Basis Of Homology Research Articles

Q-Stirling numbers: A new view

We show the classical q-Stirling numbers of the second kind can be expressed compactly as a pair of statistics on a subset of restricted growth words. The resulting expressions are polynomials in q and 1+q. We extend this enumerative result via a decomposition of a new poset Π(n,k) which we call the Stirling poset of the second kind. Its rank generating function is the q-Stirling number Sq[n,k]. The Stirling poset of the second kind supports an algebraic complex and a basis for integer homology is determined. A parallel enumerative, poset theoretic and homological study for the q-Stirling numbers of the first kind is done. Letting t=1+q we give a bijective argument showing the (q,t)-Stirling numbers of the first and second kinds are orthogonal.

Identification of Nitrogen Use Efficiency Genes in Barley: Searching for QTLs Controlling Complex Physiological Traits.

Over the past half century, the use of nitrogen (N) fertilizers has markedly increased crop yields, but with considerable negative effects on the environment and human health. Consequently, there has been a strong push to reduce the amount of N fertilizer used by maximizing the nitrogen use efficiency (NUE) of crops. One approach would be to use classical genetics to improve the NUE of a crop plant. This involves both conventional breeding and quantitative trait loci (QTL) mapping in combination with marker-assisted selection (MAS) to track key regions of the chromosome that segregate for NUE. To achieve this goal, one of initial steps is to characterize the NUE-associated genes, then use the profiles of specific genes to combine plant physiology and genetics to improve plant performance. In this study, on the basis of genetic homology and expression analysis, barley candidate genes from a variety of families that exhibited potential roles in enhancing NUE were identified and mapped. We then performed an analysis of QTLs associated with NUE in field trials and further analyzed their map-location data to narrow the search for these candidate genes. These results provide a novel insight on the identification of NUE genes and for the future prospects, will lead to a more thorough understanding of physiological significances of the diverse gene families that may be associated with NUE in barley.

Phosphinothricin Acetyltransferases Identified Using In Vivo, In Vitro, and Bioinformatic Analyses.

Acetylation of small molecules is widespread in nature, and in some cases, cells use this process to detoxify harmful chemicals. Streptomyces species utilize a Gcn5 N-acetyltransferase (GNAT), known as Bar, to acetylate and detoxify a self-produced toxin, phosphinothricin (PPT), a glutamate analogue. Bar homologues, such as MddA from Salmonella enterica, acetylate methionine analogues such as methionine sulfoximine (MSX) and methionine sulfone (MSO), but not PPT, even though Bar homologues are annotated as PPT acetyltransferases. S. enterica was used as a heterologous host to determine whether or not putative PPT acetyltransferases from various sources could acetylate PPT, MSX, and MSO. In vitro and in vivo analyses identified substrates acetylated by putative PPT acetyltransferases from Deinococcus radiodurans (DR_1057 and DR_1182) and Geobacillus kaustophilus (GK0593 and GK2920). In vivo, synthesis of DR_1182, GK0593, and GK2920 blocked the inhibitory effects of PPT, MSX, and MSO. In contrast, DR_1057 did not detoxify any of the above substrates. Results of in vitro studies were consistent with the in vivo results. In addition, phylogenetic analyses were used to predict the functionality of annotated PPT acetyltransferases in Burkholderia xenovorans, Bacillus subtilis, Staphylococcus aureus, Acinetobacter baylyi, and Escherichia coli IMPORTANCE: The work reported here provides an example of the use of a heterologous system for the identification of enzyme function. Many members of this superfamily of proteins do not have a known function, or it has been annotated solely on the basis of sequence homology to previously characterized enzymes. The critical role of Gcn5 N-acetyltransferases (GNATs) in the modulation of central metabolic processes, and in controlling metabolic stress, necessitates approaches that can reveal their physiological role. The combination of in vivo, in vitro, and bioinformatics approaches reported here identified GNATs that can acetylate and detoxify phosphinothricin.

