scholarly journals Identification of genetic variations in Necator americanus through resequencing by whole genome amplification

2019 ◽  
Vol 47 (9) ◽  
pp. 4353-4364
Author(s):  
Yumei Liu ◽  
Hongxuan Liu ◽  
Yuefeng Xie ◽  
Baohuan Zhang ◽  
Xiaoqian Zou ◽  
...  
Keyword(s):  
De Novo ◽  
Multiple Displacement Amplification ◽  
Genetic Variations ◽  
Whole Genome ◽  
Genome Resequencing ◽  
De Novo Genome Assembly ◽  
Go Analysis ◽  
Necator Americanus ◽  
New Strategy ◽  
Whole Genome Resequencing

Objective To describe a new strategy for the whole genome resequencing of small parasite samples. Methods Whole genome resequencing was based on a multiple displacement amplification (MDA) method. Sequencing reads were aligned with the reference genome, and a Bayesian model was used to calculate genotype probabilities. De novo genome assembly was conducted, and single nucleotide polymorphisms (SNPs) were detected. Gene ontology (GO) analysis was used to determine connections between SNPs and genes. Results In total, 64.12% of the parasite genome sequence was mapped to Necator americanus. fa, and 125,553 SNPs were detected. GO analysis revealed that most SNPs in coding regions were probably associated with common drug targets. Conclusion These results reveal the feasibility of a new strategy to detect genetic variations of small parasites. This study also provides a proof-of-principle for the molecular classification and epidemiological analysis of other parasites.

scholarly journals The de novo genome assembly of Tapiscia sinensis and the transcriptomic and developmental bases of androdioecy

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Peng Zhao ◽  
Guiliang Xin ◽  
Feng Yan ◽  
Huan Wang ◽  
Xiaolong Ren ◽  
...  
Keyword(s):  
Breeding System ◽  
De Novo ◽  
Whole Genome ◽  
Genome Resequencing ◽  
De Novo Genome Assembly ◽  
Genome Scans ◽  
Breeding System Evolution ◽  
Whole Genome Resequencing ◽  
Key Aspects ◽  
Shed Light

AbstractTapiscia sinensis (Tapisciaceae) possesses an unusual androdioecious breeding system that has attracted considerable interest from evolutionary biologists. Key aspects of T. sinensis biology, including its biogeography, genomics, and sex-linked genes, are unknown. Here, we report the first de novo assembly of the genome of T. sinensis. The genome size was 410 Mb, with 22,251 predicted genes. Based on whole-genome resequencing of 55 trees from 10 locations, an analysis of population genetic structure indicated that T. sinensis has fragmented into five lineages, with low intrapopulation genetic diversity and little gene flow among populations. By comparing whole-genome scans of male versus hermaphroditic pools, we identified 303 candidate sex-linked genes, 79 of which (25.9%) were located on scaffold 25. A 24-kb region was absent in hermaphroditic individuals, and five genes in that region, TsF-box4, TsF-box10, TsF-box13, TsSUT1, and TsSUT4, showed expression differences between mature male and hermaphroditic flowers. The results of this study shed light on the breeding system evolution and conservation genetics of the Tapisciaceae.

scholarly journals Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luciano Calderón ◽  
Nuria Mauri ◽  
Claudio Muñoz ◽  
Pablo Carbonell-Bejerano ◽  
Laura Bree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Somatic Mutations ◽  
Clonal Propagation ◽  
Variant Calling ◽  
Vitis Vinifera L ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Genome Resequencing ◽  
Diversity Pattern ◽  
Whole Genome Resequencing

AbstractGrapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.

scholarly journals Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Paul Stothard ◽  
Jung-Woo Choi ◽  
Urmila Basu ◽  
Jennifer M Sumner-Thomson ◽  
Yan Meng ◽  
...  
Keyword(s):  
Holstein Cattle ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals Whole-Genome Resequencing Points to Candidate DNA Loci Affecting Body Temperature under Cold Stress in Siberian Cattle Populations

Life ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 959
Author(s):  
Alexander Igoshin ◽  
Nikolay Yudin ◽  
Ruslan Aitnazarov ◽  
Andrey A. Yurchenko ◽  
Denis M. Larkin
Keyword(s):  
Body Temperature ◽  
Cold Stress ◽  
Candidate Snps ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Functional Annotations ◽  
Cold Environments ◽  
Cold Tolerant ◽  
Cold Sensitive ◽  
Whole Genome Resequencing

Despite the economic importance of creating cold resilient cattle breeds, our knowledge of the genetic basis of adaptation to cold environments in cattle is still scarce compared to information on other economically important traits. Herein, using whole-genome resequencing of animals showing contrasting phenotypes on temperature maintenance under acute cold stress combined with the existing SNP (single nucleotide polymorphism) functional annotations, we report chromosomal regions and candidate SNPs controlling body temperature in the Siberian cattle populations. The SNP ranking procedure based on regional FST calculations, functional annotations, and the allele frequency difference between cold-tolerant and cold-sensitive groups of animals pointed to multiple candidate genes. Among these, GRIA4, COX17, MAATS1, UPK1B, IFNGR1, DDX23, PPT1, THBS1, CCL5, ATF1, PLA1A, PRKAG1, and NR1I2 were previously related to thermal adaptations in cattle. Other genes, for example KMT2D and SNRPA1, are known to be related to thermogenesis in mice and cold adaptation in common carp, respectively. This work could be useful for cattle breeding strategies in countries with harsh climates, including the Russian Federation.

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