Non-redundant NCBI Research Articles

Genome sequencing and analysis of penicillin V producing Penicillium rubens strain BIONCL P45 isolated from India.

A filamentous fungus Penicillium rubens is widely recognized for producing industrially important antibiotic, penicillin at industrial scale. To better comprehend, the genetic blueprint of the wild-type P. rubens was isolated from India to identify the genetic/biosynthetic pathways for phenoxymethylpenicillin (penicillin V, PenV) and other secondary metabolites. Genomic DNA (gDNA) was isolated, and library was prepared as per Illumina platform. Whole genome sequencing (WGS) was performed according to Illumina NovoSeq platform. Further, SOAPdenovo was used to assemble the short reads validated by Bowtie-2 and SAMtools packages. Glimmer and GeneMark were used to dig out total genes in genome. Functional annotation of predicted proteins was performed by NCBI non-redundant (NR), UniProt, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Moreover, secretome analysis was performed by SignalP 4.1 and TargetP v1.1 and carbohydrate-active enzymes (CAZymes) and protease families by CAZy database. Comparative genome analysis was performed by Mauve 2.4.0. software to find genomic correlation between P. rubens BIONCL P45 and Penicillium chrysogenum Wisconsin 54-1255; also phylogeny was prepared with known penicillin producing strains by ParSNP tool. Penicillium rubens BIONCL P45 strain was isolated from India and is producing excess PenV. The 31.09Mb genome was assembled with 95.6% coverage of the reference genome P. chrysogenum Wis 54-1255 with 10687 protein coding genes, 3502 genes had homologs in NR, UniProt, KEGG, and GO databases. Additionally, 358 CAZymes and 911 transporter coding genes were found in genome. Genome contains complete pathways for penicillin, homogentisate pathway of phenyl acetic acid (PAA) catabolism, Andrastin A, Sorbicillin, Roquefortine C, and Meleagrin. Comparative genome analysis of BIONCL P45 and Wis 54-1255 revealed 99.89% coverage with 2952 common KEGG orthologous protein-coding genes. Phylogenetic analysis revealed that BIONCL P45 was clustered with Fleming's original isolate P. rubens IMI 15378. This genome can be a helpful resource for further research in developing fermentation processes and strain engineering approaches for high titer penicillin production.

Diosgenin biosynthesis investigation in medicinal herb (Tribulus terrestris) by transcriptome analysis

Next-generation sequencing (NGS) has revolutionized the analysis of specific genes, pathways, and their regulation in various species. Tribulus terrestris L., an annual medicinal herb of Zygophyllaceae family, has gained significant attention due to its diverse medicinal properties, including anti-inflammatory, antimicrobial, and anti-cancer effects. Diosgenin, a steroidal saponin, is the major bioactive compound responsible for the medicinal importance of T. terrestris. However, there is a paucity of information regarding the genes involved in the diosgenin biosynthetic pathway in T. terrestris. To address this gap, this study aimed to identify candidate genes associated with diosgenin biosynthesis through whole transcriptome profiling. A total of ∼7.9 GB of data, comprising 482 million reads, was obtained and assembled into 148,871 unigenes. Subsequently, functional annotations were assigned to 50 % of the unigenes using sequence similarity searches against the NCBI non-redundant (NR), Uniprot, KEGG, Pfam, GO, and COG databases, primarily based on Gene Ontology and KEGG-KAAS pathways. The majority of unigenes associated with the biosynthesis of the steroidal diosgenin backbone exhibited up-regulation in the fruit, leaf, and root tissues, except the SQE gene in root. The differential expression of selected genes was further validated through quantitative real-time polymerase chain reaction (qRT-PCR). Additionally, the study identified 21,026 unigenes related to transcription factors and 15,551 unigenes containing simple sequence repeats (SSR). Notably, di-nucleotide SSR motifs exhibited a high repeat frequency. These findings greatly enhance our understanding of the diosgenin biosynthesis pathway and provide a basis for future research in molecular investigation and metabolic engineering, specifically for boosting diosgenin content.