Genomic Dissection and Expression Profiling Revealed Functional Divergence in Triticum aestivum Leucine Rich Repeat Receptor Like Kinases (TaLRRKs).

The leucine rich repeat receptor like kinases (LRRK) constitute the largest subfamily of receptor like kinases (RLK), which play critical roles in plant development and stress responses. Herein, we identified 531 TaLRRK genes in Triticum aestivum (bread wheat), which were distributed throughout the A, B, and D sub-genomes and chromosomes. These were clustered into 233 homologous groups, which were mostly located on either homeologous chromosomes from various sub-genomes or in proximity on the same chromosome. A total of 255 paralogous genes were predicted which depicted the role of duplication events in expansion of this gene family. Majority of TaLRRKs consisted of trans-membrane region and localized on plasma-membrane. The TaLRRKs were further categorized into eight phylogenetic groups with numerous subgroups on the basis of sequence homology. The gene and protein structure in terms of exon/intron ratio, domains, and motifs organization were found to be variably conserved across the different phylogenetic groups/subgroups, which indicated a potential divergence and neofunctionalization during evolution. High-throughput transcriptome data and quantitative real time PCR analyses in various developmental stages, and biotic and abiotic (heat, drought, and salt) stresses provided insight into modus operandi of TaLRRKs during these conditions. Distinct expression of majority of stress responsive TaLRRKs homologous genes suggested their specified role in a particular condition. These results provided a comprehensive analysis of various characteristic features including functional divergence, which may provide the way for future functional characterization of this important gene family in bread wheat.

Crystal structures of the disulfide reductase DsbM from Pseudomonas aeruginosa.

In bacteria, many Dsb-family proteins play diverse roles in the conversion between the oxidized and reduced states of cysteine residues of substrate proteins. Most Dsb enzymes catalyze disulfide formation in periplasmic or secreted substrate proteins. Recently, a DsbM protein has been found in a Gram-negative bacterium, and was characterized as a cytosolic Dsb member with the conserved CXXC motif on the basis of sequence homology to the Dsb-family proteins. The protein was implicated in the reduction of the cytoplasmic redox-sensor protein OxyR in Pseudomonas aeruginosa. Here, crystal structures of DsbM from P. aeruginosa are presented, revealing that it consists of a modified thioredoxin domain containing the CXXC motif and a lid domain surrounding the CXXC motif. In a glutathione-linked structure, a glutathione molecule is linked to the CXXC motif of DsbM and is bound in an elongated cavity region in the thioredoxin domain, which is also suited for substrate peptide binding. A striking structural similarity to a human glutathione S-transferase was found in the glutathione-binding pocket. Further, biochemical evidence is presented suggesting that DsbM is directly involved in the reduction of the disulfide of Cys199 and Cys208 in OxyR, resulting in the acceleration of OxyR reduction in the absence of reactive oxygen species stress. These findings may help to expand the understanding of the diverse roles of redox-related proteins that contain the CXXC motif.

발아 벼로부터 tricin 4"-O-(threo-β-guaiacylglyceryl) ether 생성균주의 분리 및 동정

This study was conducted to isolate and identify a microorganism that increases tricin-O-(threo-β-guaiacylglyceryl) ether (TTGE) content in the hulls of rice (Oryza sativa L.). Bacteria from germinated rice were isolated by enrichment cultivation using yeast mold, luria bertani, potato dextrose and mannitol egg york polymyxin broths. The highest increase in TTGE content (339.30 μg/g) was achieved by a microorganism isolated by PDA enrichment cultivation. On the basis of 16S RNA sequence homology and phylogenetic analysis, the isolated bacterium was identified to have 100% similarity with Burkholderia vietnamiensis. The isolated bacteria were short rods, negative for the Gram stain, and positive for the catalase test. The highest TTGE level was 435.86 μg/g in 72-h fermented samples, representing a 2.5x increase compared with the control (175.65 μg/g). In conclusion, the bacterium isolated from germinated rice extract was Burkholderia vietnamiensis, and the optimum fermentation period to maximize TTGE levels was 72 h. These findings might help in developing functional materials using rice hulls, a waste product of rice milling.

