Full-length Open Reading Frame Research Articles

Molecular cloning and characterization of the glutathione reductase gene from Stipa purpurea

Reactive oxygen species (ROS) are a key factor in abiotic stresses; excess ROS is harmful to plants. Glutathione reductase (GR) plays an important role in scavenging ROS in plants. Here, a GR gene, named SpGR, was cloned from Stipa purpurea and characterized. The full-length open reading frame was 1497 bp, encoding 498 amino acids. Subcellular localization analysis indicated that SpGR was localized to both the plasma membrane and nucleus. The expression of SpGR was induced by cold, salt, and drought stresses. Functional analysis indicated that ectopic expression of SpGR in Arabidopsis thaliana resulted in greater tolerance to salt stress than that of wild-type plants, but no difference under cold or drought treatments. The results of GR activity and GSSG and GSH content analyses suggested that, under salt stress, transgenic plants produced more GR to reduce GSSG to GSH for scavenging ROS than wild-type plants. Therefore, SpGR may be a candidate gene for plants to resist abiotic stress.

Novel full-length major histocompatibility complex class I allele discovery and haplotype definition in pig-tailed macaques.

Pig-tailed macaques (Macaca nemestrina, Mane) are important models for human immunodeficiency virus (HIV) studies. Their infectability with minimally modified HIV makes them a uniquely valuable animal model to mimic human infection with HIV and progression to acquired immunodeficiency syndrome (AIDS). However, variation in the pig-tailed macaque major histocompatibility complex (MHC) and the impact of individual transcripts on the pathogenesis of HIV and other infectious diseases is understudied compared to that of rhesus and cynomolgus macaques. In this study, we used Pacific Biosciences single-molecule real-time circular consensus sequencing to describe full-length MHC class I (MHC-I) transcripts for 194 pig-tailed macaques from three breeding centers. We then used the full-length sequences to infer Mane-A and Mane-B haplotypes containing groups of MHC-I transcripts that co-segregate due to physical linkage. In total, we characterized full-length open reading frames (ORFs) for 313 Mane-A, Mane-B, and Mane-I sequences that defined 86 Mane-A and 106 Mane-B MHC-I haplotypes. Pacific Biosciences technology allows us to resolve these Mane-A and Mane-B haplotypes to the level of synonymous allelic variants. The newly defined haplotypes and transcript sequences containing full-length ORFs provide an important resource for infectious disease researchers as certain MHC haplotypes have been shown to provide exceptional control of simian immunodeficiency virus (SIV) replication and prevention of AIDS-like disease in nonhuman primates. The increased allelic resolution provided by Pacific Biosciences sequencing also benefits transplant research by allowing researchers to more specifically match haplotypes between donors and recipients to the level of nonsynonymous allelic variation, thus reducing the risk of graft-versus-host disease.

Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome.

Korean ginseng (Panax ginseng C.A. Meyer) has been widely used for medicinal purposes and contains potent plant secondary metabolites, including ginsenosides. To obtain transcriptomic data that offers a more comprehensive view of functional genomics in P. ginseng, we generated genome-wide transcriptome data from four different P. ginseng tissues using PacBio isoform sequencing (Iso-Seq) technology. A total of 135,317 assembled transcripts were generated with an average length of 3.2 kb and high assembly completeness. Of those unigenes, 67.5% were predicted to be complete full-length (FL) open reading frames (ORFs) and exhibited a high gene annotation rate. Furthermore, we successfully identified unique full-length genes involved in triterpenoid saponin synthesis and plant hormonal signaling pathways, including auxin and cytokinin. Studies on the functional genomics of P. ginseng seedlings have confirmed the rapid upregulation of negative feed-back loops by auxin and cytokinin signaling cues. The conserved evolutionary mechanisms in the auxin and cytokinin canonical signaling pathways of P. ginseng are more complex than those in Arabidopsis thaliana. Our analysis also revealed a more detailed view of transcriptome-wide alternative isoforms for 88 genes. Finally, transposable elements (TEs) were also identified, suggesting transcriptional activity of TEs in P. ginseng. In conclusion, our results suggest that long-read, full-length or partial-unigene data with high-quality assemblies are invaluable resources as transcriptomic references in P. ginseng and can be used for comparative analyses in closely related medicinal plants.