Transcriptomic Identification and Expression Profile Analysis of Odorant-Degrading Enzymes from the Asian Corn Borer Moth, Ostrinia furnacalis.

The Asian corn borer moth Ostrinia furnacalis is an important lepidopteran pest of maize in Asia. Odorant-degrading enzymes (ODEs), including carboxylesterases (CCEs), glutathione S-transferases (GSTs), cytochrome P450s (CYPs), UDP-glycosyltransferases (UGTs), and aldehyde oxidases (AOXs), are responsible for rapid inactivation of odorant signals in the insect antennae. In this study, we performed a transcriptome assembly for the antennae of O. furnacalis to identify putative ODE genes. Transcriptome sequencing revealed 35,056 unigenes, and 21,012 (59.94%) of these were annotated by searching against the reference sequences in the NCBI non-redundant (NR) protein database. For functional classification, these unigenes were subjected to Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations. We identified 79 genes encoding putative ODEs: 19 CCEs, 17 GSTs, 24 CYPs, 13 UGTs, and 6 AOXs. BLASTX best hit results indicated that these genes shared quite high amino acid identities with their respective orthologs from other lepidopteran species. Reverse transcription-quantitative PCR showed that OfurCCE2, OfurCCE5, and OfurCCE18 were enriched in male antennae, while OfurCCE7 and OfurCCE10 were enriched in female antennae. OfurCCE14 and OfurCCE15 were expressed at near-equal amounts in the antennae of both sexes. Our findings establish a solid foundation for future studies aimed at understanding the olfactory functions of these genes in O. furnacalis.

De novo genome assembly and functional annotation for Fusarium langsethiae

BackgroundFusarium langsethiae is a T-2 and HT-2 mycotoxins producing species firstly characterised in 2004. It is commonly isolated from oats in Northern Europe. T-2 and HT-2 mycotoxins exhibit immunological and haemotological effects in animal health mainly through inhibition of protein, RNA and DNA synthesis. The development of a high-quality and comprehensively annotated assembly for this species is therefore essential in providing the molecular understanding and the mechanism of T-2 and HT-2 biosynthesis in F. langsethiae to help develop effective control strategies.ResultsThe F. langsethiae assembly was produced using PacBio long reads, which were then assembled independently using Canu, SMARTdenovo and Flye. A total of 19,336 coding genes were identified using RNA-Seq informed ab-initio gene prediction. Finally, predicting genes were annotated using the basic local alignment search tool (BLAST) against the NCBI non-redundant (NR) genome database and protein hits were annotated using InterProScan. Genes with blast hits were functionally annotated with Gene Ontology.ConclusionsWe developed a high-quality genome assembly of a total length of 59 Mb and N50 of 3.51 Mb. Raw sequence reads and assembled genome is publicly available and can be downloaded from: GenBank under the accession JAFFKB000000000.All commands used to generate this assembly are accessible via GitHub: https://github.com/FadyMohareb/fusarium_langsethiae.

A highly alkaline pectate lyase from the Himalayan hot spring metagenome and its bioscouring applications

From the vast enzymatic weaponry encrypted in the metagenomic resource of the Himalayan hot spring, a novel gene encoding pectate lyase (eplM) was identified. Mapping against the nucleotide non-redundant NCBI database could not reveal any match for this gene sequence. At the protein level, it was about 56.86% identical to an uncharacterized sequence from Rheinheimera tangshanensis. The novel gene, eplM, was cloned and expressed in a heterologous host, Escherichia coli. The purified protein, EPLM, was biochemically characterized for pectate lyase activity towards pectin. It exhibited the maximum activity in the alkaline pH range, with optimum activity at 11.0 pH (1524.10 U/mg). The enzyme was functional in the temperature range of 30–50 °C, with the optimum activity at 40 °C. EPLM was found to be a calcium-dependent enzyme that can efficiently act on the methylated pectin obtained from a diverse source of plant biomass. The catalytic utility of EPLM was tested by demonstrating bioscouring of banana pseudostem biomass. The micrographic changes in surface structures of the fibers and release of unsaturated galacturonides endorsed EPLM as a promising biocatalyst for pectin-removal processing applications.