Combined Transcriptomic and Proteomic Analysis of the Posterior Salivary Gland from the Southern Blue-Ringed Octopus and the Southern Sand Octopus.

This study provides comprehensive proteomic profiles from the venom producing posterior salivary glands of octopus (superorder Octopodiformes) species. A combined transcriptomic and proteomic approach was used to identify 1703 proteins from the posterior salivary gland of the southern blue-ringed octopus, Hapalochlaena maculosa and 1300 proteins from the posterior salivary gland of the southern sand octopus, Octopus kaurna. The two proteomes were broadly similar; clustering of proteins into orthogroups revealed 937 that were shared between species. Serine proteases were particularly diverse and abundant in both species. Other abundant proteins included a large number of secreted proteins, many of which had no known conserved domains, or homology to proteins with known function. On the basis of homology to known venom proteins, 23 putative toxins were identified in H.maculosa and 24 in O.kaurna. These toxins span nine protein families: CAP (cysteine rich secretory proteins, antigen 5, parthenogenesis related), chitinase, carboxylesterase, DNase, hyaluronidase, metalloprotease, phospholipase, serine protease and tachykinin. Serine proteases were responsible for 70.9% and 86.3% of putative toxin expression in H.maculosa and O.kaurna, respectively, as determined using intensity based absolute quantification (iBAQ) measurements. Phylogenetic analysis of the putative toxin serine proteases revealed a similar suite of diverse proteins present in both species. Posterior salivary gland composition of H.maculosa and O.kaurna differ in several key aspects. While O.kaurna expressed the proteinaceous neurotoxin, tachykinin, this was absent from H.maculosa, perhaps reflecting the acquisition of a potent nonproteinaceous neurotoxin, tetrodotoxin (TTX) produced by bacteria in the salivary glands of that species. The dispersal factor, hyaluronidase was particularly abundant in H.maculosa. Chitinase was abundant in both species and is believed to facilitate envenomation in chitinous prey such as crustaceans. Cephalopods represent a largely unexplored source of novel proteins distinct from all other venomous taxa and are of interest for further inquiry, as novel proteinaceous toxins derived from venoms may contribute to pharmaceutical design.

Genome sequence and gene expression studies reveal novel hydrogenases mediated hydrogen production by Clostridium biohydrogenum sp. nov., MCM B-509T

The present study describes Clostridium biohydrogenum sp. nov., MCM B-509T as one of the most efficient hydrogen producing dark fermentative bacteria. MCM B-509 produced 3.35 mol hydrogen per mole of glucose consumed. The draft genome sequence of MCM B-509 provided insights into gene repertoire involved in hydrogen metabolism. Genome analysis revealed the presence of key enzymes such as Fe hydrogenase, NiFe Hydrogenases, NAD dependent hydroxy-butyrate dehydrogenase and D-3 Phosphoglycerate dehydrogenase. Fe-hydrogenases were identified as novel hydrogenases on the basis of low sequence homology with the reference sequences in GenBank database as well as predicted 3D structure. Gene expression studies revealed genes encoding hydrogenases were upregulated and solventogenic pathway down regulated during exponential growth phase. Reverse was observed during stationary growth phase explaining high hydrogen production and decline during respective growth phases. This paper illustrates genetic investigation to explain high hydrogen production potential of C. biohydrogenum sp. nov., MCM B-509T.

