De novo assembly and inferred functional annotation of the transcriptome of Heterosigma akashiwo

Heterosigma akashiwo is a eukaryotic, cosmopolitan, and unicellular alga (class: Raphidophyceae), and produces fish-killing blooms. There is a substantial scientific and practical interest in its ecophysiological characteristics that determine bloom dynamics and its adaptation to broad climate zones. A well-annotated genomic/genetic sequence information enables researchers to characterize organisms using modern molecular technology. The Chloroplast and the mitochondrial genome sequences and transcriptome sequence assembly (TSA) datasets with limited sizes for H. akashiwo are available in NCBI nucleotide database on December 2021: there is no doubt that more genetic information of the species will greatly enhance the progress of biological characterization of the species. Here, we conducted H. akashiwo RNA sequencing, a de novo transcriptome assembly (NCBI TSA ICRV01) of a large number of high-quality short-read sequences, and the functional annotation of predicted genes. Based on our transcriptome, we confirmed that the organism possesses genes that were predicted to function in phagocytosis, supporting the earlier observations of H. akashiwo bacterivory. Along with its capability for photosynthesis, the mixotrophy of H. akashiwo may partially explain its high adaptability to various environmental conditions. Our study here will provide an important toehold to decipher H. akashiwo ecophysiology at a molecular level.

De novo assembly and inferred functional annotation of the transcriptome of Heterosigma akashiwo

Heterosigma akashiwo is a eukaryotic, cosmopolitan, and unicellular alga (class: Raphidophyceae), and produces fish-killing blooms. There is a substantial scientific and practical interest in its ecophysiological characteristics that determine bloom dynamics and its adaptation to broad climate zones. A well-annotated genomic/genetic sequence information enables researchers to characterize organisms using modern molecular technology. The Chloroplast and the mitochondrial genome sequences and transcriptome sequence assembly (TSA) datasets with limited sizes for H. akashiwo are available in NCBI nucleotide database on December 2021: there is no doubt that more genetic information of the species will greatly enhance the progress of biological characterization of the species. Here, we conducted H. akashiwo RNA sequencing, a de novo transcriptome assembly (NCBI TSA ICRV01) of a large number of high-quality short-read sequences, and the functional annotation of predicted genes. Based on our transcriptome, we confirmed that the organism possesses genes that were predicted to function in phagocytosis, supporting the earlier observations of H. akashiwo bacterivory. Along with its capability for photosynthesis, the mixotrophy of H. akashiwo may partially explain its high adaptability to various environmental conditions. Our study here will provide an important toehold to decipher H. akashiwo ecophysiology at a molecular level.

Screening of Agricultural Wastes for Substrates in Oxalic Acid Production Using Aspergillus niger

The disposal and attendant problems associated with agro-wastes have remained a challenge to the environment. Three agricultural wastes (cassava whey, banana peels and groundnut shells) were collected from the Choba and Yam zone markets in Rivers State, Nigeria and screened for their potential as substrates in the formulation of fermentation media to produce oxalic acid. The inoculum for the study was isolated from the banana peels and identified using the megablast search for highly similar sequences from the NCBI non-redundant nucleotide database. The microbial load and proximate composition of the substrates were determined, and the fermentation media formulated. The organism used for the study was identified as Aspergillus niger MW188538. The results showed a total bacterial count of 9.5x104 cfu/ml, 1.87 x 105 cfu/ml, and 4.0 x 104 cfu/g for cassava whey, banana peels and groundnut shell respectively. The carbohydrates of the cassava whey, banana peels and groundnut shells were 67.74 %w/v, 53.24%w/v and 38.8% w/v respectively. After 12 days of fermentation, the substrates from cassava whey, banana peels, groundnut shells accumulated 2.5 ppm, 1.8 ppm and 1.3 ppm of oxalic acid respectively. The study hypothetically indicates that agro-wastes could be utilized as media components for production of industrial organics.

Exposure of Exiguobacterium spp. to dengue vector, Aedes aegypti reduces growth and reproductive fitness

