleshed sweet potato provides insights into the molecular mechanism of anthocyanin biosynthesis

Sweet potato, <i>Ipomoea batatas</i>, is a globally important food crop. The purple-fleshed sweet potato, rich in anthocyanins, has great potential for both nutritional and pharmaceutical uses. In this study, we characterized the root transcriptomes of the purple-fleshed sweet potato cv. Jingshu 6 and its mutant JS6-5 with high anthocyanin content by high-throughput RNA sequencing. A total of 22873364 and 27955097 high quality reads were obtained from Jingshu 6 and JS6-5, respectively, and assembled into 35592 unigenes. In all, we obtained 1566 differentially expressed genes (DEGs). Among them, 994 were upregulated and 572 were downregulated in JS6-5 compared to the expression in Jingshu 6. A total of 1436 DEGs were annotated, in which 847 DEGs had gene ontology (GO) terms and 329 DEGs were assigned to 84 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most importantly, 23 differentially expressed genes and 24 transcription factors were identified as candidate genes involved in anthocyanin biosynthesis. In addition, 2349 SSRs were detected. This study not only provides the candidate genes but also provides insights into the molecular mechanism of anthocyanin biosynthesis in sweet potato.

Quality Control of Common and Rare Variants.

Thorough data quality control (QC) is a key step to the success of high-throughput genotyping approaches. Following extensive research several criteria and thresholds have been established for data QC at the sample and variant level. Sample QC is aimed at the identification and removal (when appropriate) of individuals with (1) low call rate, (2) discrepant sex or other identity-related information, (3) excess genome-wide heterozygosity and homozygosity, (4) relations to other samples, (5) ethnicity differences, (6) batch effects, and (7) contamination. Variant QC is aimed at identification and removal or refinement of variants with (1) low call rate, (2) call rate differences by phenotypic status, (3) gross deviation from Hardy-Weinberg Equilibrium (HWE), (4) bad genotype intensity plots, (5) batch effects, (6) differences in allele frequencies with published data sets, (7) very low minor allele counts(MAC), (8) low imputation quality score, (9) low variant quality score log-odds, and (10) few or low quality reads.

Robust inference of population structure from next-generation sequencing data with systematic differences in sequencing.

Inferring population structure is important for both population genetics and genetic epidemiology. Principal components analysis (PCA) has been effective in ascertaining population structure with array genotype data but can be difficult to use with sequencing data, especially when low depth leads to uncertainty in called genotypes. Because PCA is sensitive to differences in variability, PCA using sequencing data can result in components that correspond to differences in sequencing quality (read depth and error rate), rather than differences in population structure. We demonstrate that even existing methods for PCA specifically designed for sequencing data can still yield biased conclusions when used with data having sequencing properties that are systematically different across different groups of samples (i.e. sequencing groups). This situation can arise in population genetics when combining sequencing data from different studies, or in genetic epidemiology when using historical controls such as samples from the 1000 Genomes Project. To allow inference on population structure using PCA in these situations, we provide an approach that is based on using sequencing reads directly without calling genotypes. Our approach is to adjust the data from different sequencing groups to have the same read depth and error rate so that PCA does not generate spurious components representing sequencing quality. To accomplish this, we have developed a subsampling procedure to match the depth distributions in different sequencing groups, and a read-flipping procedure to match the error rates. We average over subsamples and read flips to minimize loss of information. We demonstrate the utility of our approach using two datasets from 1000 Genomes, and further evaluate it using simulation studies. TASER-PC software is publicly available at http://web1.sph.emory.edu/users/yhu30/software.html. yijuan.hu@emory.edu. Supplementary data are available at Bioinformatics online.

De novo RNA sequencing transcriptome of Rhododendron obtusum identified the early heat response genes involved in the transcriptional regulation of photosynthesis.