Molecular characterization and expression analysis of the large yellow croaker (Larimichthys crocea) chemokine receptors CXCR2, CXCR3, and CXCR4 after bacterial and poly I:C challenge

The large yellow croaker (Larimichthys crocea) has a well-developed innate immune system. We studied a component of this system, chemokine receptor CXCR family. In this study, we report the full-length open reading frames, as well as the identification and characterization of the chemokine receptor genes CXCR2 (LycCXCR2), CXCR3 (LycCXCR3), and CXCR4 (LycCXCR4) of large yellow croaker. We report that LycCXCR3 and LycCXCR4 are evolving neutrally according to PAML analyses. Quantitative real-time PCR analysis revealed that CXCR transcripts were expressed in all examined tissues. The expression of chemokine receptors LycCXCR2, LycCXCR3, and LycCXCR4 was elevated in the kidney, spleen, and particularly the liver of the large yellow croaker after challenge with Vibrio anguillarum and polyinosinic:polycytidylic acid (poly I:C). These results suggest that LycCXCR2, LycCXCR3, and LycCXCR4 may be important immune-related genes, playing crucial roles in immune defence against bacterial infection.

Interaction of heat shock protein 90 B1 (Hsp90B1) with liposome reveals its potential role in protection the integrity of lipid membranes

Heat shock proteins of 90kDa (Hsp90) are molecular chaperones essential for protein homeostasis. Besides chaperone activity, Hsp90 exhibits other cellular functions at membranes, yet how it interacts with membranes remains elusive. We report here that Hsp90B1 interacts with phospholipid membranes. We first cloned the full-length open reading frame of Hsp90B1 from Anas platyrhnchos (ApHsp90B1), and the gene was then heterologously expressed and purified. SPR analysis show the purified ApHsp90B1 interacts with phospholipid membranes with high affinity (KD 176±25nM), and the interaction occurs over a wide range of pH, which is especially distinct under acidic conditions. Tryptophan fluorescence and far-UV CD spectra studies find that the interaction of ApHsp90B1 with phospholipid membrane induces microenvironment changes of tryptophan residues and conformational change of some regions in ApHsp90B1, which might be the reason of its increased ATPase activity upon addition phospholipid vesicles. Importantly, the interaction of ApHsp90B1 with phospholipid vesicles significantly reduces lipolysis of the membrane phospholipid, suggesting that the interaction of Hsp90B1 with membrane could preserve membrane integrity. The present study therefore demonstrates for the first time that Hsp90B1 exhibits high affinity for phospholipid membrane and suggest Hsp90B1 play an important role in membrane-stabilizing via its interaction with membrane phospholipids.

MiR171 and its target gene SCL6 contribute to embryogenic callus induction and torpedo-shaped embryo formation during somatic embryogenesis in two lily species

Somatic embryogenesis (SE) is the capacity of plant somatic cells to form embryos through a process resembling zygotic embryogenesis. This process is used as a model system to study zygotic embryo development. miRNAs play a crucial role in regulating the occurrence and development of plant SE. In our previous study, miR171 showed differential expression in the various developmental stages of SE in Lilium pumilum DC. Fisch. and Lilium davidii var. unicolor. However, little is known about the regulatory mechanism of miR171 and its target genes during Lilium SE. Here, the mature sequences of lpu-miR171a, lpu-miR171b, lda-miR171a and lda-miR171c were cloned using stem-loop RT-PCR. Furthermore, SCL6 transcription factors were verified to be the targets of miR171 using RLM-RACE. In addition, the full-length open reading frames for three target genes were cloned. The qRT-PCR results indicate that expression profiles differ among members of the miR171 family. lpu-miR171a expresses at high levels in the embryonic callus stage, while lda-miR171a, lda-miR171c and lpu-miR171b have the highest expression levels in the torpedo-shaped embryo stage. The expression levels of targets were negatively correlated with those of lpu-miR171a and lpu-miR171b; however, the levels of lda-miR171a and lda-miR171c were positively correlated with those of their target genes. The developmental stage-specific expression profiles of miR171 and SCL6 genes during SE implied that they have different regulatory functions during lily SE. According to the relationships between the expression files of miR171 and its target, the miR171 family functions in the regulation of SE, especially in the development of torpedo-shaped embryos.