Background Aedes aegypti is a major insect vector because it transmits dreadful viruses as adults that cause disease in humans and other vertebrates. The use of mosquito’s microbiota has shown great potential impacts on vector control and mosquito reproductive competence. The present study aimed to examine the resident bacteria of mosquitoes which are used as a potent range to reduce the A. aegypti fitness. Isolated resident-bacterial strains from blood-fed Aedes species were characterized using gene sequencing and phylogenetic analysis, to assess the inhabitant bacterial strains survival rate in A. aegypti midgut, instar developmental duration, malformation and reproductive competence. Results The genetic distinctiveness of isolated bacterial strains belong to the genus Exiguobacterium spp. and further non-redundant nucleotide database search revealed that the species of effective strains were E. aestuarii (MN629357) and E. profundum (MN625885). Exposure of the freshly hatched larvae with these bacteria cell densities extended the developmental duration. For instance, exposure of A. aegypti larva with 0.42 × 108, 0.84 × 108 and 1.68 × 108 cells/mL of E. aestuarii extended the total developmental duration to 11.41, 14.29 and 14.78 days, respectively. It also reduced the fecundity and hatchability of A. aegypti female, with exposure to these bacteria, from 1033.33 eggs/10 females in the control series to 656.67 eggs/10 females. Conclusions These present findings indicate that the resident-bacterial strains from blood-fed mosquito not only extend the larval durations but also rendered the A. aegypti females sterile to various extents.

From e-voucher to genomic data: Preserving archive specimens as demonstrated with medically important mosquitoes (Diptera: Culicidae) and kissing bugs (Hemiptera: Reduviidae)

Scientific collections such as the U.S. National Museum (USNM) are critical to filling knowledge gaps in molecular systematics studies. The global taxonomic impediment has resulted in a reduction of expert taxonomists generating new collections of rare or understudied taxa and these large historic collections may be the only reliable source of material for some taxa. Integrated systematics studies using both morphological examinations and DNA sequencing are often required for resolving many taxonomic issues but as DNA methods often require partial or complete destruction of a sample, there are many factors to consider before implementing destructive sampling of specimens within scientific collections. We present a methodology for the use of archive specimens that includes two crucial phases: 1) thoroughly documenting specimens destined for destructive sampling—a process called electronic vouchering, and 2) the pipeline used for whole genome sequencing of archived specimens, from extraction of genomic DNA to assembly of putative genomes with basic annotation. The process is presented for eleven specimens from two different insect subfamilies of medical importance to humans: Anophelinae (Diptera: Culicidae)—mosquitoes and Triatominae (Hemiptera: Reduviidae)—kissing bugs. Assembly of whole mitochondrial genome sequences of all 11 specimens along with the results of an ortholog search and BLAST against the NCBI nucleotide database are also presented.

New genotypes of Helicobacter Pylori VacA d-region identified from global strains

Background Pathogenesis of Helicobacter Pylori (HP) vacuolating toxin A (vacA) depends on polymorphic diversity within the signal (s), middle (m), intermediate (i), deletion (d) and c-regions. These regions show distinct allelic diversity. The s-region, m-region and the c-region (a 15 bp deletion at the 3′-end region of the p55 domain of the vacA gene) exist as 2 types (s1, s2, m1, m2, c1 and c2), while the i–region has 3 allelic types (i1, i2 and i3). The locus of d-region of the vacA gene has also been classified into 2 genotypes, namely d1 and d2. We investigated the “d-region”/“loop region” through bioinformatics, to predict its properties and relation to disease. One thousand two hundred fifty-nine strains from the NCBI nucleotide database and the dryad database with complete vacA sequences were included in the study. The sequences were aligned using BioEdit and analyzed using Lasergene and BLAST. The secondary structure and physicochemical properties of the region were predicted using PredictProtein. Results We identified 31 highly polymorphic genotypes in the “d-region”, with a mean length of 34 amino acids (9 ~ 55 amino acids). We further classified the 31 genotypes into 3 main types, namely K-type (strains starting with the KDKP motif in the “d-region”), Q-type (strains starting with the KNQT motif), and E-type (strains starting with the ESKT motif) respectively. The most common type, K-type, is more prevalent in cancer patients (80.87%) and is associated with the s1i1m1c1 genotypes (P < .01). Incidentally, a new region expressing sequence diversity (2 aa deletion) at the C-terminus of the p55 domain of vacA was identified during bioinformatics analysis. Conclusions Prediction of secondary structures shows that the “d-region” adopts a loop conformation and is a disordered region.