Characterization and valuable applications of xylanase from endophytic fungus Aspergillus terreus KP900973 isolated from Corchorus olitorius

Abstract Isolated fungal strains from molokhia stalks (Corchorus olitorius) were screened for the production of xylanase enzyme. Aspergillus terreus KP900973 was selected as potential xylanase producer and was identified on the basis of 18S rDNA gene homology. Screening was done by Congo red test for xylanase, based on the light coloured zone around the sample in xylan agar plates. Optimization of xylanase production was performed using low cost substrates through submerged fermentation (SMF). Using a mixture of untreated molokhia stalks and pea peel with no nutrients added enhanced enzyme production by 100.73%. Optimal assay temperature and pH were 50 °C and 5.5, respectively. At pH 4.0 the activity decreased to 91.23%, moreover, at pH 9.0 the enzyme had 67.25% of its activity. The enzyme retained about 97% of its activity after being stored for 46 days at −18 °C. A. terreus is free from tested mycotoxins and considered as a non-toxigenic strain, so, some industrial applications of crude xylanase were tested. Wheat bran was found to be the most susceptible substrate for hydrolysis with the highest level of fermentable sugars and saccharification yield (16%) after 48 h. The greatest clarification degree of orange juice (64%) was observed after 72 h using crude enzyme preparation. Xylanase can even substitute the addition of emulsifiers and additives used in bread production enhancing dough-raising as compared to the control about 2-fold.

IDENTIFICATION AND CLASSIFICATION OF BACTERIAL AUTOTRANSPORTERS

Bacterial Autotransporters is a huge and assorted super family of proteins present in external boundary of the gram negative bacteria. Autotransporters consists of C-terminal beta domain, N-terminal passenger domain and a pathogenic function. The beta domain of the bacterial autotransporter is associated with pathogenicity with three types of functions namely adhesions, esterase and proteases. Identification and classification of a bacterial autotransporter is important in order to target it and hinder its ability to cause disease. Identification and classification therefore has become a challenging problem due to its homology sequence. In this paper, we ought to establish a web based tool that could identify and classify bacterial autotransporters on basis of homology with already reported bacterial autotransporters. The input required for tool amino acid sequence in FASTA format. The tool will analyze the query based on similarity with already reported sequence in database and generate output with information in terms of function, organism, class, length, protein ID and symbol. Further, this user friendly and freely accessible tool is integrated with NCBI, InterPro, Pfam, pubmed. Moreover, newly detected bacterial autotransporter can be easily added in the Bacterial Autotransporter Detector tool database with authentic reference

VIP: an integrated pipeline for metagenomics of virus identification and discovery.

Identification and discovery of viruses using next-generation sequencing technology is a fast-developing area with potential wide application in clinical diagnostics, public health monitoring and novel virus discovery. However, tremendous sequence data from NGS study has posed great challenge both in accuracy and velocity for application of NGS study. Here we describe VIP (“Virus Identification Pipeline”), a one-touch computational pipeline for virus identification and discovery from metagenomic NGS data. VIP performs the following steps to achieve its goal: (i) map and filter out background-related reads, (ii) extensive classification of reads on the basis of nucleotide and remote amino acid homology, (iii) multiple k-mer based de novo assembly and phylogenetic analysis to provide evolutionary insight. We validated the feasibility and veracity of this pipeline with sequencing results of various types of clinical samples and public datasets. VIP has also contributed to timely virus diagnosis (~10 min) in acutely ill patients, demonstrating its potential in the performance of unbiased NGS-based clinical studies with demand of short turnaround time. VIP is released under GPLv3 and is available for free download at: https://github.com/keylabivdc/VIP.

Genetic linkage mapping of loci conferring resistance to Blue butterfly (Lampides boeticus L.) and Plume moth (Exelastis atomosa Wals.) on chromosome 2 (CcLG02) in Pigeonpea

