scholarly journals Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yawo Mawunyo Nevame Adedze ◽  
Xia Lu ◽  
Yingchun Xia ◽  
Qiuyue Sun ◽  
Chofong G. Nchongboh ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Pcr Amplification ◽  
Reference Sequence ◽  
Whole Genome ◽  
Sequencing Data ◽  
Fresh Market ◽  
Breeding Lines ◽  
Indel Markers ◽  
Indel Polymorphisms ◽  
Hybrid Seeds

AbstractInsertion and Deletion (InDel) are common features in genomes and are associated with genetic variation. The whole-genome re-sequencing data from two parents (X1 and X2) of the elite cucumber (Cucumis sativus) hybrid variety Lvmei No.1 was used for genome-wide InDel polymorphisms analysis. Obtained sequence reads were mapped to the genome reference sequence of Chinese fresh market type inbred line ‘9930’ and gaps conforming to InDel were pinpointed. Further, the level of cross-parents polymorphism among five pairs of cucumber breeding parents and their corresponding hybrid varieties were used for evaluating hybrid seeds purity test efficiency of InDel markers. A panel of 48 cucumber breeding lines was utilized for PCR amplification versatility and phylogenetic analysis of these markers. In total, 10,470 candidate InDel markers were identified for X1 and X2. Among these, 385 markers with more than 30 nucleotide difference were arbitrary chosen. These markers were selected for experimental resolvability through electrophoresis on an Agarose gel. Two hundred and eleven (211) accounting for 54.81% of markers could be validated as single and clear polymorphic pattern while 174 (45.19%) showed unclear or monomorphic genetic bands between X1 and X2. Cross-parents polymorphism evaluation recorded 68 (32.23%) of these markers, which were designated as cross-parents transferable (CPT) InDel markers. Interestingly, the marker InDel114 presented experimental transferability between cucumber and melon. A panel of 48 cucumber breeding lines including parents of Lvmei No. 1 subjected to PCR amplification versatility using CPT InDel markers successfully clustered them into fruit and common cucumber varieties based on phylogenetic analysis. It is worth noting that 16 of these markers were predominately associated to enzymatic activities in cucumber. These agarose-based InDel markers could constitute a valuable resource for hybrid seeds purity testing, germplasm classification and marker-assisted breeding in cucumber.

scholarly journals Harnessing the 100,000 Genomes Project whole genome sequencing data - an unbiased systematic tool to filter by biologically validated regions of functionality

2020 ◽  
Author(s):  
Sihao Xiao ◽  
Zhentian Kai ◽  
David Brown ◽  
Claire L Shovlin ◽  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Diagnostics ◽  
Reference Sequence ◽  
Whole Genome Sequencing Data ◽  
Disease Genes ◽  
Full Potential ◽  
Hereditary Haemorrhagic Telangiectasia ◽  
Whole Genome ◽  
Sequencing Data

SUMMARYWhole genome sequencing (WGS) is championed by the UK National Health Service (NHS) to identify genetic variants that cause particular diseases. The full potential of WGS has yet to be realised as early data analytic steps prioritise protein-coding genes, and effectively ignore the less well annotated non-coding genome which is rich in transcribed and critical regulatory regions. To address, we developed a filter, which we call GROFFFY, and validated in WGS data from hereditary haemorrhagic telangiectasia patients within the 100,000 Genomes Project. Before filter application, the mean number of DNA variants compared to human reference sequence GRCh38 was 4,867,167 (range 4,786,039-5,070,340), and one-third lay within intergenic areas. GROFFFY removed a mean of 2,812,015 variants per DNA. In combination with allele frequency and other filters, GROFFFY enabled a 99.56% reduction in variant number. The proportion of intergenic variants was maintained, and no pathogenic variants in disease genes were lost. We conclude that the filter applied to NHS diagnostic samples in the 100,000 Genomes pipeline offers an efficient method to prioritise intergenic, intronic and coding gDNA variants. Reducing the overwhelming number of variants while retaining functional genome variation of importance to patients, enhances the near-term value of WGS in clinical diagnostics.

scholarly journals Development and Application of Novel Indel Markers in Flax (Linum Usitatissimum L.) Through Whole-genome Re-sequencing

2021 ◽  
Author(s):  
Hui Jiang ◽  
Gen Pan ◽  
Touming Liu ◽  
Li Chang ◽  
Siqi Huang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Snp Markers ◽  
Diversity Analysis ◽  
Whole Genome ◽  
Chromosome 2 ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Genetic Diversity Analysis ◽  
Indel Markers

Abstract Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87-3 and 84-3) with the flax reference genome. The length of InDels ranged from 1–277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and chromosome 2 (1505) showed the highest number of InDels among flax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using 32 pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535 and lus10025284) tightly linked to InDel-26 or InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the markers into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.

