Analysis of virome by high-throughput sequencing disclosed multiple infection in a single grapevine plant / Análise do viroma por sequenciamento de alto rendimento revelou infecção múltipla em uma planta de videira

Among phytosanitary problems of the grapevine, viruses stand out for their capacity of reducing the quality and yield of grapes. However, detecting and identifying viral infections in grapevines can be challenging. This study performed a high throughput sequencing (HTS) of the viral pathogens present in a vine showing virus-like symptoms to elucidate the etiology. HTS analysis reported in a hybrid grapevine with mild curling down of leaf edges, the presence of four viruses and viroids, which were probably implicated in the observed symptoms. The determined complete genomes showed high genetic identities with previously characterized isolates of homologous pathogens.

Dentre os problemas fitossanitários da videira, os vírus se destacam pela capacidade de reduzir a qualidade e o rendimento da uva. No entanto, detectar e identificar infecções virais em videiras pode ser um desafio. O objetivo do estudo foi realizar um sequenciamento de alto rendimento (HTS) para determinar os patógenos virais presentes em uma videira com sintomas de virose e elucidar a etiologia. Com o HTS foi detectada, em uma videira híbrida com leve enrolamento dos bordos foliares, a presença de quatro vírus e viroides, os quais provavelmente estavam implicados com os sintomas observados. Os genomas completos determinados mostraram altas identidades genéticas com isolados previamente caracterizados de patógenos homólogos.

Exploring the rumen microbial community in Guizhou White goats at different ages

This study evaluated the changes in rumen microbiome during the process of age development of farming Guizhou White goats from Southwest China. We conducted high-throughput 16S rRNA gene sequencing to investigate the diversity, structure, and composition of goat rumen microbiota (RM) of 21 goats of different age groups (1, 6, and 12 months). We found that volatile fatty acids (i.e., acetate, propionate, and butyrate) fermented by microbes were found to increase significantly in the sixand one-month-old goats. Results of the genera abundance analysis showed that abundance of eight and seven taxa decreased in six- and one-month-old goats, respectively, compared with that in 12-month-old goats. Additionally, differences in six taxa in six-month-old goats and in one taxon in one-month-old goats were found. In addition, specific gut microbiome was found, which was significantly correlated with rumen fermentation parameters in Guizhou White goats. These results revealed the signature microbiota in RM during various developmental stages in goats raised in Southwest China and can also provide a guiding tool for evaluating rumen health of ruminants worldwide.(AU)

Analysis of microbial diversity in the root of Astragalus mongholicus / Análise da diversidade microbiana em raízes de astrágalo

The dry root of Astragalus mongholicus has therapeutic effects such as tonifing the middle - jiao, replenishing qi, solidifing the surface, promoting diuresis, dispelling sepsis outwards and nourishing muscle. There are some slices having black spots after slicing the root of astragalus. The diversity of endophytic fungi between slices with black spots and normal slices was analysed in this paper. The endophytic fungal sequences obtained by high-throughput sequencing were 298,044 and 297,396, and the 116 OTU subsets obtained after clustering belonged to 3 phyla, 9 classes, 22 orders, 38 families and 46 genera. The dominant classes were Eurotiomycetes and Leotiomycetes. The dominant order is Eurotiales and Helotiales. The dominant families are Helotiales_fam_Incertae_sedis and Aspergillaceae. The dominant genera are Cadophora and Aspergillus. There are some peculiar fungal flora in both normal slices and spotted slices. The study on endophytic fungi diversity of astragalus slices will provide some help for drug development of this plant.