Inheritance of host resistance to blue butterfly (PBB1) and plume moth (PPM1) in interspecific mapping populations (F2, F3 and BC1) derived from a cross involving Cajanus cajan (cv. ICP-26) × Cajanus scarabaeoides (acc. ICPW-94) appeared to be under monogenic control either by a single major gene or a cluster of tightly linked genes. Bulked segregant analysis using 237 [85 simple sequence repeats (SSR), 143 random amplified polymorphic DNA (RAPD) and nine inter simple sequence repeats (ISSR)] parental polymorphic primers led to the identification of 43 markers that distinguished the resistant and susceptible bulks alike to parents, and which were also segregating among F2 progenies. Linkage analysis of these markers along with interaction phenotype score for both traits generated a linkage group consisting of 11 markers (two SSR, seven RAPD and two ISSR) and two trait loci (PBB1 and PPM1). This linkage group distributed over 133.9 cM with an average marker interval of 10.3 cM. The PBB1 and PPM1 loci were linked to each other by 11.2 cM (rf 0.110), and were flanked by ISSR marker UBC8722000 (15.9 cM), and RAPD marker OPA09910 (15.3 cM), respectively. On the basis of sequence homology of linked marker OPA09910 these two loci were assigned to chromosome 2 (CcLG02). Composite interval mapping led to the detection of two major quantitative trait loci (qPBB2.1 and qPPM2.1) controlling blue butterfly and plume moth resistance, respectively and the quantitative trait locus peaks coinciding with PBB1 and PPM1 loci on the map.

Torsion homology growth and cycle complexity of arithmetic manifolds

Let M be an arithmetic hyperbolic 3-manifold, such as a Bianchi manifold. We conjecture that there is a basis for the second homology of M, where each basis element is represented by a surface of `low' genus, and give evidence for this. We explain the relationship between this conjecture and the study of torsion homology growth.

Production and Optimization of Alkaline Pectin Lyase fromBacillus cereusUnder Submerged Fermentation

Bacillus cereus was isolated from soil sample and selected as maximum pectin lyase producing bacterium under alkaline conditions. The morphological, cultural and biochemical characteristics of bacterium were studied and it was identified on the basis of nucleotide homology and phylogenetic analysis by 16S rDNA analysis. Pectin lyase gave considerable activity with pectin (3% w/v) as a sole carbon source, there was a significant increase in enzyme activity (p<0.001). A combination of both yeast extract and peptone (0.5% w/v each) as nitrogen source also showed significant increase in enzyme activity (p<0.001). Enzyme gave maximum activity with inoculum age of 18 h, inoculum size of 2% (v/v), at temperature of 40°C and pH 10.0 for 24 h incubation time. The glycine-NaOH buffer (0.25M) of pH 10.0 was found to be the most appropriate buffer and optimum reaction temperature and incubation time observed were 30°C and 55 min respectively. Enzyme showed greater affinity towards pectin (0.5% w/v) as substrate. Among all the metal ions studied only Mn2+ ion was effective to stimulate the activity whereas other metal ions inhibited the enzyme activity. SDS was found to be the strongest inhibitor and among thiols, L-cysteine and ascorbic acid stimulated enzyme activity. All the phenolics studied inhibited the enzyme activity. The enzyme gave half-life of 150 min at optimized pH 10.0. Optimal enzyme concentration observed was 0.01mg/ml. This enzyme has tremendous potential in textile industry and paper and pulp industry.

Structural comparison of O-antigen gene clusters of Legionella pneumophila and its application of a serogroup-specific multiplex PCR assay.

The Legionella pneumophila serogroups O1, O4, O6, O7, O10 and O13 are pathogenic strains associated with pneumonia. The surface O-antigen gene clusters of L. pneumophila serogroups O4, O6, O7, O10 and O13 were sequenced and analyzed, with the function annotated on the basis of homology to that of the genes of L. pneumophila serogroup O1 (L. pneumophila subsp. pneumophila str. Philadelphia 1). The gene locus of the six L. pneumophila serogroups contains genes of yvfE, neuABCD, pseA-like for nucleotide sugar biosynthesis, wecA for sugar transfer, and wzm as well as wzt for O-antigen processing. The detection of O-antigen genes allows the fine differentiation at species and serogroup level without the neccessity of nucleotide sequencing. The O-antigen-processing genes wzm and wzt, which were found to be distinctive for different for different serogroups, have been used as the target genes for the detection and identification of L. pneumophila strains of different O serogroups. In this report, a multiplex PCR assay based on wzm or wzt that diferentiates all the six serogroups by amplicon size was developed with the newly designed specific primer pairs for O1 and O7, and the specific primer pairs for O4, O6, O10, and O13 reported previously. The array was validated by analysis of 34 strains including 15 L. pneumophila O-standard reference strains, eight reference strains of other Legionella non-pneumophila species, six other bacterial species, and five L. pneumophila environmental isolates. The detection sensitivity was one ng genomic DNA. The accurate and sensitive assay is suitable for the identification and detection of strains of these serogroups in environmental and clinical samples.