Rhododendron spp. is an important ornamental species that is widely cultivated for landscape worldwide. Heat stress is a major obstacle for its cultivation in south China. Previous studies on rhododendron principally focused on its physiological and biochemical processes, which are involved in a series of stress tolerance. However, molecular or genetic properties of rhododendron’s response to heat stress are still poorly understood. The phenotype and chlorophyll fluorescence kinetics parameters of four rhododendron cultivars were compared under normal or heat stress conditions, and a cultivar with highest heat tolerance, “Yanzhimi” (R. obtusum) was selected for transcriptome sequencing. A total of 325,429,240 high quality reads were obtained and assembled into 395,561 transcripts and 92,463 unigenes. Functional annotation showed that 38,724 unigenes had sequence similarity to known genes in at least one of the proteins or nucleotide databases used in this study. These 38,724 unigenes were categorized into 51 functional groups based on Gene Ontology classification and were blasted to 24 known cluster of orthologous groups. A total of 973 identified unigenes belonged to 57 transcription factor families, including the stress-related HSF, DREB, ZNF, and NAC genes. Photosynthesis was significantly enriched in the Kyoto Encyclopedia of Genes and Genomes pathway, and the changed expression pattern was illustrated. The key pathways and signaling components that contribute to heat tolerance in rhododendron were revealed. These results provide a potentially valuable resource that can be used for heat-tolerance breeding.

Quality control of regional wall motion analysis in stress Echo 2020

BackgroundThe trial “Stress Echo (SE) 2020” evaluates novel applications of SE beyond coronary artery disease. The aim of the study was control quality and harmonize reading criteria. MethodsOne reader from 78 centers of the SE 2020 network asked for credentials to read a set of 20 SE video-clips selected by the core lab. All aspiring centers met the pre-requisite of high-volume and the years of experience in SE ranged from 5 to 31years (mean value 18years). The diagnostic gold standard was a reading by the core lab. The a priori determined pass threshold was 18/20 (≥90%). ResultsOf the initial 78 who started, 57 completed the first attempt: individual readers' score on first attempt ranged from 07/20 to 20/20 (accuracy from 35% to 100%, mean 78.7±13%) and 44 readers passed it. There was a very poor correlation between years of experience and the reader's score on first attempt (r=−0.161, p=0.231). Of the 13 readers who failed the first attempt, 12 took it again after the web-based session and their accuracy improved (74% vs. 96%, p<0.001). The kappa inter-observer agreement before and after web-based training was 0.59 on first attempt and rose to 0.91 on the last attempt. ConclusionsIn SE reading, the volume of activity or years of experience is not synonymous with diagnostic quality. Qualitative analysis and operator-dependence can become a limiting weakness in clinical practice, in the absence of strict pathways of learning, credentialing and audit.

De novo assembly of Koelreuteria transcriptome and analysis of major gene related to leaf etiolation

As an important small deciduous tree, Koelreuteria bipinnata var. integrifoliola ‘Jinyan’ possesses high ornamental value. Understanding its coloring processes in leaves may help scientists breed the best plant type. Here, we report the first transcriptome generated from the leaves of K. bipinnata var. integrifoliola ‘Jinyan’ and K. bipinnata var. integrifoliola through de novo high-throughput transcriptome sequencing. A total of 94,125 unigenes were obtained from more than 156 million of high quality reads using de novo assembly, of which 47,341 unigenes were annotated in various protein databases, including the Nr, Swiss-Prot, GO, COG, KOG and KEGG. Moreover, 482,377 SNPs and 9414 SSRs were identified in assembled unigenes, and 13,670 DEGs with up-regulated or down-regulated expression levels were detected in all samples. Finally, 9 and 14 genes, which are responsible for encoding enzyme, were screened in porphyrin and chlorophyll metabolism and carotenoid biosynthesis pathways respectively. Taken together, this transcriptome data may be further utilized in functional genomics and genetics studies on Koelreuteria.

Next Generation Sequencing: Approach for Assessment and enrichment of raw data

Next-generation sequencing (NGS) is a non-sanger technique based on high-throughput capacity for determining the exact order of nucleotide in the given DNA & RNA molecule. Modern high-throughput sequencer’s produce millions of sequences read in a single run. The quality of these data are not perfect because they contains artefacts like poor quality reads, adapter contamination, wrong base calls and INDELs due to instrument failure or chemical process error. In this study, a procedure has been designed for the refinement and improvement of quality of NGS data for further biological processes.

A Transcriptome Approach Toward Understanding Fruit Softening in Persimmon.