A raiz seca de astrágalo tem a função de tonificar o zhongjiao, qi benéfico, superfície sólida, diurético, remoção externa de veneno e fortalecimento muscular. Depois de cortar o astrágalo em fatias finas, algumas fatias têm pontos pretos. Neste trabalho foi analisada a diversidade de fungos endofíticos em fatias de ponto negro versus fatias normais. O sequenciamento de alto rendimento resultou em 314.998 e 315.051 sequências de fungos endofíticos, respectivamente, que após agrupamento resultaram em 116 subgrupos de OTU, pertencentes a três filos, nove classes, 22 ordens, 38 famílias e 46 gêneros. As classes dominantes são Eurotiomycetes e Leotiomycetes. A ordem principal é euclides e hilllows. As famílias predominantes foram aspergilaceae e aspergilaceae. Os gêneros predominantes foram leucostilla e aspergillus. Tanto as seções normais como as secções manchadas apresentam uma flora fúngica distinta. O estudo da diversidade de fungos endofíticos em fatias de astrágalo pode contribuir para o desenvolvimento de fármacos para esta planta.

Type C botulism in dogs from rural properties located in Goiânia, Brazil

Botulism is a disease usually fatal, caused by the ingestion of neurotoxins produced by Clostridium botulinum. In dogs, intoxication is caused by the ingestion of botulinum toxin type C, and animals often recover spontaneously. The present study describes the occurrence of type C botulism in two dogs domiciled on neighboring rural properties in the municipality of Goiânia, state of Goiás, Brazil, probably associated with ingestion of decomposing bovine carcass. Upon clinical evaluation, the dogs were alert in the lateral decubitus position with ascending flaccid paralysis, absence of eyelid reflexes, and reduced muscle tone. Due to their worsening clinical symptoms, the animals died within 12 h and 3 days after supportive treatment. Botulinum toxin type C was identified, in the serum and feces of both dogs, by seroneutralization in mice with homologous monovalent antitoxin. The results of the high-throughput gene sequencing showed that the abundance of C. botulinum in the fecal microbiota of one of the affected dogs was low (0.53%). In this way, the present study highlights the need of sanitary practices related to the appropriate collection and disposal of bovine carcasses in rural areas since they represent a risk factor for the occurrence of botulism in dogs domiciled on rural properties.

Toxinology in the proteomics era: a review on arachnid venom proteomics

Abstract The word venomics was coined to acknowledge the studies that use omics to investigate venom proteins and peptides. Venomics has evolved considerably over the last 20 years. The first works on scorpion or spider venomics were published in the early 2000s. Such studies relied on peptide mass fingerprinting (PMF) to characterize venom complexity. After the introduction of new mass spectrometers with higher resolution, sensitivity and mass accuracy, and the next-generation nucleotide sequencing, the complexity of data reported in research on scorpion and spider venomics increased exponentially, which allowed more comprehensive studies. In the present review article, we covered key publications on scorpion venomics and spider venomics, presenting historical grounds and implemented technologies over the last years. The literature presented in this review was selected after searching the PubMed database using the terms (scorpion venom) AND (proteome) for scorpion venomics, and (spider venom) AND (proteome) for publications on spider venomics. We presented the key aspects related to proteomics in the covered papers including, but not restricted to, the employed proteomic strategy (i.e., PMF, two-dimensional gel electrophoresis, shotgun/bottom-up and/or top-down/peptidome), and the type of mass spectrometer used. Some conclusions can be drawn from the present study. For example, the scorpion genus Tityus is the most studied concerning venomics, followed by Centruroides; whereas for spiders the studied genera were found more equally distributed. Another interesting conclusion is the lack of high throughput studies on post-translational modifications (PTMs) of scorpion and spider proteins. In our opinion, PTMs should be more studied as they can modulate the activity of scorpion and spider toxins.