Increasing the power of interpretation for soil metaproteomics data

BackgroundSoil and sediment microorganisms are highly phylogenetically diverse but are currently largely under-represented in public molecular databases. Their functional characterization by means of metaproteomics is usually performed using metagenomic sequences acquired for the same sample. However, such hugely diverse metagenomic datasets are difficult to assemble; in parallel, theoretical proteomes from isolates available in generic databases are of high quality. Both these factors advocate for the use of theoretical proteomes in metaproteomics interpretation pipelines. Here, we examined a number of database construction strategies with a view to increasing the outputs of metaproteomics studies performed on soil samples.ResultsThe number of peptide-spectrum matches was found to be of comparable magnitude when using public or sample-specific metagenomics-derived databases. However, numbers were significantly increased when a combination of both types of information was used in a two-step cascaded search. Our data also indicate that the functional annotation of the metaproteomics dataset can be maximized by using a combination of both types of databases.ConclusionsA two-step strategy combining sample-specific metagenome database and public databases such as the non-redundant NCBI database and a massive soil gene catalog allows maximizing the metaproteomic interpretation both in terms of ratio of assigned spectra and retrieval of function-derived information.4F9sWsX3PjS31f5TKAyCkGVideo abstract

The Developmental Transcriptome of Bagworm, Metisa plana (Lepidoptera: Psychidae) and Insights into Chitin Biosynthesis Genes.

Bagworm, Metisa plana (Lepidoptera: Psychidae) is a ubiquitous insect pest in the oil palm plantations. M. plana infestation could reduce the oil palm productivity by 40% if it remains untreated over two consecutive years. Despite the urgency to tackle this issue, the genome and transcriptome of M. plana have not yet been fully elucidated. Here, we report a comprehensive transcriptome dataset from four different developmental stages of M. plana, comprising of egg, third instar larva, pupa and female adult. The de novo transcriptome assembly of the raw data had produced a total of 193,686 transcripts, which were then annotated against UniProt, NCBI non-redundant (NR) database, Gene Ontology, Cluster of Orthologous Group, and Kyoto Encyclopedia of Genes and Genomes databases. From this, 46,534 transcripts were annotated and mapped to 146 known metabolic or signalling KEGG pathways. The paper further identified 41 differentially expressed transcripts encoding seven genes in the chitin biosynthesis pathways, and their expressions across each developmental stage were further analysed. The genetic diversity of M. plana was profiled whereby there were 21,516 microsatellite sequences and 379,895 SNPs loci found in the transcriptome of M. plana. These datasets add valuable transcriptomic resources for further study of developmental gene expression, transcriptional regulations and functional gene activities involved in the development of M. plana. Identification of regulatory genes in the chitin biosynthesis pathway may also help in developing an RNAi-mediated pest control management by targeting certain pathways, and functional studies of the genes in M. plana.

Proteomic investigation of Peristenus spretus ovary and characterization of an ovary-enriched heat shock protein.