Identification and characterization of the steroid 15α-hydroxylase gene from Penicillium raistrickii.

Penicillium raistrickii ATCC 10490 is used for the commercial preparation of 15α-13-methy-estr-4-ene-3,17-dione, a key intermediate in the synthesis of gestodene, which is a major component of third-generation contraceptive pills. Although it was previously shown that a cytochrome P450 enzyme in P. raistrickii is involved in steroid 15α-hydroxylation, the gene encoding the steroid 15α-hydroxylase remained unknown. In this study, we report the cloning and characterization of the 15α-hydroxylase gene from P. raistrickii ATCC 10490 by combining transcriptomic profiling with functional heterologous expression in Saccharomyces cerevisiae. The full-length open reading frame (ORF) of the 15α-hydroxylase gene P450pra is 1563bp and predicted to encode a cytochrome P450 protein of 520 amino acids. Targeted gene deletion revealed that P450pra is solely responsible for 15α-hydroxylation activity on 13-methy-estr-4-ene-3,17-dione in P. raistrickii ATCC 10490. The identification of the 15α-hydroxylase gene from P. raistrickii should help elucidate the molecular basis of regio- and stereo-specificity of steroid 15α-hydroxylation and aid in the engineering of more efficient industrial strains for useful steroid 15α-hydroxylation reactions.

Cloning and identification of a novel steroid 11α-hydroxylase gene from Absidia coerulea

Steroid 11-hydroxylation by filamentous fungi is a major route for industrial scale production of key intermediates in the synthesis of steroid drugs. Although it is well established that enzymes involved in fungal hydroxylation of steroids are cytochrome P450s (CYP), few fungal steroid hydroxylase genes have been identified. In this study, we identified a novel 11α-hydroxylase gene CYP5311B1 from Absidia coerulea AS3.65 by a combination of transcriptome sequencing, real-time qRT-PCR and heterologous expression in Pichia pastoris. The full-length open reading frame (ORF) of CYP5311B1 is predicted to encode a CYP protein of 527 amino acids whose expression in Pichia cells was confirmed by western blot. In addition, the major hydroxylation product was characterized by HPLC and 2D NMR. CYP5311B1 was highly induced by steroid substrate at the transcriptional level. The cloning and identification of an 11α-hydroxylase gene from A. coerulea should aid in a better understanding of the structural basis underlying regio- and stereoselectivity, and substrate specificity of fungal steroid 11α-hydroxylases, thus facilitating the engineering of more efficient steroid hydroxylases for industrial applications.

Cloning and characterization of the ammonium transporter genes BaAMT1;1 and BaAMT1;3 from Chinese kale