Toxinology in the proteomics era: a review on arachnid venom proteomics

The word venomics was coined to acknowledge the studies that use omics to investigate venom proteins and peptides. Venomics has evolved considerably over the last 20 years. The first works on scorpion or spider venomics were published in the early 2000's. Such studies relied on peptide mass fingerprinting (PMF) to characterize venom complexity. After the introduction of new mass spectrometers with higher resolution, sensitivity and mass accuracy, and the next-generation nucleotide sequencing, the complexity of data reported in research on scorpion and spider venomics increased exponentially, which allowed more comprehensive studies. In the present review article, we covered key publications on scorpion venomics and spider venomics, presenting historical grounds and implemented technologies over the last years. The literature presented in this review was selected after searching the PubMed database using the terms "(scorpion venom) AND (proteome)" for scorpion venomics, and "(spider venom) AND (proteome)" for publications on spider venomics. We presented the key aspects related to proteomics in the covered papers including, but not restricted to, the employed proteomic strategy (i.e., PMF, two-dimensional gel electrophoresis, shotgun/bottom-up and/or top-down/peptidome), and the type of mass spectrometer used. Some conclusions can be drawn from the present study. For example, the scorpion genus Tityus is the most studied concerning venomics, followed by Centruroides; whereas for spiders the studied genera were found more equally distributed. Another interesting conclusion is the lack of high throughput studies on post-translational modifications (PTMs) of scorpion and spider proteins. In our opinion, PTMs should be more studied as they can modulate the activity of scorpion and spider toxins.(AU)

Effects of dietary lysozyme on immune response and fecal microflora in both sows and their offspring

Two studies were conducted to investigate the effects of dietary lysozyme on immune response, fecal microflora in sows and their offspring fed lysozyme from late gestation to the onset of lactation, and growth performance in weaned piglets. Four antibiotic-based treatments (chlortetracycline, colistin, and lysozyme) were applied in experiment 1. Lysozyme addition significantly increased final body weight, average daily gain, and average daily feed intake, improved feed:gain ratio (F:G), and decreased diarrhea rate in weaned piglets. In experiment 2, postpartum sows were fed diets either with amoxicillin and cephalosporin (SC) or lysozyme (SE). Piglets from SC sows were administered enrofloxacin and those from SE sows were administered lysozyme. Lysozyme treatment decreased serum IL-1, IL-6, and IL-10, but did not influence IL-8, TNF-α, or IFN-γ in weaned piglets. Sequencing revealed that lysozyme significantly decreased Chao-1 index in sows and weaned piglets, increased Bifidobacterium longum in sows, and Lactobacillus coleohominis, L. mucosae, L. amylovorus, and L. hamsteri in weaned piglets. The results suggest that dietary supplementation of lysozyme improved the growth performance of weaned piglets, and dietary supplementation of lysozyme for sows increased immune function and modulated the intestinal flora structure in sows and their offspring.

Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)

Pimelodus yuma (formerly Pimelodus blochii) is a freshwater fish, endemic to the Colombian Magdalena-Cauca and Caribbean basins that experiences habitat disturbances resulting from anthropogenic activities. Due to the lack of information about the population genetics of this species, this study developed 14 species-specific microsatellite loci to assess the genetic diversity and population structure of samples from the lower section of the Cauca River. The studied species showed genetic diversity levels higher than the average values reported for Neotropical Siluriformes and significant inbreeding levels as was described for some congeners. Furthermore, P. yuma comprises two coexisting genetic groups that exhibit gene flow along the lower section of the Cauca River. This information constitutes a baseline for future monitoring of the genetic diversity and population structure in an anthropic influenced sector of the Magdalena-Cauca basin.(AU)

Pimelodus yuma (anteriormente Pimelodus blochii) es un pez dulceacuícola endémico de las cuencas colombianas Magdalena-Cauca y Caribe que experimenta alteraciones del hábitat como resultado de actividades antropogénicas. Debido a la falta de información sobre la genética poblacional de esta especie, este estudio desarrolló 14 loci microsatélites especie-específicos para evaluar la diversidad genética y la estructura poblacional de muestras de la sección baja del río Cauca. La especie estudiada mostró niveles de diversidad genética más altos que los valores promedio reportados para Siluriformes neotropicales y niveles de endogamia significativos como se describió para algunos congéneres. Además, P. yuma comprende dos grupos genéticos coexistentes que exhiben flujo de genes a lo largo de la sección baja del río Cauca. Esta información constituye una línea base para futuros monitoreos de la diversidad genética y la estructura poblacional en un sector de influencia antrópica de la cuenca Magdalena-Cauca.(AU)

Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)

Pimelodus yuma (formerly Pimelodus blochii) is a freshwater fish, endemic to the Colombian Magdalena-Cauca and Caribbean basins that experiences habitat disturbances resulting from anthropogenic activities. Due to the lack of information about the population genetics of this species, this study developed 14 species-specific microsatellite loci to assess the genetic diversity and population structure of samples from the lower section of the Cauca River. The studied species showed genetic diversity levels higher than the average values reported for Neotropical Siluriformes and significant inbreeding levels as was described for some congeners. Furthermore, P. yuma comprises two coexisting genetic groups that exhibit gene flow along the lower section of the Cauca River. This information constitutes a baseline for future monitoring of the genetic diversity and population structure in an anthropic influenced sector of the Magdalena-Cauca basin.(AU)

Pimelodus yuma (anteriormente Pimelodus blochii) es un pez dulceacuícola endémico de las cuencas colombianas Magdalena-Cauca y Caribe que experimenta alteraciones del hábitat como resultado de actividades antropogénicas. Debido a la falta de información sobre la genética poblacional de esta especie, este estudio desarrolló 14 loci microsatélites especie-específicos para evaluar la diversidad genética y la estructura poblacional de muestras de la sección baja del río Cauca. La especie estudiada mostró niveles de diversidad genética más altos que los valores promedio reportados para Siluriformes neotropicales y niveles de endogamia significativos como se describió para algunos congéneres. Además, P. yuma comprende dos grupos genéticos coexistentes que exhiben flujo de genes a lo largo de la sección baja del río Cauca. Esta información constituye una línea base para futuros monitoreos de la diversidad genética y la estructura poblacional en un sector de influencia antrópica de la cuenca Magdalena-Cauca.(AU)

Characterization of the seminal bacterial microbiome of healthy, fertile stallions using next-generation sequencing

Abstract High-throughput sequencing studies have shown the important role microbial communities play in the male reproductive tract, indicating differences in the semen microbial composition between fertile and infertile males. Most of these studies were made on human beings but little is known regarding domestic animals. Seminal bacteria studies made in stallions mostly focus on pathogenic bacteria and on their impact on reproductive technology. However, little is known about stallion commensal seminal microflora. That ultimately hinders our capacity to associate specific bacteria to conditions or seminal quality. Therefore, the aim of this study was to characterize the seminal microbial composition of 12 healthy, fertile stallion using next-generation sequencing. Hypervariable region V3 was chosen for bacterial identification. A total of nine phyla was detected. The most abundant ones were Bacteroidetes (46.50%), Firmicutes (29.92%) and Actinobacteria (13.58%). At family level, we found 69 bacterial families, but only nine are common in all samples. Porphyromonadaceae (33.18%), Peptoniphilaceae (14.09%), Corynebacteriaceae (11.32%) and Prevotellaceae (9.05%) were the most representative ones, while the Firmicutes phylum displayed the highest number of families (23, a third of the total). Samples showed high inter-subject variability. Findings previously described in other species notably differ from our findings. Families found in human such as Lactobacillaceae, Staphylococcaceae and Streptococcaceae only represented a 0.00%, 0.17% and 0.22% abundance in our samples, respectively. In conclusion, Porphyromonadaceae, Prevotellaceae, Peptoniphilaceae and Corynebacteriaceae families are highly represented in the seminal microbiome of healthy, fertile stallions. A high variation among individuals is also observed.