Peristenus spretus (Hymenoptera: Braconidae) is one of the most important endoparasitoids used for biological control of the green mirid bug, Apolygus lucorum Meyer-Dür (Heteroptera: Miridae). However, what we know about its reproductive genetics is very limited. Here, the composition of ovarian proteins in P. spretus was analyzed. Mass spectrum data searched against the non-redundant NCBI protein and UniProt protein database identified 1382 proteins and revealed an enrichment of the heat shock protein 83 (HSP83) in P. spretus ovary. The Pshsp83 complete cDNA is 2175 bp in length and encodes a protein of 724 amino acids with a calculated molecular mass of 83.4 kDa and a theoretical isoelectric point of 4.87. Transcription of Pshsp83 appeared from days 1 to 13 post-emergence and peaked at 13th day. Immuno-localization showed that the HSP83 protein was present in cytoplasm of germarium and in egg chambers of the whole ovariole. The transcript abundance of Pshsp83 fluctuated drastically after heat shocks at different temperatures and the maximum emerged at 35°C. The exposure to 35°C caused no dramatic effects on reproductive parameters of adult females such as pupation rate, cocoon weight, emergence rate, sex ratio and developmental duration, but did on longevity. These results suggested that the HSP83 protein is involved in life-span regulation in the P. spretus.

Quantitative proteomics to reveal the composition of Southern India spectacled cobra (Naja naja) venom and its immunological cross-reactivity towards commercial antivenom

Indian cobra (Naja naja) envenomation is frequently reported across Indian subcontinent. Geographical differences in the venom composition of a particular species of snake often leads to inconsistencies in the antivenom neutralization. Consequently, determining the venom proteome from every locale is necessary for the production of effective antivenom. In this study, we deciphered the proteome composition of N. naja venom (NnV) from southern India (SI) by label-free quantitative proteomics that identified 45 proteins (toxins) belonging to 14 venom protein families when searched against Elapidae (taxid: 8602) protein entries in the non-redundant NCBI database. Low molecular mass (<15 kDa) toxins such as PLA2 (18.2%) and 3FTx (37.4%) are the most abundant enzymatic and non-enzymatic proteins, respectively, in SI NnV. Nevertheless, the relative abundance of 3FTxs in SI NnV was found to be lower than the relative abundance of these toxins in previously determined eastern and western India NnV samples. Immuno-recognition and in vitro neutralization of some enzymatic activities and pharmacological properties of SI NnV by commercial polyvalent antivenom evidently demonstrated poor recognition of the most abundant low molecular mass toxins of SI NnV. This finding points to the need for new strategies for antivenom production for the successful treatment of cobra bite.

The Single-molecule long-read sequencing of Scylla paramamosain

Scylla paramamosain is an important aquaculture crab, which has great economical and nutritional value. To the best of our knowledge, few full-length crab transcriptomes are available. In this study, a library composed of 12 different tissues including gill, hepatopancreas, muscle, cerebral ganglion, eyestalk, thoracic ganglia, intestine, heart, testis, ovary, sperm reservoir, and hemocyte was constructed and sequenced using Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology. A total of 284803 full-length non-chimeric reads were obtained, from which 79005 high-quality unique transcripts were obtained after error correction and sequence clustering and redundant. Additionally, a total of 52544 transcripts were annotated against protein database (NCBI nonredundant, Swiss-Prot, KOG, and KEGG database). A total of 23644 long non-coding RNAs (lncRNAs) and 131561 simple sequence repeats (SSRs) were identified. Meanwhile, the isoforms of many genes were also identified in this study. Our study provides a rich set of full-length cDNA sequences for S. paramamosain, which will greatly facilitate S. paramamosain research.

Comparative transcriptome analysis of translucent flesh disorder in mangosteen (Garcinia mangostana L.) fruits in response to different water regimes.

