Identification of high-quality single-nucleotide polymorphisms in Glycine latifolia using a heterologous reference genome sequence

We sequenced the genomes of a Brahman, an Africander and a Tuli bull because tropically adapted breeds of cattle have so far not been well characterised at the level of DNA variation. In excess of 16 Gb of Illumina GA-II sequence was obtained for each animal in the form of 75-bp paired-end reads, generating more than 6× coverage of each genome, and between 86.7 and 88.8% of the bases of each genome sequence was covered by one or more sequence reads. A total of 6.35 million single nucleotide polymorphisms (SNP) were discovered in the three animals, adding 3.56 million new SNP to dbSNP. The Brahman animal had nearly twice as many SNP as either the Tuli or the Africander. Comparing genome sequence to genotypic array data, genotype accuracy from sequencing was more than 98% for homozygotes that had at least six high quality sequence reads and for heterozygotes that had at least two high quality reads containing the alternative allele. Intergenic and intronic SNP were found at higher densities closer to coding sequences, and there was a reduction in numbers of SNP within 5 bp of a splice site, features consistent with genetic selection. On average, slightly more SNP per Mb, and slightly higher average reads per SNP per Mb, were found towards the ends of chromosomes, especially towards the telomeric end of the chromosome. At least one autosome in each animal showed a large stretch of homozygosity, the largest was 58 Mb long in the Tuli, although the animals are not known to have recent inbreeding.

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Complete Genome Sequence of Geobacillus thermoglucosidasius NCIMB 11955, the Progenitor of a Bioethanol Production Strain

Genome Announcements ◽

10.1128/genomea.01065-16 ◽

2016 ◽

Vol 4 (5) ◽

Cited By ~ 3

Author(s):

Lili Sheng ◽

Ying Zhang ◽

Nigel P. Minton

Keyword(s):

Single Nucleotide Polymorphisms ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Bioethanol Production ◽

Nucleotide Polymorphisms ◽

Industrial Strain ◽

Single Nucleotide ◽

Geobacillus Thermoglucosidasius ◽

Production Strain

The industrially important thermophile Geobacillus thermoglucosidasius has the potential to produce chemicals and fuels from biomass-derived sugar feedstocks. Here, we present the genome sequence of strain NCIMB 11955, the progenitor of an ethanologenic industrial strain, revealing 11 single-nucleotide polymorphisms and 2 indels compared to strain DSM 2542 and two novel plasmids.

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

F1000Research ◽

10.12688/f1000research.18316.1 ◽

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.

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

10.21203/rs.3.rs-1176760/v1 ◽

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.

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Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97

Genome Announcements ◽

10.1128/genomea.00157-17 ◽

2017 ◽

Vol 5 (14) ◽

Cited By ~ 22

Author(s):

Kerri M. Malone ◽

Damien Farrell ◽

Tod P. Stuber ◽

Olga T. Schubert ◽

Ruedi Aebersold ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Mycobacterium Bovis ◽

Genome Sequence ◽

Bovine Tuberculosis ◽

Reference Genome ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Coding Sequences ◽

Content Type ◽

Reference Genome Sequence

ABSTRACT We report here an update to the reference genome sequence of the bovine tuberculosis bacillus Mycobacterium bovis AF2122/97, generated using an integrative multiomics approach. The update includes 42 new coding sequences (CDSs), 14 modified annotations, 26 single-nucleotide polymorphism (SNP) corrections, and disclosure that the RD900 locus, previously described as absent from the genome, is in fact present.

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Single-Nucleotide Polymorphisms in the Whole-Genome Sequence Data of Shiga Toxin-Producing Escherichia coli O157:H7/H- Strains by Cultivation

Current Microbiology ◽

10.1007/s00284-017-1208-z ◽

2017 ◽

Vol 74 (4) ◽

pp. 425-430 ◽

Cited By ~ 3

Author(s):

Eiji Yokoyama ◽

Shinichiro Hirai ◽

Taichiro Ishige ◽

Satoshi Murakami

Keyword(s):

Escherichia Coli ◽

Single Nucleotide Polymorphisms ◽

Genome Sequence ◽

Shiga Toxin ◽

Sequence Data ◽

Whole Genome Sequence ◽

Whole Genome ◽

Escherichia Coli O157 ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

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High-Quality and -Quantity DNA Extraction from Frozen Archival Blood Clots for Genotyping of Single-Nucleotide Polymorphisms

Genetic Testing and Molecular Biomarkers ◽

10.1089/gtmb.2012.0429 ◽

2013 ◽

Vol 17 (6) ◽

pp. 501-503 ◽

Cited By ~ 14

Author(s):

Steffen Bank ◽

Bjørn Andersen Nexø ◽

Vibeke Andersen ◽

Ulla Vogel ◽

Paal Skytt Andersen

Keyword(s):

Single Nucleotide Polymorphisms ◽

Dna Extraction ◽

Nucleotide Polymorphisms ◽

High Quality ◽

Single Nucleotide ◽

Blood Clots

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

Microorganisms ◽

10.3390/microorganisms9030570 ◽

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.

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