Gonadotropin inhibitory hormone downregulates steroid hormone secretion and genes expressions in duck granulosa cells

Abstract The mechanisms by which GnIH regulates the steroid synthesis pathway in duck granulosa cells remain poorly understood. In this study, we measured steroid hormone secretion by ELISA and reproduction-associated gene expression by quantitative real-time Polymerase Chain Reaction (qPCR) in duck granulosa cells treated with different concentrations of GnIH (0, 0.1, 1, 10, and 100 ng/mL) for 24 h. The genome-wide expression profiles of GnIH-treated cells (0 and 10 ng/mL) were evaluated by high-throughput RNA sequencing. Compared with untreated cells, the secretion of the steroid hormones E2, E1, P4, and T was downregulated, with that of E1 and P4 reaching statistical significance (P<0.05); in contrast, the secretion of ACV and INH was significantly upregulated (P<0.05) after treatment with 10 and 100 ng/mL GnIH. The expression of encoding steroidogenic proteins and enzymes genes (STAR, CYP11A1, CYP17A1, CYP19A1, and 3-β-HSD) and encoding gonadotropin receptors genes (FSHR, LHR) were significantly declined (P<0.05) in the 10 and 100 ng/mL GnIH treatments. Transcriptome sequencing identified 348 differentially expressed genes (DEGs), including 253 upregulated and 95 downregulated genes. The DEGs were mainly involved in cell growth and death, immune response, and steroid biosynthesis pathways. We identified four novel DEGs (MROH5, LOC113840576, SDR42E1, and LOC113841457) with key roles in the regulation of steroid hormone biosynthesis. Our study revealed changes in gonadal steroid hormone secretion and steroid biosynthesis pathway-related gene expression in duck granulosa cells under the inhibitory effect of GnIH. These data contribute to our understanding of the molecular and genetic mechanisms underlying reproduction in ducks.

Gonadotropin inhibitory hormone downregulates steroid hormone secretion and genes expressions in duck granulosa cells

The mechanisms by which GnIH regulates the steroid synthesis pathway in duck granulosa cells remain poorly understood. In this study, we measured steroid hormone secretion by ELISA and reproduction-associated gene expression by quantitative real-time Polymerase Chain Reaction (qPCR) in duck granulosa cells treated with different concentrations of GnIH (0, 0.1, 1, 10, and 100 ng/mL) for 24 h. The genome-wide expression profiles of GnIH-treated cells (0 and 10 ng/mL) were evaluated by high-throughput RNA sequencing. Compared with untreated cells, the secretion of the steroid hormones E2, E1, P4, and T was downregulated, with that of E1 and P4 reaching statistical significance (P<0.05); in contrast, the secretion of ACV and INH was significantly upregulated (P<0.05) after treatment with 10 and 100 ng/mL GnIH. The expression of encoding steroidogenic proteins and enzymes genes (STAR, CYP11A1, CYP17A1, CYP19A1, and 3-β-HSD) and encoding gonadotropin receptors genes (FSHR, LHR) were significantly declined (P<0.05) in the 10 and 100 ng/mL GnIH treatments. Transcriptome sequencing identified 348 differentially expressed genes (DEGs), including 253 upregulated and 95 downregulated genes. The DEGs were mainly involved in cell growth and death, immune response, and steroid biosynthesis pathways. We identified four novel DEGs (MROH5, LOC113840576, SDR42E1, and LOC113841457) with key roles in the regulation of steroid hormone biosynthesis. Our study revealed changes in gonadal steroid hormone secretion and steroid biosynthesis pathway-related gene expression in duck granulosa cells under the inhibitory effect of GnIH. These data contribute to our understanding of the molecular and genetic mechanisms underlying reproduction in ducks.(AU)

Characterization of the seminal bacterial microbiome of healthy, fertile stallions using next-generation sequencing