Chinese kale (Brassica alboglabra L.) is a popular vegetable rich in important nutrients. Fertilization with appropriate ammonium:nitrate ratios enhances biomass production and quality. AMT-type ammonium transporters have been shown to mediate ammonium uptake across the plasma membrane. However, very little is known about the molecular regulation of growth and development by ammonium in Chinese kale, including how ammonium regulates the expression of AMT1 genes. In this study, we identified and characterized two AMT1 genes from B. alboglabra, BaAMT1;1 and BaAMT1;3. The full-length open reading frames of BaAMT1;1 and BaAMT1;3 were 1512 bp and 1515 bp, respectively. Transient expression of the fusion proteins pBE-EGFP-BaAMT1;1 and pBE-EGFP-BaAMT1;3 in onion epidermal cells indicated that these transporters are located on the plasma membrane. BaAMT1;1 and BaAMT1;3 were functional in yeast and complemented a mutant defective in ammonium transport. BaAMT1;1 was expressed in vegetative organs and at high levels in roots, while BaAMT1;3 expression was root specific. In addition, we observed opposite responses of BaAMT1;1 and BaAMT1;3 expression to nitrogen starvation and ammonium resupply in roots. These results provide new insights into the molecular mechanisms underlying ammonium absorption in Chinese kale.

Molecular cloning and expression analysis of two lectin genes in Sophora flavescens

Plant lectins are greatly introduced in modern medical diagnostics, which play a key role to diagnose the degrees of malignant tumor and used to inhibit different types of cancer cells. To further characterize the structure and function of plant lectins, we cloned, expressed and analyzed two lectin genes from a Chinese medicinal plant Sophora flavescens (sfl1, sfl2). The two genes were successfully cloned by reverse transcription-polymerase chain reaction (RT-PCR). The full-length open reading frame (ORF) of the sfl1 contained 864bp encoding SFL1 protein with 287 amino acids, whereas the sfl2 contained 891bp encoding SFL2 protein of 296 amino acids. The two genes were subcloned to pET-22b(+) vector and the recombinant plasmids pET-22b(+)-sfl1 and pET-22b(+)-sfl2 were transformed into E. coli BL21 for protein expression. The two expressed proteins were detected by Western-blotting. The physicochemical properties, homologous proteins and evolution, secondary structures, and three dimensional (3D) structures of the SFL1 and SFL2 proteins were analyzed by bioinformatic tools. Our results provide a foundation for exploring plant lectins as anti-cancer drugs.

De Novo Genome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis).

The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by short reads (80 ×) and checked for accuracy by congruency against an independent short read assembly. We scaffolded the assembly using the exon–gene models derived from 9805 full-length open reading frames (FL-ORFs) constructed from the beaver leukocyte and muscle transcriptomes. The final assembly comprised 22,515 contigs with an N50 of 278,680 bp and an N50-scaffold of 317,558 bp. Maximum contig and scaffold lengths were 3.3 and 4.2 Mb, respectively, with a combined scaffold length representing 92% of the estimated genome size. The completeness and accuracy of the scaffold assembly was demonstrated by the precise exon placement for 91.1% of the 9805 assembled FL-ORFs and 83.1% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set used to assess the quality of genome assemblies. Well-represented were genes involved in dentition and enamel deposition, defining characteristics of rodents with which the beaver is well-endowed. The study provides insights for genome assembly and an important genomics resource for Castoridae and rodent evolutionary biology.

Molecular characterization of HOXC8 gene and methylation status analysis of its exon 1 associated with the length of cashmere fiber in Liaoning cashmere goat.

Homeobox protein Hox-C8 (HOXC8) is a member of Hox family. It is expressed in the dermal papilla of the skin and is thought to be associated with the hair inductive capacity of dermal papilla cells. In the present study, we isolated and characterized a full-length open reading frame of HOXC8 cDNA from the skin tissue of Liaoning cashmere goat, as well as, established a phylogenetic relationship of goat HOXC8 with that of other species. Also, we investigated the effect of methylation status of HOXC8 exon 1 at anagen secondary hair follicle on the cashmere fiber traits in Liaoning cashmere goat. The sequence analysis indicated that the obtained cDNA was 1134-bp in length containing a complete ORF of 729-bp. It encoded a peptide of 242 amino acid residues in length. The structural analysis indicated that goat HOXC8 contained a typical homeobox domain. The phylogenetic analysis revealed that Capra hircus HOXC8 had a closer genetic relationship with that of Ovis aries, followed by Bos Taurus and Bubalus bubalis. The methylation analysis suggested that the methylation degree of HOXC8 exon 1 in anagen secondary hair follicle might be involved in regulating the growth of cashmere fiber in Liaoning cashmere goat. Our results provide new evidence for understanding the molecular structural and evolutionary characteristics of HOXC8 in Liaoning cashmere goat, as well as, for further insight into the role of methylation degree of HOXC8 exon 1 regulates the growth of cashmere fiber in goat.