Translucent flash disorder (TFD) is one of the important physiological disorders in mangosteen (Garcinia mangostana L.). TFD has symptoms such as flesh arils that become firm and appear transparent similar to watercore in apple or pear. Information on the changes of gene expression in TFD-affected tissues remain limited, and investigations into the effects of different water regimes still need to be undertaken. Through an RNA sequencing approach using the Ion Proton, 183,274 contigs with length ranging from 173–13,035 bp were constructed by de novo assembly. Functional annotation was analyzed using various public databases such as non-redundant protein NCBI, SwissProt, and Gene Ontology, and KEGG pathway. Our studies compared different water regimes to incidence and differentially expressed genes of TFD-like physiological disorders. From the differentially expressed gene (DEG) between normal air and TFD-affected aril, we identified DEG-related TFD events, which 6228 DEGs in the control condition and 3327 DEGs in under water stress treatment condition remained, and confirmed these with RT-qPCR, including sucrose synthase (SUSY), endoglucanase (GUN), xyloglucan endotransglucosylase/hydrolase (XTH), and polygalacturonase (PG) showed statistically significant. In addition, transcription factors also indicated changes in MYB, NAC and WRKY between tissues and different water regimes.

Transcriptome sequencing and de novo analysis of the northern snakehead, Ophiocephalus argus

Northern snakehead, Ophiocephalus argus Cantor, is an endemic freshwater fish in China. However, wild stocks of O. argus are dwindling sharply. Further, water conservancy projects, environmental pollution and human activities have caused the decrease of wild stocks, which has attracted much attention. Here, we have investigated the genomic information of O. argus using IlluminaHiseq 4000 sequencing. The transcriptomes of O. argus were sequenced by Illumina technology. A total of 67,564 sequences from 79,500,964 paired-end reads were generated, 33,710 unigenes were annotated based on protein databases (NCBI nonredundant (NR) databases). In total, 7182 unigenes had the clusters of orthologous group (COG) classifications, 33,710 unigenes were assigned to 59 gene ontology (GO) terms. Further, a total of 21,464 simple sequence repeats (SSRs) from 67,564 unigenes and 113,518 single nucleotide polymorphism (SNP) sites among 335 Mclean reads were yielded for O. argus based on a transcriptome-wide search. The new transcriptome data which is presented in this study for O. argus will provide valuable information for gene discovery and downstream applications, such as phylogenetic analysis, gene-expression profiling and identification of genetic markers (SSRs andSNP).

A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining

Microorganisms are useful environmental indicators, able to deliver essential insights to processes regarding mine land rehabilitation. To compare microbial communities from a chronosequence of mine land rehabilitation to pre-disturbance levels from references sites covered by native vegetation, we sampled non-rehabilitated, rehabilitating and reference study sites from the Urucum Massif, Southwestern Brazil. From each study site, three composed soil samples were collected for chemical, physical, and metagenomics analysis. We used a paired-end library sequencing technology (NextSeq 500 Illumina); the reads were assembled using MEGAHIT. Coding DNA sequences (CDS) were identified using Kaiju in combination with non-redundant NCBI BLAST reference sequences containing archaea, bacteria, and viruses. Additionally, a functional classification was performed by EMG v2.3.2. Here, we provide the raw data and assembly (reads and contigs), followed by initial functional and taxonomic analysis, as a base-line for further studies of this kind. Further investigation is needed to fully understand the mechanisms of environmental rehabilitation in tropical regions, inspiring further researchers to explore this collection for hypothesis testing.

Deep sequencing analysis of toad Rhinella schneideri skin glands and partial biochemical characterization of its cutaneous secretion

BackgroundAnimal poisons and venoms are sources of biomolecules naturally selected. Rhinella schneideri toads are widespread in the whole Brazilian territory and they have poison glands and mucous gland. Recently, protein from toads’ secretion has gaining attention. Frog skin is widely known to present great number of host defense peptides and we hypothesize toads present them as well. In this study, we used a RNA-seq analysis from R. schneideri skin and biochemical tests with the gland secretion to unravel its protein molecules.MethodsTotal RNA from the toad skin was extracted using TRizol reagent, sequenced in duplicate using Illumina Hiseq2500 in paired end analysis. The raw reads were trimmed and de novo assembled using Trinity. The resulting sequences were submitted to functional annotation against non-redundant NCBI database and Database of Anuran Defense Peptide. Furthermore, we performed caseinolytic activity test to assess the presence of serine and metalloproteases in skin secretion and it was fractionated by fast liquid protein chromatography using a reverse-phase column. The fractions were partially sequenced by Edman’s degradation.ResultsWe were able to identify several classes of antimicrobial peptides, such as buforins, peroniins and brevinins, as well as PLA2, lectins and galectins, combining protein sequencing and RNA-seq analysis for the first time. In addition, we could isolate a PLA2 from the skin secretion and infer the presence of serine proteases in cutaneous secretion.ConclusionsWe identified novel toxins and proteins from R. schneideri mucous glands. Besides, this is a pioneer study that presented the in depth characterization of protein molecules richness from this toad secretion. The results obtained herein showed evidence of novel AMP and enzymes that need to be further explored.