High-throughput sequencing studies have shown the important role microbial communities play in the male reproductive tract, indicating differences in the semen microbial composition between fertile and infertile males. Most of these studies were made on human beings but little is known regarding domestic animals. Seminal bacteria studies made in stallions mostly focus on pathogenic bacteria and on their impact on reproductive technology. However, little is known about stallion commensal seminal microflora. That ultimately hinders our capacity to associate specific bacteria to conditions or seminal quality. Therefore, the aim of this study was to characterize the seminal microbial composition of 12 healthy, fertile stallion using next-generation sequencing. Hypervariable region V3 was chosen for bacterial identification. A total of nine phyla was detected. The most abundant ones were Bacteroidetes (46.50%), Firmicutes (29.92%) and Actinobacteria (13.58%). At family level, we found 69 bacterial families, but only nine are common in all samples. Porphyromonadaceae (33.18%), Peptoniphilaceae (14.09%), Corynebacteriaceae (11.32%) and Prevotellaceae (9.05%) were the most representative ones, while the Firmicutes phylum displayed the highest number of families (23, a third of the total). Samples showed high inter-subject variability. Findings previously described in other species notably differ from our findings. Families found in human such as Lactobacillaceae, Staphylococcaceae and Streptococcaceae only represented a 0.00%, 0.17% and 0.22% abundance in our samples, respectively. In conclusion, Porphyromonadaceae, Prevotellaceae, Peptoniphilaceae and Corynebacteriaceae families are highly represented in the seminal microbiome of healthy, fertile stallions. A high variation among individuals is also observed.(AU)

De novo venom gland transcriptomics of Calliophis bivirgata flaviceps: uncovering the complexity of toxins from the Malayan blue coral snake

The Malayan blue coral snake, Calliophis bivirgata flaviceps, is a medically important venomous snake in Southeast Asia. However, the complexity and diversity of its venom genes remain little explored. Methods: To address this, we applied high-throughput next-generation sequencing to profile the venom gland cDNA libraries of C. bivirgata flaviceps. The transcriptome was de novo assembled, followed by gene annotation, multiple sequence alignment and analyses of the transcripts. Results: A total of 74 non-redundant toxin-encoding genes from 16 protein families were identified, with 31 full-length toxin transcripts. Three-finger toxins (3FTx), primarily delta-neurotoxins and cardiotoxin-like/cytotoxin-like proteins, were the most diverse and abundantly expressed. The major 3FTx (Cb_FTX01 and Cb_FTX02) are highly similar to calliotoxin, a delta-neurotoxin previously reported in the venom of C. bivirgata. This study also revealed a conserved tyrosine residue at position 4 of the cardiotoxin-like/cytotoxin-like protein genes in the species. These variants, proposed as Y-type CTX-like proteins, are similar to the H-type CTX from cobras. The substitution is conservative though, preserving a less toxic form of elapid CTX-like protein, as indicated by the lack of venom cytotoxicity in previous laboratory and clinical findings. The ecological role of these toxins, however, remains unclear. The study also uncovered unique transcripts that belong to phospholipase A2 of Groups IA and IB, and snake venom metalloproteinases of PIII subclass, which show sequence variations from those of Asiatic elapids. Conclusion: The venom gland transcriptome of C. bivirgata flaviceps from Malaysia was de novo assembled and annotated. The diversity and expression profile of toxin genes provide insights into the biological and medical importance of the species.(AU)

De novo venom gland transcriptomics of Calliophis bivirgata flaviceps: uncovering the complexity of toxins from the Malayan blue coral snake