A plasmid library of full-length zebrafish rab proteins for in vivo cell biology.

The zebrafish is an emerging model for highly sophisticated medium-throughput experiments such as genetic and chemical screens. However, studies of entire protein families within this context are often hampered by poor genetic resources such as clone libraries. Here we describe a complete collection of 76 full-length open reading frame clones for the zebrafish rab protein family. While the mouse genome contains 60 rab genes and the human genome 63, we find that 18 zebrafish rab genes have 2, and in the case of rab38, 3 paralogues. In contrast, we were unable to identify zebrafish orthologues of the mammalian Rab2b, Rab17 or Rab29. We make this resource available through the Addgene repository to facilitate cell biologic approaches using this model.

Molecular Cloning and Characterization of Babesia orientalis Rhoptry Neck 2 BoRON2 Protein.

Babesiosis caused by Babesia orientalis is one of the most prevalent infections of water buffalo transmitted by Rhipicephalus haemaphysaloides causing a parasitic and hemolytic disease. The organelles proteins localized in apical membrane especially rhoptries neck and microneme protein form a complex called moving junction important during invasion process of parasites belonging to apicomplexan group, including Babesia species. A truncated fragment coding a 936 bps fragment was cloned in pMD-19T and subcloned into pET32 (a)+ expression vector, expressed in E. coli BL21. Purified recombinant BoRON2 was used to produce polyclonal antibody against BoRON2. Here, we identified the full sequence of gene encoding the rhoptry neck 2 protein that we named BoRON2 which is 4035 bp in full-length open reading frame without introns, encoding a polypeptide of 1345 amino acids. Western blot of rBoRON2 probed with buffalo positive serum analysis revealed a band of around 150 kDa in parasite lysates, suggesting an active involvement during invasion process. These findings most likely are constructive in perspective of ongoing research focused particularly on water buffalo babesiosis prevention and therapeutics and globally provide new information for genes comparative analysis.

Identification and Expression Analyses of Equine Endogenous Retroviruses in Horses.

Endogenous retroviruses (ERVs) have been integrated into vertebrate genomes and have momentously affected host organisms. Horses (Equus caballus) have been domesticated and selected for elite racing ability over centuries. ERVs played an important role in the evolutionary diversification of the horse genome. In the present study, we identified six equine ERV families (EqERVs-E1, I1, M2, P1, S1, and Y4), their full-length viral open reading frames (ORFs), and elucidated their phylogenetic relationships. The divergence time of EqERV families assuming an evolutionary rate of 0.2%/Myr indicated that EqERV-S3 (75.4 million years ago; mya) on chromosome 10 is an old EqERV family and EqERV-P5 (1.2 Mya) on chromosome 12 is a young member. During the evolutionary diversification of horses, the EqERV-I family diverged 1.7 Mya to 38.7 Mya. Reverse transcription quantitative real-time PCR (RT-qPCR) amplification of EqERV pol genes showed greater expression in the cerebellum of the Jeju horse than the Thoroughbred horse. These results could contribute further dynamic studies for horse genome in relation to EqERV gene function.