Biodegradation of Petrochemical Hydrocarbons Using an Efficient Bacterial Consortium: A2457

Petrochemical hydrocarbons are considered to be the most significant environmental pollutants and need to be removed. In present study, the biodegradation of used engine oil and diesel oil was achieved under shake flask conditions using an efficient bacterial consortium A2457: comprising bacterial strains of Stenotrophomonas maltophilia, Bacillus cereus and Bacillus pumilus. The strains were isolated and screened by enrichment technique. The bacterial strains were identified on the basis of 16S rRNA gene sequence homology. The percent removal and biodegradation of the petrochemicals was evaluated through UV–Vis spectrophotometer and FTIR spectrometry. The bacterial consortium resulted in significant degradation of diesel oil (94.13 %) and used engine oil (99.77 %) under experimental conditions. FTIR spectra of the hydrocarbons, before and after biodegradation experiments, also revealed significant changes in the characteristic peaks in the wavenumber range of 4000–600 cm−1. The consortium displayed significant biosurfactant production and lipase activity during 28 days of incubation and reduced the surface tension of culture medium to 27.95 ± 0.3 mN m−1. The petrochemical hydrocarbon degradation by the bacterial consortium: A2457 of present study could be attributed with the production of biosurfactants and lipases to utilize diesel oil and used engine oil as sole source of carbon and energy.

TAL effectors and the executor R genes.

Transcription activator-like (TAL) effectors are bacterial type III secretion proteins that function as transcription factors in plants during Xanthomonas/plant interactions, conditioning either host susceptibility and/or host resistance. Three types of TAL effector associated resistance (R) genes have been characterized—recessive, dominant non-transcriptional, and dominant TAL effector-dependent transcriptional based resistance. Here, we discuss the last type of R genes, whose functions are dependent on direct TAL effector binding to discrete effector binding elements in the promoters. Only five of the so-called executor R genes have been cloned, and commonalities are not clear. We have placed the protein products in two groups for conceptual purposes. Group 1 consists solely of the protein from pepper, BS3, which is predicted to have catalytic function on the basis of homology to a large conserved protein family. Group 2 consists of BS4C-R, XA27, XA10, and XA23, all of which are relatively short proteins from pepper or rice with multiple potential transmembrane domains. Group 2 members have low sequence similarity to proteins of unknown function in closely related species. Firm predictions await further experimentation on these interesting new members to the R gene repertoire, which have potential broad application in new strategies for disease resistance.