Proteomic Analysis and Immuno-Profiling of Eastern India Russell's Viper ( Daboia russelii) Venom: Correlation between RVV Composition and Clinical Manifestations Post RV Bite.

The proteomes of Russell's viper venom (RVV) from Burdwan (RVV B) and Nadia (RVV N), the two districts of West Bengal, eastern India (EI), were investigated by gel-filtration chromatography (GFC) followed by tandem mass spectrometry of tryptic fragments of the fractions. A total of 73 and 69 proteins belonging to 15 snake venom protein families were identified in RVV B and RVV N, respectively, by MS/MS search against Viperidae (taxid 8689) protein entries of the nonredundant NCBI database. The minor differences in venom composition of both the EI RV were established unequivocally by their biochemical and pharmacological properties and by SDS-PAGE, gel filtration chromatography, and LC-MS/MS analyses. The composition of EI RVVs was well correlated with published reports on the pathophysiology of RV-envenomed patients from this part of the country. Venom-antivenom cross-reactivity determined by ELISA, Western blotting, and antivenomics approaches demonstrated poor recognition of low molecular mass (<20 kDa) RVV proteins by commercial polyvalent antivenoms, which was substantiated by neutralization of RVV enzymes by antivenom.

Quantitative proteomic analysis and antivenom study revealing that neurotoxic phospholipase A2 enzymes, the major toxin class of Russell's viper venom from southern India, shows the least immuno-recognition and neutralization by commercial polyvalent antivenom

The proteome composition of Russell's viper venom (RVV) from southern India (SI) was investigated by 1D-SDS-PAGE of venom followed by tandem mass spectrometry analysis of protein bands. A total of 66 proteins belonging to 14 snake venom protein families were identified by LC-MS/MS analysis against Viperidae (taxid 8689) protein entries from the non-redundant NCBI database. Phospholipase A2 (43.25%) and snaclec (14.57%) represented the most abundant enzymatic and non-enzymatic proteins, respectively. SI RVV was characterized as containing a higher quantity of PLA2 and a lower amount of Kunitz-type serine protease inhibitors, in comparison to RVV from other regions of the Indian subcontinent. The enzymatic activities, pharmacological properties, and clinical manifestations of RV envenomation in SI were well correlated with its proteome composition; however, ATPase, ADPase, and hyaluronidase enzymes were not identified by LC-MS/MS analysis, owing to paucity of the existing database. Neurological symptoms exhibited by RV-bite patients in SI were correlated to the presence of abundant neurotoxic phospholipase A2 enzymes (15.66%) in SI RVV. Neutralization studies, immunological cross-reactivity, and antivenomics studies unequivocally demonstrated the poor recognition and lowest neutralization of PLA2 enzymes by commercial polyvalent antivenom, which is a major concern for the treatment of RV-envenomed patients in SI.

Genomic analysis of bifunctional Class C-Class D β-lactamases in environmental bacteria.