The Multifunctional Protein, Snd1, Involved in tRNA Splicing of the Fission Yeast

By screening a bank of temperature sensitive mutants of Schizosaccharomyces pombe, we had previously isolated six pre-tRNA splicing mutants named ptp1 to ptp6. We cloned the ptp4-2 + gene from a genomic DNA library by complementation of the growth defect. The recovered plasmid contains a 2.4 kb insert and complements the growth defect of the ptp4 - mutant by 87%. The 2.0 kb subclone of this plasmid showed 60% complementation of the growth defect. Introduction of the ptp4-2 + genes into the ptp4 - mutant cells restores the ability to splice tRNA. The nucleotide sequence of the ptp4-2+ gene was identical to the part of sequence of S. pombe chromosome III in the database of National Center for Biotechnology Information. There was only one truncated open reading frame in entire 2.4 kb sequence. The full-length open reading frame encodes Snd1, the multifunctional protein involved in various cellular processes. The 2.4 kb or 2.0 kb yeast DNA of the ptp4-2 + subclone contains only staphylococcal nuclease (SN) domains of the Snd1, suggesting that the SN domains of the Snd1 protein may participate in tRNA splicing. Snd1 is known to be involved in carcinogenesis and over-expressed in cancer cells. Considering that all tRNA expression is increased in cancer cells, the results in here may shed light in understanding the connection between tRNA and Snd1 in tumor cells as well as the mechanisms of carcinogenesis by Snd1.

Molecular and functional characterization of pigeon (Columba livia) tumor necrosis factor receptor-associated factor 3

Tumor necrosis factor receptor-associated factor 3 (TRAF3) plays a key antiviral role by promoting type I interferon production. We cloned the pigeon TRAF3 gene (PiTRAF3) according to its predicted mRNA sequence to investigate its function. The 1704-bp full-length open reading frame encodes a 567-amino acid protein. One Ring finger, two TRAF-type Zinc fingers, one Coiled coil, and one MATH domain were inferred. RT-PCR showed that PiTRAF3 was expressed in all tissues, with relatively weak expression in the heart and liver. In HEK293T cells, over-expression of wild-type, △Ring, △Zinc finger, and △Coiled coil PiTRAF3, but not a △MATH form, significantly increased IFN-β promoter activity. Zinc finger and Coiled coil domains were essential for NF-κB activation. In chicken HD11 cells, PiTRAF3 increased IFN-β promoter activity and four domains were all contributing. R848 stimulation of pigeon peripheral blood mononuclear cells and splenocytes significantly increased expression of PiTRAF3 and the inflammatory cytokine genes CCL5, IL-8, and IL-10. These data demonstrate TRAF3's innate immune function and improve understanding of its involvement in poultry antiviral defense.

Enzymatic modification by point mutation and functional analysis of an omega-6 fatty acid desaturase from Arctic Chlamydomonas sp.

ABSTRACTArctic Chlamydomonas sp. is a dominant microalgal strain in cold or frozen freshwater in the Arctic region. The full-length open reading frame of the omega-6 fatty acid desaturase gene (AChFAD6) was obtained from the transcriptomic database of Arctic Chlamydomonas sp. from the KOPRI culture collection of polar micro-organisms. Amino acid sequence analysis indicated the presence of three conserved histidine-rich segments as unique characteristics of omega-6 fatty acid desaturases, and three transmembrane regions transported to plastidic membranes by chloroplast transit peptides in the N-terminal region. The AChFAD6 desaturase activity was examined by expressing wild-type and V254A mutant (Mut-AChFAD6) heterologous recombinant proteins. Quantitative gas chromatography indicated that the concentration of linoleic acids in AChFAD6-transformed cells increased more than 3-fold [6.73 ± 0.13 mg g−1 dry cell weight (DCW)] compared with cells transformed with vector alone. In contrast, transformation with Mut-AChFAD6 increased the concentration of oleic acid to 9.23 ± 0.18 mg g−1 DCW, indicating a change in enzymatic activity to mimic that of stearoyl-CoA desaturase. These results demonstrate that AChFAD6 of Arctic Chlamydomonas sp. increases membrane fluidity by enhancing denaturation of C18 fatty acids and facilitates production of large quantities of linoleic fatty acids in prokaryotic expression systems.