Metagenomic profiling of host-associated bacteria from 8 datasets of the red alga Porphyra purpurea, with MetaPhlAn 3.0

Microbial communities play a fundamental role in the association with marine algae, in fact they are recognized to be actively involved in growth and morphogenesis.Porphyra purpurea is a red algae commonly found in the intertidal zone with an high economical value, indeed several species belonging to the genus Porphyra are intensely cultivated in the Eastern Asian countries. Moreover, P. purpurea is widely used as model species in different fields, mainly due to its peculiar life cycle. Despite of that, little is known about the microbial community associated to this species. Here we report the microbial-associated diversity of P. purpurea in four different localities (Ireland, Italy United Kingdom and USA) through the analysis of eight metagenomic datasets obtained from the publicly available metagenomic nucleotide database (https://www.ebi.ac.uk/ena/). The metagenomic datasets were quality controlled with FastQC version 0.11.8, pre-processed with Trimmomatic version 0.39 and analysed with Methaplan 3.0, with a reference database containing clade specific marker genes from ~ 99.500 bacterial genomes, following the pan-genome approach, in order to identify the putative bacterial taxonomies and their relative abundances. Furthermore, we compared the results to the 16S rRNA metagenomic analysis pipeline of MGnify database to evaluate the effectiveness of the two methods. Out of the 43 bacterial species identified with MetaPhlAn 3.0 only 5 were common with the MGnify results and from the 21 genera, only 9 were common. This approach highlighted the different taxonomical resolution of a 16S rRNA OTU-based method in contrast to the pan-genome approach deployed by MetaPhlAn 3.0.

The increasing prevalence of CPV-2c in domestic dogs in China

Background Canine parvovirus type 2 (CPV-2), a serious pathogen, leads to high morbidity and mortality in dogs and several wild carnivore species. Although it is a DNA virus, it evolves particularly rapidly, with a genomic substitution rate of approximately 10−4 substitutions/site/year, close to that of some RNA viruses. Tracing the prevalence of CPV-2 in dogs is significant. Methods In this study, an aetiological survey was carried out from 2016 to 2019 in Guangdong Province, China, involving Guangzhou, Shenzhen and Dongguan. Furthermore, to systematically analyse the prevalence of CPV-2 in China, the VP2 gene sequences of all Chinese isolates were downloaded from the NCBI nucleotide database in December 2019, and changes in CPV-2 variants were examined. Results A total of 55.7% (34/61) of samples were CPV-2 positive by PCR detection and virus isolation. In addition to different variants circulating in dogs, coinfection with multiple variants was identified, as was coinfection with other canine enteric pathogens in some cases. Two previously reported amino acid sites, A5G and Q370R of CPV-2c mutants, reported in variants in China were assessed, and several CPV-2 isolates with P13S and K582N mutations were detected in this study. Finally, we speculate on the prevalence of different CPV-2 variants in China. According to the VP2 gene sequence obtained from the NCBI nucleotide database, the proportion of different variants in China has changed, and CPV-2c appears to be growing rapidly. In conclusion, this aetiology survey suggests that CPV-2 continues to be common in China and that the prevalence of CPV-2c is increasing.

PSVI-7 Variation in bitter taste receptor genes in three breeds of goats

The objective of this study was to detect bitter taste receptor (T2Rs) variants in three breeds of goats. The ability to taste bitter taste impacts feed intake, digestion, and rejection of potentially toxic substances. Blood was collected from three breeds of goats (Spanish, Savannah, and Boer n = 5 /breed). Genomic DNA was extracted. The concentration and purity of DNA was determined using the Nanodrop spectrophotometer. Primers specific for seven T2R gene variants (T2R3, T2R4, T2R10, T2R12, T2R13, T2R16, and T2R67) were used to detect the goat T2R gene based on average threshold cycle. DNA products were commercially sequenced (Eurofins Genomics). The sequenced products were used in BLAST against the Capra hircus redundant nucleotide database. All seven taste gene variants were detected in the Savannah breed, In Spanish goats T2R4 and T213 were not detected, In Boer goats only T2R3, T2R16 and T2R13 were detected. Polymorphisms in T2R impact dietary preference, innate immunity and health. Thus, studies are needed to ascertain the possible functional significance of this variation using a larger sample size

Diat.barcode, an open-access curated barcode library for diatoms

Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. They display a huge diversity, which makes them excellent ecological indicators of aquatic ecosystems. Usually, diatoms are identified using characteristics of their exoskeleton morphology. DNA-barcoding is an alternative to this and the use of High-Throughput-Sequencing enables the rapid analysis of many environmental samples at a lower cost than analyses under microscope. However, to identify environmental sequences correctly, an expertly curated reference library is needed. Several curated libraries for protists exists; none, however are dedicated to diatoms. Diat.barcode is an open-access library dedicated to diatoms which has been maintained since 2012. Data come from two sources (1) the NCBI nucleotide database and (2) unpublished sequencing data of culture collections. Since 2017, several experts have collaborated to curate this library for rbcL, a chloroplast marker suitable for species-level identification of diatoms. For the latest version of the database (version 7), 605 of the 3482 taxonomical names originally assigned by the authors of the rbcL sequences were modified after curation. The database is accessible at https://www6.inra.fr/carrtel-collection_eng/Barcoding-database.