scholarly journals A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

Nature ◽  
2001 ◽  
Vol 409 (6822) ◽  
pp. 928-933 ◽  
Author(s):  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Human Genome ◽  
Genome Sequence ◽  
Sequence Variation ◽  
Human Genome Sequence ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 455 ◽  
Author(s):  
Shuai Zeng ◽  
Jing Yang ◽  
Brian Hon-Yin Chung ◽  
Yu Lau ◽  
Wanling Yang
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Human Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Functional Impact

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

2016 ◽  
Vol 4 (5) ◽  
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.

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 Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genome

2003 ◽  
Vol 13 (3) ◽  
pp. 335-342 ◽  
Author(s):  
Thomas G. Schulze ◽  
Kui Zhang ◽  
Yu-Sheng Chen ◽  
Nirmala Akula ◽  
Fengzhu Sun ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Human Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Haplotype Blocks
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