De Novo Transcriptomes of Forsythia koreana Using a Novel Assembly Method: Insight into Tissue- and Species-Specific Expression of Lignan Biosynthesis-Related Gene.

Forsythia spp. are perennial woody plants which are one of the most extensively used medicinal sources of Chinese medicines and functional diets owing to their lignan contents. Lignans have received widespread attention as leading compounds in the development of antitumor drugs and healthy diets for reducing the risks of lifestyle-related diseases. However, the molecular basis of Forsythia has yet to be established. In this study, we have verified de novo deep transcriptome of Forsythia koreana leaf and callus using the Illumina HiSeq 1500 platform. A total of 89 million reads were assembled into 116,824 contigs using Trinity, and 1,576 of the contigs displayed the sequence similarity to the enzymes responsible for plant specialized metabolism including lignan biosynthesis. Notably, gene ontology (GO) analysis indicated the remarkable enrichment of lignan-biosynthetic enzyme genes in the callus transcriptome. Nevertheless, precise annotation and molecular phylogenetic analyses were hindered by partial sequences of open reading frames (ORFs) of the Trinity-based contigs. To obtain more numerous contigs harboring a full-length ORF, we developed a novel overlapping layout consensus-based procedure, virtual primer-based sequence reassembly (VP-seq). VP-seq elucidated 709 full-length ORFs, whereas only 146 full-length ORFs were assembled by Trinity. The comparison of expression profiles of leaf and callus using VP-seq-based full-length ORFs revealed 50-fold upregulation of secoisolariciresinol dehydrogenase (SIRD) in callus. Expression and phylogenetic cluster analyses predicted candidates for matairesinol-glucosylating enzymes. We also performed VP-seq analysis of lignan-biosynthetic enzyme genes in the transcriptome data of other lignan-rich plants, Linum flavum, Linum usitatissimum and Podophyllum hexandrum. The comparative analysis indicated both common gene clusters involved in biosynthesis upstream of matairesinol such as SIRD and plant lineage-specific gene clusters, in particular, genes responsible for biosynthetic pathways for production of podophyllotoxin; CYP71BE54, a key enzyme gene for podophyllotoxin biosynthesis in P. hexandrum, was not found in L. flavum, although both P. hexandrum. and L. flavum yield podophyllotoxin. Altogether, these data have established the fruitful molecular basis of Forsythia and provided insight into the molecular evolution and diversity of lignan biosynthetic pathways.

Cloning, characterization, and expression analysis of LGP2 cDNA from goose, Anser cygnoides

Laboratory of genetics and physiology 2 (LGP2) is a homologue of the retinoic acid inducible gene-I and melanoma differentiation associated gene 5 that lacks the caspase activation and recruitment domain required for signaling. It plays a pivotal role in host immune response. In this study, we cloned and characterized the full-length open reading frame (ORF) sequence of LGP2 in the Qingyuan goose (Anser cygnoides) and evaluated the mRNA expression of this gene post infection with an H5N1 highly pathogenic avian influenza virus (HPAIV). The full-length goose LGP2 ORF (2,028 bp) encoded a polypeptide of 675 amino acids. The deduced amino acid sequence contained 5 main overlapping structural domains—2 DEAD/DEAH box helicase domains, one conserved restriction domain of bacterial type III restriction enzyme, one helicase superfamily C-terminal domain and one C-terminal regulatory domain. Quantitative real-time PCR analysis indicated that goose LGP2 was constitutively expressed in all 19 investigated tissues, but the expression level was different among them. It was high expressed in the trachea, jejunum, bursa, kidney and heart, but low in the glandular stomach, lung, liver, spleen, crop and muscular stomach. A significant increase in the transcription of LGP2 was detected in the brain, spleen and lungs of geese post infection with H5N1 HPAIV versus uninfected tissues. These findings indicated that goose LGP2 was an important receptor that is involved in the host antiviral innate immune defense to H5N1 HPAIV in geese.