Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus

The mulberry silkworm, Bombyx mori (L.), is a model organism of lepidopteran insects with high economic importance. The viral diseases of the silkworm caused by Bombyx mori nucleopolyhedrovirus (BmNPV) and Bombyx mori bidensovirus (BmBDV) inflict huge economic losses and significantly impact the sericulture industry of India and other countries. To understand the distribution of Indian isolates of the BmNPV and to investigate their genetic composition, an in-depth population structure analysis was conducted using comprehensive and newly developed genomic analysis methods. The seven new Indian BmNPV isolates from Anantapur, Dehradun, Ghumarwin, Jammu, Kashmir, Mysore and Salem grouped in the BmNPV clade, and are most closely related to Autographa californica multiple nucleopolyhedrovirus and Rachiplusia ou multiple nucleopolyhedrovirus on the basis of gene sequencing and phylogenetic analyses of the partial polh, lef-8 and lef-9 gene fragments. The whole genome sequencing of three Indian BmNPV isolates from Mysore (-My), Jammu (-Ja) and Dehradun (-De) was conducted, and intra-isolate genetic variability was analyzed on the basis of variable SNP positions and the frequencies of alternative nucleotides. The results revealed that the BmNPV-De and BmNPV-Ja isolates are highly similar in their genotypic composition, whereas the population structure of BmNPV-My appeared rather pure and homogenous, with almost no or few genetic variations. The BmNPV-De and BmNPV-Ja samples further contained a significant amount of BmBDV belonging to the Bidnaviridae family. We elucidated the genotype composition within Indian BmNPV and BmBDV isolates, and the results presented have broad implications for our understanding of the genetic diversity and evolution of BmNPV and co-occurring BmBDV isolates.

Korelasi fenotip antara ukuran bagian tubuh dengan bobot badan dari silangan ayam pedaging, kate dan lokal sabu pada umur dua belas minggu

ABSTRACT The purpose of this research was to know the relationship between the the weight and body measurements at age of 12 weeks of crossbreds of three chicken types that were broiler, kate and Sabu chicken. The relationship of body weight with the body measurements was used as a consideration for selecting the body weight. The research material was 30 tails of crossbreds with genotype composition was ½ broiler 1/4 Kate ¼ Sabu chicken. The method of research was experiment and directly weighting and measuring of the body measuremens. All chickens were given freely the same food and waters. The observed parameters were body weight, backbone length, chest circumference, shank circumference and wing span. Data was analised using the correlation analysis. Research results obtained the koefisien of correlation between chest circumference, backbone length, shank length and wing span with body weight were 0.62; 0.32; 031 and 0.20. Correlations between body weight and body measurements of chicken crossbreds with genotype composision ½ broiler ¼ Kate ¼ Sabu were positip.

Bacsnp: Using Single Nucleotide Polymorphism (SNP) Specificities and Frequencies to Identify Genotype Composition in Baculoviruses

Natural isolates of baculoviruses (as well as other dsDNA viruses) generally consist of homogenous or heterogenous populations of genotypes. The number and positions of single nucleotide polymorphisms (SNPs) from sequencing data are often used as suitable markers to study their genotypic composition. Identifying and assigning the specificities and frequencies of SNPs from high-throughput genome sequencing data can be very challenging, especially when comparing between several sequenced isolates or samples. In this study, the new tool “bacsnp”, written in R programming langue, was developed as a downstream process, enabling the detection of SNP specificities across several virus isolates. The basis of this analysis is the use of a common, closely related reference to which the sequencing reads of an isolate are mapped. Thereby, the specificities of SNPs are linked and their frequencies can be used to analyze the genetic composition across the sequenced isolate. Here, the downstream process and analysis of detected SNP positions is demonstrated on the example of three baculovirus isolates showing the fast and reliable detection of a mixed sequenced sample.

Cutibacterium acnes (Propionibacterium acnes) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification

ABSTRACT The human skin surface harbors huge numbers of microbes. The skin microbiota interacts with its host and forms a skin microbiome profile that is specific for each individual. It has been reported that the skin microbiota that is left on an individual’s possessions can act as a sort of “fingerprint” and be used for owner identification. However, this approach needs to be improved to take into account any long-term instability of skin microbiota and contamination from nonspecific bacteria. Here, we took advantage of single-nucleotide polymorphisms (SNPs) in the 16S-encoding rRNA gene of Cutibacterium acnes, the most common and abundant bacterium on human skin, to perform owner identification. We first developed a high-throughput genotyping method based on next-generation sequencing to characterize the SNPs of the C. acnes 16S rRNA gene and found that the genotype composition of C. acnes 16S rRNA is individual specific. Owner identification accuracy of around 90% based on random forest machine learning was achieved by using a combination of C. acnes 16S rRNA genotype and skin microbiome profile data. Furthermore, our study showed that the C. acnes 16S rRNA genotype remained more stable over time than the skin microbiome profile. This characteristic of C. acnes was further confirmed by the analysis of publicly available human skin metagenome data. Our approach, with its high precision, good reproducibility, and low costs, thus provides new possibilities in the field of microbiome-based owner identification and forensics in general. IMPORTANCE Cutibacterium acnes is the most common and abundant bacterial species on human skin, and the gene that encodes its 16S rRNA has multiple single-nucleotide polymorphisms. In this study, we developed a method to efficiently determine the C. acnes 16S rRNA genotype composition from microbial samples taken from the hands of participants and from their possessions. Using the C. acnes 16S rRNA genotype composition, we could predict the owner of a possession with around 90% accuracy when the 16S rRNA gene-based microbiome profile was included. We also showed that the C. acnes 16S rRNA genotype composition was more stable over time than the skin microbiome profile and thus is more suitable for owner identification.

Development and Application of a Quantitative PCR Assay to Assess Genotype Dynamics and Anatoxin Content in Microcoleus autumnalis-Dominated Mats

Microcoleus is a filamentous cyanobacteria genus with a global distribution. Some species form thick, cohesive mats over large areas of the benthos in rivers and lakes. In New Zealand Microcoleus autumnalis is an anatoxin producer and benthic proliferations are occurring in an increasing number of rivers nationwide. Anatoxin content in M. autumnalis-dominated mats varies spatially and temporally, making understanding and managing proliferations difficult. In this study a M. autumnalis-specific TaqMan probe quantitative PCR (qPCR) assay targeting the anaC gene was developed. The assay was assessed against 26 non-M. autumnalis species. The assay had a detection range over seven orders of magnitude, with a limit of detection of 5.14 × 10−8 ng μL−1. The anaC assay and a cyanobacterial specific 16S rRNA qPCR were then used to determine toxic genotype proportions in 122 environmental samples collected from 19 sites on 10 rivers in New Zealand. Anatoxin contents of the samples were determined using LC-MS/MS and anatoxin quota per toxic cell calculated. The percentage of toxic cells ranged from 0 to 30.3%, with significant (p < 0.05) differences among rivers. The anatoxin content in mats had a significant relationship with the percentage of toxic cells (R2 = 0.38, p < 0.001), indicating that changes in anatoxin content in M. autumnalis-dominated mats are primarily related to the dominance of toxic strains. When applied to more extensive samples sets the assay will enable new insights into how biotic and abiotic parameters influence genotype composition, and if applied to RNA assist in understanding anatoxin production.

Trichothecene Genotype Composition of Fusarium graminearum Not Differentiated Among Isolates from Maize Stubble, Maize Ears, Wheat Spikes, and the Atmosphere in New York

In order to test the hypothesis that the trichothecene genotype composition of local populations of Fusarium graminearum is structured by specific habitats, a collection of 1,407 isolates was obtained from overwintered maize stubble, mature maize ears and wheat spikes, and the atmosphere 1.5 m aboveground during the flowering stage of these crops. These isolates were sampled at three diverse agricultural locations in New York State: namely, Aurora (sampled in 2012 and 2013) in central New York, Belmont (sampled in 2013) in southwestern New York, and Willsboro (sampled in 2013) in northeastern New York. Approximately 100 isolates of F. graminearum from each habitat were collected within a 10-mile2 area in each location. Polymerase chain reaction assays were used to identify three main B-trichothecene genotypes—3-acetyldeoxynivalenol (3-ADON), 15-ADON, or nivalenol (NIV)—based on amplification of portions of Tri3 and Tri12 genes. All but the NIV genotype were detected. The 15-ADON genotype predominated in most locations; frequencies were 92% (652/709) at Aurora, 78% (332/379) at Belmont, and 53% (167/319) at Willsboro. Frequencies of any genotype did not differ in general among the four habits in each location. An exception was in Aurora 2012, where only 5 in 24 3-ADON isolates were found in samplings from the air and grains of both crops. As viewed by the composition of trichothecene genotypes, local populations of F. graminearum appear not to be structured by these four habitats inclusive of pathogenic and saprophytic phases of the fungus life cycle. The similar frequency of 3-ADON and 15-ADON in eastern New York (Willsboro), which is less than 400 km away from the Aurora sampling location in the central area of the state, suggests that regional populations may be differentiated based on selection associated with climatic or landscape features not currently identified.