scholarly journals Whole genome sequence and genome-wide distributed single nucleotide polymorphisms (SNPs) of the Black Bengal goat

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 318
Author(s):  
Md. Bazlur Rahman Mollah ◽  
Md. Shamsul Alam Bhuiyan ◽  
M.A.M. Yahia Khandoker ◽  
Md. Abdul Jalil ◽  
Gautam Kumar Deb ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Single Nucleotide ◽  
Genome Wide ◽  
High Quality Snps ◽  
Black Goat ◽  
Black Bengal Goat

The Black Bengal goat (BBG) is a dwarf sized heritage goat (Capra hircus) breed from Bangladesh, and is well known for its high fertility, excellent meat and skin quality. Here we present the first whole genome sequence and genome-wide distributed single nucleotide polymorphisms (SNPs) of the BBG. A total of 833,469,900 raw reads consisting of 125,020,485,000 bases were obtained by sequencing one male BBG sample. The reads were aligned to the San Clemente and the Yunnan black goat genome which resulted in 98.65% (properly paired, 94.81%) and 98.50% (properly paired, 97.10%) of the reads aligning, respectively. Notably, the estimated sequencing coverages were 48.22X and 44.28X compared to published San Clemente and the Yunnan black goat genomes respectively. On the other hand, a total of 9,497,875 high quality SNPs (Q ≥ 20) along with 1,023,359 indels, and 8,746,849 high quality SNPs along with 842,706 indels were identified in BBG against the San Clemente and Yunnan black goat genomes respectively. The dataset is publicly available from NCBI BioSample (SAMN10391846), Sequence Read Archive (SRR8182317, SRR8549413 and SRR8549904), with BioProject ID PRJNA504436. These data might be useful genomic resources in conducting genome wide association studies, identification of quantitative trait loci (QTLs) and functional genomic analysis of the Black Bengal goat.

scholarly journals Whole-Genome Sequencing of a Year-Round Fruiting Jackfruit Variety Reveals Very High Single Nucleotide Polymorphisms in Inter-Genic Regions

2021 ◽  
Author(s):  
Tofazzal Islam ◽  
Nadia Afroz ◽  
ChuShin Koh ◽  
M. Nazmul Haque ◽  
Md. Jillur Rahman ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genome Sequence ◽  
De Novo ◽  
Agricultural Research ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Tropical Fruit

Abstract Background Jackfruit (Artocarpus heterophyllus Lam.) is a tropical and sub-tropical fruit tree distributed in Asia, Africa, and South America. It is the national fruit of Bangladesh and produces fruit in the summer season only. However, a year-round jackfruit variety, BARI Kanthal-3 developed by Bangladesh Agricultural Research Institute (BARI) provides fruits from September to June. This study aimed to evaluate the agronomic performance of BARI Kanthal-3 and to generate a draft whole genome sequence to obtain molecular insights of this important unique variety. Results Number of fruits, average each fruit weight, fruit yield per plant, edible portion in fruit and ß carotene content of BARI Kanthal-3 (n = 5) were 422/plant/year, 5.60 kg, 236.32 kg/year, 53.5% and 3614 mg/100g, respectively. During de novo assembly, 817.7 Mb of the BARI Kanthal-3 genome was scaffolded. However, in the reference-guided genome assembly, almost 843 Mb of the BARI Kanthal-3 genome was scaffolded. Through BUSCO assessment, 97.2% of the core genes were represented in the assembly with 1.3% and 1.5% either fragmented or missing, respectively. By comparing the single copy orthologues (SCOs) in three closely and one distantly related species of BARI Kanthal-3, 706 SCOs were found to be shared across the genomes of the five species. The phylogenetic analysis of the shared SCOs showed that A. heterophyllus is the closest species to BARI Kantal-3. The estimated genome size of BARI Kanthal-3 was 1.04 giga base pairs (Gbp) with a heterozygosity rate of 1.62%. The estimated GC content was 34.10%. Variant analysis revealed that BARI Kanthal-3 includes 5.7 M (35%) and 10.4 M (65%) simple and heterozygous single nucleotide polymorphisms (SNPs), and about 90% of all these polymorphisms are located in inter-genic regions. Conclusion The whole-genome sequence of A. heterophyllus cv. BARI Kanthal-3 reveals extremely high single nucleotide polymorphisms in inter-genic regions. The findings of this study will help better understanding the evolution, domestication, phylogenetic relationships, year-round fruiting and the markers development for molecular breeding of this highly nutritious fruit crop.

scholarly journals Whole Genome Sequence Analysis of Brucella abortus Isolates from Various Regions of South Africa

2021 ◽  
Vol 9 (3) ◽  
pp. 570
Author(s):  
Maphuti Betty Ledwaba ◽  
Barbara Akorfa Glover ◽  
Itumeleng Matle ◽  
Giuseppe Profiti ◽  
Pier Luigi Martelli ◽  
...  
Keyword(s):  
South Africa ◽  
Single Nucleotide Polymorphisms ◽  
South African ◽  
Genome Sequence ◽  
Brucella Abortus ◽  
Whole Genome Sequence ◽  
Snp Analysis ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