The Malayan blue coral snake, Calliophis bivirgata flaviceps, is a medically important venomous snake in Southeast Asia. However, the complexity and diversity of its venom genes remain little explored. Methods: To address this, we applied high-throughput next-generation sequencing to profile the venom gland cDNA libraries of C. bivirgata flaviceps. The transcriptome was de novo assembled, followed by gene annotation, multiple sequence alignment and analyses of the transcripts. Results: A total of 74 non-redundant toxin-encoding genes from 16 protein families were identified, with 31 full-length toxin transcripts. Three-finger toxins (3FTx), primarily delta-neurotoxins and cardiotoxin-like/cytotoxin-like proteins, were the most diverse and abundantly expressed. The major 3FTx (Cb_FTX01 and Cb_FTX02) are highly similar to calliotoxin, a delta-neurotoxin previously reported in the venom of C. bivirgata. This study also revealed a conserved tyrosine residue at position 4 of the cardiotoxin-like/cytotoxin-like protein genes in the species. These variants, proposed as Y-type CTX-like proteins, are similar to the H-type CTX from cobras. The substitution is conservative though, preserving a less toxic form of elapid CTX-like protein, as indicated by the lack of venom cytotoxicity in previous laboratory and clinical findings. The ecological role of these toxins, however, remains unclear. The study also uncovered unique transcripts that belong to phospholipase A2 of Groups IA and IB, and snake venom metalloproteinases of PIII subclass, which show sequence variations from those of Asiatic elapids. Conclusion: The venom gland transcriptome of C. bivirgata flaviceps from Malaysia was de novo assembled and annotated. The diversity and expression profile of toxin genes provide insights into the biological and medical importance of the species.(AU)

In-depth transcriptome reveals the potential biotechnological application of Bothrops jararaca venom gland

Lack of complete genomic data of Bothrops jararaca impedes molecular biology research focusing on biotechnological applications of venom gland components. Identification of full-length coding regions of genes is crucial for the correct molecular cloning design. Methods: RNA was extracted from the venom gland of one adult female specimen of Bothrops jararaca. Deep sequencing of the mRNA library was performed using Illumina NextSeq 500 platform. De novo assembly of B. jararaca transcriptome was done using Trinity. Annotation was performed using Blast2GO. All predicted proteins after clustering step were blasted against non-redundant protein database of NCBI using BLASTP. Metabolic pathways present in the transcriptome were annotated using the KAAS-KEGG Automatic Annotation Server. Toxins were identified in the B. jararaca predicted proteome using BLASTP against all protein sequences obtained from Animal Toxin Annotation Project from Uniprot KB/Swiss-Pro database. Figures and data visualization were performed using ggplot2 package in R language environment. Results: We described the in-depth transcriptome analysis of B. jararaca venom gland, in which 76,765 de novo assembled isoforms, 96,044 transcribed genes and 41,196 unique proteins were identified. The most abundant transcript was the zinc metalloproteinase-disintegrin-like jararhagin. Moreover, we identified 78 distinct functional classes of proteins, including toxins, inhibitors and tumor suppressors. Other venom proteins identified were the hemolytic lethal factors stonustoxin and verrucotoxin. Conclusion: It is believed that the application of deep sequencing to the analysis of snake venom transcriptomes may represent invaluable insight on their biotechnological potential focusing on candidate molecules.(AU)

Intercropping of wheat changed cucumber rhizosphere bacterial community composition and inhibited cucumber Fusarium wilt disease

Enhancing the plant rhizosphere microbial community function by increasing plant diversity in the field is a promising strategy for enhancing agricultural sustainability. This study evaluated the effectiveness of the intercropping of wheat in controlling cucumber Fusarium wilt disease. Bacterial community diversity and abundance in cucumber rhizosphere were estimated by high-throughput amplicon sequencing and quantitative polymerase chain reaction (PCR). Results showed that the intercropping of wheat inhibited the severity of cucumber seedling Fusarium wilt disease, increased the alpha diversity and altered the composition of the bacterial community in cucumber rhizosphere. Compared with monocropped cucumber, intercropped cucumber had higher relative abundances of Anaerolineae, Deltaproteobacteria, Phycisphaerae and Planctomycetacia, and lower Alphaproteobacteria and Cyanobacteria. Moreover, the intercropping of wheat promoted bacterial genera with plant-beneficial potential (e.g. Pseudomonas, Haliangium and Archangium spp.) in cucumber rhizosphere. Quantitative PCR confirmed that Pseudomonas spp. abundance was higher in intercropped cucumber rhizosphere than in monocropped cucumber rhizosphere. Overall, the intercropping of wheat decreased the severity of Fusarium wilt of cucumber and promoted potential plant-beneficial microbes in cucumber rhizosphere.