Persimmon (Diospyros kaki Thunb.), which is a climacteric fruit, softens in 3–5 weeks after harvest. However, little is known regarding the transcriptional changes that underlie persimmon ripening. In this study, high-throughput de novo RNA sequencing was performed to examine differential expression between freshly harvested (FH) and softened (ST) persimmon fruit peels. Using the Illumina HiSeq platform, we obtained 259,483,704 high quality reads and 94,856 transcripts. After the removal of redundant sequences, a total of 31,258 unigenes were predicted, 1,790 of which were differentially expressed between FH and ST persimmon (1,284 up-regulated and 506 down-regulated in ST compared with FH). The differentially expressed genes (DEGs) were further subjected to KEGG pathway analysis. Several pathways were found to be up-regulated in ST persimmon, including “amino sugar and nucleotide sugar metabolism.” Pathways down-regulated in ST persimmon included “photosynthesis” and “carbon fixation in photosynthetic organisms.” Expression patterns of genes in these pathways were further confirmed using quantitative real-time RT-PCR. Ethylene gas production during persimmon softening was monitored with gas chromatography and found to be correlated with the fruit softening. Transcription involved in ethylene biosynthesis, perception and signaling was up-regulated. On the whole, this study investigated the key genes involved in metabolic pathways of persimmon fruit softening, especially implicated in increased sugar metabolism, decreased photosynthetic capability, and increased ethylene production and other ethylene-related functions. This transcriptome analysis provides baseline information on the identity and modulation of genes involved in softening of persimmon fruits and can underpin the future development of technologies to delay softening in persimmon.

Virome analysis for identification of novel mammalian viruses in bats from Southeast China

Bats have been shown as important mammal resevoirs to carry a variety of zoonotic pathogens. To analyze pathogenic species in bats from southeast coastal regions of China, we performed metagenomic sequencing technology for high throughput sequencing of six sentinels from southeast coastal area of China. We obtained 5,990,261 high quality reads from intestine and lung tissue of 235 bats, including 2,975,371 assembled sequences. 631,490 reads predicted overlapping sequences for the open reading frame (ORF), which accounts for 2.37% of all the sequences (15,012/631,490). Further, the acquired virus sequences were classified into 25 viral families, including 16 vertebrate viruses, four plant viruses and five insect viruses. All bat samples were screened by specific PCR and phylogenetic analysis. Using these techniques, we discovered many novel bat viruses and some bat viruses closely-related to known human/animal pathogens, including coronavirus, norovirus, adenovirus, bocavirus, astrovirus, and circovirus. In summary, this study extended our understanding of bats as the viral reservoirs. Additionally, it also provides a basis for furher studying the transmission of viruses from bats to humans.

Transcriptomic profiling of Tibetan highland fish (Gymnocypris przewalskii) in response to the infection of parasite ciliate Ichthyophthirius multifiliis

Gymnocypris przewalskii is a native cyprinid in the Lake Qinghai of the Qinghai-Tibetan Plateau. G. przewalskii is highly susceptible to the infection of a parasite, Ichthyophthirius multifiliis, in the artificial propagation and breeding. To better understand the host immune reaction to I. multifiliis infection, we characterize the gene expression profiles in the spleen of healthy and I. multifiliis infected G. przewalskii by RNA-seq. Totally, the transcriptomic analysis produces 463,031,110 high quality reads, which are assembled to 213,538 genes with N50 of 1918 bp and the average length of 1205 bp. Of assembled genes, 90.52% are annotated by public databases. The expression analysis shows 744 genes are significantly changed by the infection of I. multifiliis, which are validated by qRT-PCR with the correlation coefficient of 0.896. The differentially expressed genes are classified into 689 GO terms and 230 KEGG pathways, highlighting the promoted innate immunity in I. multifiliis infected G. przewalskii at 2 days post infection. Our results pinpoint that the up-regulated genes are enriched in TLR signaling pathway, inflammatory response and activation of immune cell migration. On the contrary, complement genes are down-regulated, indicating the evasion of host complement cascades by I. multifiliis. The repressed genes are also enriched in the pathways related to metabolism and endocrine, suggesting the metabolic disturbance in I. multifiliis treated G. przewalskii. In summary, the present study profiles the gene expression signature of G. przewalskii in the responses to I. multifiliis infection, and improves our understanding on molecular mechanisms of host-parasite interaction in G. przewalskii, which focuses the crucial function of TLRs, cytokines and complement components in the host defense against I. multifiliis.