β-lactamases, which are found in several bacterial species and environments, are the main cause of resistance to β-lactams in Gram-negative bacteria. In 2009, a protein (LRA-13) with two β-lactamase domains (one class C domain and one class D domain) was experimentally characterised, and an extended action spectrum against β-lactams consistent with two functional domains was found. Here, we present the results of searches in the non-redundant NCBI protein database that revealed the existence of a group of homologous bifunctional β-lactamases in the genomes of environmental bacteria. These findings suggest that bifunctional β-lactamases are widespread in nature; these findings also raise concern that bifunctional β-lactamases may be transferred to bacteria of clinical importance through lateral gene transfer mechanisms.

Head Kidney Transcriptome Analysis and Characterization for the Sub-Antarctic Notothenioid Fish Eleginops maclovinus

This study describes de novo transcriptome sequencing and annotation analyses for the head kidney of the sub-Antarctic notothenioid fish Eleginops maclovinus, a sister group of the Antarctic notothenioid fish clade. Moreover, E. maclovinus is one of the most eurythermal and euryhaline representatives of the Notothenioidei suborder. RNA-seq data were generated by the 454 GS Junior system, resulting in 11,207 contigs that were then assembled by the Genomic Workbench CLC software. The transcriptome was annotated by BLASTing each sequence against the universal, non-redundant NCBI database (National Center for Biotechnology Information) using the AUSTRAL-omics computer cluster. A significant number of transcripts related to innate and adaptive immunity were found in the sequences, which could be used as references in future immunological studies in E. maclovinus.

Gene expression profiling of the unfed nymphal Dermacentor silvarum (Acari: Ixodidae) in response to low temperature

The tick Dermacentor silvarum is recognized as an emerging vector of marked medical and veterinary significance. The current study investigated the gene expression profiling of the unfed nymphal D. silvarum in response to low temperature using high-throughput transcriptome sequencing. A total of approximately 12-giga base pairs were produced, which yielded 87,500 unigenes, and among them, 29,815 unigenes were successfully annotated by all available databases (NCBI nonredundant, Swissprot, UniProtKB/TrEMBL, the clusters of orthologous groups databases, the Kyoto encyclopedia of genes and genomes database, and pfam database). After low temperature treatment (4°C for 10 days), 2,241 genes, including 1,160 up-regulated and 1,081 down-regulated genes, were differentially expressed. The differentially expressed genes were further enriched to GO terms and KEGG pathways, and our results showed that 133 genes were enriched in molecular function, 90 genes were enriched in cellular components, 107 genes were enriched in biological processes and 202 genes were assigned into different KEGG pathways. This study establishes a molecular basis for gene function analysis in the tick D. silvarum, and will provide theoretical information for mechanistic studies on the overwintering adaptations of ticks.

Transcriptome Characterization of the Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook.) and Expression Analysis of Candidate Phosphate Transporter Genes

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most important afforestation tree species in China because of its excellent timber quality and high yield. However, the limited availability of phosphorus in forest soils is widespread and has become an important factor in the declining productivity of Chinese fir plantations. Here we used the Illumina HiSeq™ 2000 DNA sequencing platform to sequence root, stem, and leaf transcriptomes of one-year old Chinese fir clones with phosphorus treatment. Approximately 236,529,278 clean reads were obtained and generated 35.47 G of sequencing data. These reads were assembled into 413,806 unigenes with a mean length of 520 bp. In total, 109,596 unigenes were annotated in the NR (NCBI non-redundant) database, 727,287 genes were assigned for GO (Gene Ontology) terms, information for 92,001 classified unigenes was assigned to 26 KOG (Karyotic Orthologous Groups) categories, and 57,042 unigenes were significantly matched with 132 KEGG (Kyoto Encyclopedia of Genes and Genomes) predicted pathways. In total, 49 unigenes were identified as exhibiting inorganic phosphate transporter activity, and 14 positive genes’ expression patterns in different phosphorus deficiency treatments were analyzed by qRT-PCR to explore their putative functions. This study provides a basic foundation for functional genomic studies of the phosphate transporter in Chinese fir, and also presents an extensive annotated sequence resource for molecular research.