Abstract 3762: The landscape of therapeutic targetable fusions

Abstract Gene fusions are an important class of cancer-contributing somatic alteration, and have an important significance as a tumor-initiating event and as a molecular therapeutic target for specific tumors. We analyzed RNA sequencing, DNA copy number and gene mutation data from 4,366 primary tumor samples to comprehensively detect fusion events in 13 tumor types. To reduce the number of false-positive predictions, we developed strict quality criteria on the basis of gene homology, transcript allele fraction (TAF), and partner gene variety. In addition, we used fusions detected in RNAseq data from 364 normal tissue samples to extract tumor-specific fusions. In total, 7,887 fusion transcripts with high confidence were detected across 13 tumor types. Our fusion prediction was validated by supporting evidence for a genomic rearrangement for 78 of 79 fusions in 48 glioma samples where whole genome sequencing data was available. Fusion transcript frequency was positively correlated with the levels of genomic instability in cancers, whereas tumor samples harboring fusions contained statistically significantly fewer driver gene mutations. We identified 221 fusion transcripts involving a tumor suppressor gene and these were wildtype in majority (98.2%), suggesting the fusion has a disruptive effect and a role in tumorigenesis. We identified at least one in-frame protein kinase fusion in 324 of 4,366 samples (7.4%). Potentially therapeutic targetable kinase fusions such as ALK, ROS, RET, NTRK, and FGFR gene families were detected in thyroid carcinoma (8.7%), glioblastoma (4.4%), bladder carcinoma (3.3%), lung squamous cell carcinoma (2.3%), lung adenocarcinoma (1.6%), lower grade glioma (1.5%), and head and neck cancer (1.0%), suggesting a potential for application of kinase inhibitors for multiple tumor types. In-frame fusion transcripts involving histone methyltransferase or histone demethylase genes, which may also be considered as therapeutic targets, were detected in 111 samples (2.5%). In summary, the landscape of transcript fusions detected across a large number of tumor samples revealed fusion events with clinical relevance that have not been previously recognized. Our findings support the concept of basket clinical trials where patients are matched with experimental therapies based on their genomic profile rather than the tissue where the tumor originated. Citation Format: Kosuke Yoshihara, Qianghu Wang, Wandaliz Torres-Garcia, Siyuan Zheng, Rahulsimham Vegesna, Hoon Kim, Roel GW Verhaak. The landscape of therapeutic targetable fusions. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3762. doi:10.1158/1538-7445.AM2015-3762

Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler.

Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence. Among various sequencing platforms available, Illumina is the most widely used platform based on data quality, quantity and cost. Various de novo transcriptome assemblers are also available today for construction of de novo transcriptome.In this study, we aimed at obtaining an ameliorated de novo transcriptome assembly with sequence reads obtained from Illumina platform and assembled using Trinity Assembler. We found that, primary transcriptome assembly obtained as a result of Trinity can be ameliorated on the basis of transcript length, coverage, and depth and protein homology. Our approach to ameliorate is reproducible and could enhance the sensitivity and specificity of the assembled transcriptome which could be critical for validation of the assembled transcripts and for planning various downstream biological assays.

Transcriptome and venom proteome of the box jellyfish Chironex fleckeri.

BackgroundThe box jellyfish, Chironex fleckeri, is the largest and most dangerous cubozoan jellyfish to humans. It produces potent and rapid-acting venom and its sting causes severe localized and systemic effects that are potentially life-threatening. In this study, a combined transcriptomic and proteomic approach was used to identify C. fleckeri proteins that elicit toxic effects in envenoming.ResultsMore than 40,000,000 Illumina reads were used to de novo assemble ∼ 34,000 contiguous cDNA sequences and ∼ 20,000 proteins were predicted based on homology searches, protein motifs, gene ontology and biological pathway mapping. More than 170 potential toxin proteins were identified from the transcriptome on the basis of homology to known toxins in publicly available sequence databases. MS/MS analysis of C. fleckeri venom identified over 250 proteins, including a subset of the toxins predicted from analysis of the transcriptome. Potential toxins identified using MS/MS included metalloproteinases, an alpha-macroglobulin domain containing protein, two CRISP proteins and a turripeptide-like protease inhibitor. Nine novel examples of a taxonomically restricted family of potent cnidarian pore-forming toxins were also identified. Members of this toxin family are potently haemolytic and cause pain, inflammation, dermonecrosis, cardiovascular collapse and death in experimental animals, suggesting that these toxins are responsible for many of the symptoms of C. fleckeri envenomation.ConclusionsThis study provides the first overview of a box jellyfish transcriptome which, coupled with venom proteomics data, enhances our current understanding of box jellyfish venom composition and the molecular structure and function of cnidarian toxins. The generated data represent a useful resource to guide future comparative studies, novel protein/peptide discovery and the development of more effective treatments for jellyfish stings in humans. (Length: 300).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1568-3) contains supplementary material, which is available to authorized users.