The availability of whole genome sequences in public databases permits genome-wide comparative studies of various bacterial species. Whole genome sequence-single nucleotide polymorphisms (WGS-SNP) analysis has been used in recent studies and allows the discrimination of various Brucella species and strains. In the present study, 13 Brucella spp. strains from cattle of various locations in provinces of South Africa were typed and discriminated. WGS-SNP analysis indicated a maximum pairwise distance ranging from 4 to 77 single nucleotide polymorphisms (SNPs) between the South African Brucella abortus virulent field strains. Moreover, it was shown that the South African B. abortus strains grouped closely to B. abortus strains from Mozambique and Zimbabwe, as well as other Eurasian countries, such as Portugal and India. WGS-SNP analysis of South African B. abortus strains demonstrated that the same genotype circulated in one farm (Farm 1), whereas another farm (Farm 2) in the same province had two different genotypes. This indicated that brucellosis in South Africa spreads within the herd on some farms, whereas the introduction of infected animals is the mode of transmission on other farms. Three B. abortus vaccine S19 strains isolated from tissue and aborted material were identical, even though they originated from different herds and regions of South Africa. This might be due to the incorrect vaccination of animals older than the recommended age of 4–8 months or might be a problem associated with vaccine production.

scholarly journals Classification of cannabis strains in the Canadian market with discriminant analysis of principal components using genome-wide single nucleotide polymorphisms

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253387
Author(s):  
Dan Jin ◽  
Philippe Henry ◽  
Jacqueline Shan ◽  
Jie Chen
Keyword(s):  
Discriminant Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Principal Components ◽  
Large Scale ◽  
Therapeutic Potential ◽  
Morphological Characteristics ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide

The cannabis community typically uses the terms “Sativa” and “Indica” to characterize drug strains with high tetrahydrocannabinol (THC) levels. Due to large scale, extensive, and unrecorded hybridization in the past 40 years, this vernacular naming convention has become unreliable and inadequate for identifying or selecting strains for clinical research and medicinal production. Additionally, cannabidiol (CBD) dominant strains and balanced strains (or intermediate strains, which have intermediate levels of THC and CBD), are not included in the current classification studies despite the increasing research interest in the therapeutic potential of CBD. This paper is the first in a series of studies proposing that a new classification system be established based on genome-wide variation and supplemented by data on secondary metabolites and morphological characteristics. This study performed a whole-genome sequencing of 23 cannabis strains marketed in Canada, aligned sequences to a reference genome, and, after filtering for minor allele frequency of 10%, identified 137,858 single nucleotide polymorphisms (SNPs). Discriminant analysis of principal components (DAPC) was applied to these SNPs and further identified 344 structural SNPs, which classified individual strains into five chemotype-aligned groups: one CBD dominant, one balanced, and three THC dominant clusters. These structural SNPs were all multiallelic and were predominantly tri-allelic (339/344). The largest portion of these SNPs (37%) occurred on the same chromosome containing genes for CBD acid synthases (CBDAS) and THC acid synthases (THCAS). The remainder (63%) were located on the other nine chromosomes. These results showed that the genetic differences between modern cannabis strains were at a whole-genome level and not limited to THC or CBD production. These SNPs contained enough genetic variation for classifying individual strains into corresponding chemotypes. In an effort to elucidate the confused genetic backgrounds of commercially available cannabis strains, this classification attempt investigated the utility of DAPC for classifying modern cannabis strains and for identifying structural SNPs.

scholarly journals Utilizing Big Data to Identify Tiny Toxic Components: Digitalis

Foods ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1794
Author(s):  
Elizabeth Sage Hunter ◽  
Robert Literman ◽  
Sara M. Handy
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Dietary Supplements ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Sequence Data ◽  
Genus Level

The botanical genus Digitalis is equal parts colorful, toxic, and medicinal, and its bioactive compounds have a long history of therapeutic use. However, with an extremely narrow therapeutic range, even trace amounts of Digitalis can cause adverse effects. Using chemical methods, the United States Food and Drug Administration traced a 1997 case of Digitalis toxicity to a shipment of Plantago (a common ingredient in dietary supplements marketed to improve digestion) contaminated with Digitalis lanata. With increased accessibility to next generation sequencing technology, here we ask whether this case could have been cracked rapidly using shallow genome sequencing strategies (e.g., genome skims). Using a modified implementation of the Site Identification from Short Read Sequences (SISRS) bioinformatics pipeline with whole-genome sequence data, we generated over 2 M genus-level single nucleotide polymorphisms in addition to species-informative single nucleotide polymorphisms. We simulated dietary supplement contamination by spiking low quantities (0–10%) of Digitalis whole-genome sequence data into a background of commonly used ingredients in products marketed for “digestive cleansing” and reliably detected Digitalis at the genus level while also discriminating between Digitalis species. This work serves as a roadmap for the development of novel DNA-based assays to quickly and reliably detect the presence of toxic species such as Digitalis in food products or dietary supplements using genomic methods and highlights the power of harnessing the entire genome to identify botanical species.

scholarly journals Whole-Genome Sequence of a Reemerging Listeria monocytogenes Serovar 1/2a Strain in Central Italy

2018 ◽  
Vol 7 (23) ◽  
Author(s):  
Massimiliano Orsini ◽  
Marina Torresi ◽  
Claudio Patavino ◽  
Patrizia Centorame ◽  
Antonio Rinaldi ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Single Nucleotide Polymorphisms ◽  
Genome Sequence ◽  
Central Italy ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Content Type

We report the whole-genome sequence of a Listeria monocytogenes strain isolated from a child in central Italy. Interestingly, the sequence showed a difference of only 13 single-nucleotide polymorphisms (SNPs) from a strain responsible for a severe listeriosis outbreak that occurred between January 2015 and March 2016 in the same region.

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