Intercropping of wheat changed cucumber rhizosphere bacterial community composition and inhibited cucumber Fusarium wilt disease

Enhancing the plant rhizosphere microbial community function by increasing plant diversity in the field is a promising strategy for enhancing agricultural sustainability. This study evaluated the effectiveness of the intercropping of wheat in controlling cucumber Fusarium wilt disease. Bacterial community diversity and abundance in cucumber rhizosphere were estimated by high-throughput amplicon sequencing and quantitative polymerase chain reaction (PCR). Results showed that the intercropping of wheat inhibited the severity of cucumber seedling Fusarium wilt disease, increased the alpha diversity and altered the composition of the bacterial community in cucumber rhizosphere. Compared with monocropped cucumber, intercropped cucumber had higher relative abundances of Anaerolineae, Deltaproteobacteria, Phycisphaerae and Planctomycetacia, and lower Alphaproteobacteria and Cyanobacteria. Moreover, the intercropping of wheat promoted bacterial genera with plant-beneficial potential (e.g. Pseudomonas, Haliangium and Archangium spp.) in cucumber rhizosphere. Quantitative PCR confirmed that Pseudomonas spp. abundance was higher in intercropped cucumber rhizosphere than in monocropped cucumber rhizosphere. Overall, the intercropping of wheat decreased the severity of Fusarium wilt of cucumber and promoted potential plant-beneficial microbes in cucumber rhizosphere.(AU)

Identification and characterisation of alternative splice variants of HOXB9 and their correlation with melanogenesis in the black-boned chicken

Homeobox B9 (HOXB9) gene has been demonstrated to be associated with melanogenesis in chicken plumage by high-throughput RNA sequencing. In this study, we cloned and characterised HOXB9 in black-boned chickens. Two alternative splice variants (HOXB9-1 and HOXB9-2) were identified in chicken feather bulbs. Expression analysis of HOXB9 in 11 different chicken tissues by RT-PCR indicated that the two transcripts were only expressed in the kidney, abdominal fat, feather bulbs, skin, and small intestine. No HOXB9-1 or HOXB9-2 transcripts were detected in the breast muscle or the ovary. The two HOXB9 variants were expressed at significantly different levels in black feather bulbs and white feather bulbs (p<0.01), and in black skin compared with white skin (p<0.01). The results indicate that HOXB9-1 and HOXB9-2 may be involved in melanin formation in the plumage and skin. The expression of HOXB9-2 was higher in white than in black muscles (p<0.05), HOXB9-2 may play a role in muscle melanogenesis. Our results suggest that HOXB9, which is partially regulated by alternative splicing, may be involved in the process of melanogenesis in the black-boned chicken.(AU)

Identification and characterisation of alternative splice variants of HOXB9 and their correlation with melanogenesis in the black-boned chicken

Homeobox B9 (HOXB9) gene has been demonstrated to be associated with melanogenesis in chicken plumage by high-throughput RNA sequencing. In this study, we cloned and characterised HOXB9 in black-boned chickens. Two alternative splice variants (HOXB9-1 and HOXB9-2) were identified in chicken feather bulbs. Expression analysis of HOXB9 in 11 different chicken tissues by RT-PCR indicated that the two transcripts were only expressed in the kidney, abdominal fat, feather bulbs, skin, and small intestine. No HOXB9-1 or HOXB9-2 transcripts were detected in the breast muscle or the ovary. The two HOXB9 variants were expressed at significantly different levels in black feather bulbs and white feather bulbs (p<0.01), and in black skin compared with white skin (p<0.01). The results indicate that HOXB9-1 and HOXB9-2 may be involved in melanin formation in the plumage and skin. The expression of HOXB9-2 was higher in white than in black muscles (p<0.05), HOXB9-2 may play a role in muscle melanogenesis. Our results suggest that HOXB9, which is partially regulated by alternative splicing, may be involved in the process of melanogenesis in the black-boned chicken.