scholarly journals First phylogenetic analysis of Malian SARS-CoV-2 sequences provide molecular insights into the genomic diversity of the Sahel region

2020 ◽  
Author(s):  
Bourema Kouriba ◽  
Angela Duerr ◽  
Alexandra Rehn ◽  
Abdoul Karim Sangare ◽  
Brehima Youssouf Traoure ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Sequencing ◽  
Sequence Data ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Sequencing Data ◽  
Genome Sequences ◽  
Spreading Dynamics ◽  
Sahel Region ◽  
Limited Sequence

We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occuring in the Wuhan region, China, in December 2019. From China the virus has spread to 188 countries and regions worldwide, reaching the Sahel region on the 2nd of March 2020. Since whole genome sequencing (WGS) data is very crucial to understand the spreading dynamics of the ongoing pandemic, but only limited sequence data is available from the Sahel region to date, we have focused our efforts on generating the first Malian sequencing data available. Screening of 217 Malian patient samples for the presence of SARS-CoV-2 resulted in 38 positive isolates from which 21 whole genome sequences were generated. Our analysis shows that both, the early A (19B) and the fast evolving B (20A/C) clade, are present in Mali indicating multiple and independent introductions of the SARS-CoV-2 to the Sahel region.

scholarly journals Phylogenetic Analysis of Mycobacterium tuberculosis Strains in Wales by Use of Core Genome Multilocus Sequence Typing To Analyze Whole-Genome Sequencing Data

2019 ◽  
Vol 57 (6) ◽  
Author(s):  
R. C. Jones ◽  
L. G. Harris ◽  
S. Morgan ◽  
M. C. Ruddy ◽  
M. Perry ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Data Set

ABSTRACT An inability to standardize the bioinformatic data produced by whole-genome sequencing (WGS) has been a barrier to its widespread use in tuberculosis phylogenetics. The aim of this study was to carry out a phylogenetic analysis of tuberculosis in Wales, United Kingdom, using Ridom SeqSphere software for core genome multilocus sequence typing (cgMLST) analysis of whole-genome sequencing data. The phylogenetics of tuberculosis in Wales have not previously been studied. Sixty-six Mycobacterium tuberculosis isolates (including 42 outbreak-associated isolates) from south Wales were sequenced using an Illumina platform. Isolates were assigned to principal genetic groups, single nucleotide polymorphism (SNP) cluster groups, lineages, and sublineages using SNP-calling protocols. WGS data were submitted to the Ridom SeqSphere software for cgMLST analysis and analyzed alongside 179 previously lineage-defined isolates. The data set was dominated by the Euro-American lineage, with the sublineage composition being dominated by T, X, and Haarlem family strains. The cgMLST analysis successfully assigned 58 isolates to major lineages, and the results were consistent with those obtained by traditional SNP mapping methods. In addition, the cgMLST scheme was used to resolve an outbreak of tuberculosis occurring in the region. This study supports the use of a cgMLST method for standardized phylogenetic assignment of tuberculosis isolates and for outbreak resolution and provides the first insight into Welsh tuberculosis phylogenetics, identifying the presence of the Haarlem sublineage commonly associated with virulent traits.

scholarly journals First Phylogenetic Analysis of Malian SARS-CoV-2 Sequences Provides Molecular Insights into the Genomic Diversity of the Sahel Region

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1251
Author(s):  
Bourema Kouriba ◽  
Angela Dürr ◽  
Alexandra Rehn ◽  
Abdoul Karim Sangaré ◽  
Brehima Y. Traoré ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Sequencing Data ◽  
Genome Sequences ◽  
Spreading Dynamics ◽  
Sahel Region

We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occurring in the Wuhan region of China in December 2019. From China, the virus has spread to 188 countries and regions worldwide, reaching the Sahel region on 2 March 2020. Since whole genome sequencing (WGS) data is very crucial to understand the spreading dynamics of the ongoing pandemic, but only limited sequencing data is available from the Sahel region to date, we have focused our efforts on generating the first Malian sequencing data available. Screening 217 Malian patient samples for the presence of SARS-CoV-2 resulted in 38 positive isolates, from which 21 whole genome sequences were generated. Our analysis shows that both the early A (19B) and the later observed B (20A/C) clade are present in Mali, indicating multiple and independent introductions of SARS-CoV-2 to the Sahel region.

scholarly journals Development of InDel Markers and Fingerprinting of Bitter Gourd (Momordica Charantia) Based on Whole Genome Re-sequencing

2021 ◽  
Author(s):  
Liwen Su ◽  
Lianlian Ma ◽  
Xiaochun Huang ◽  
Wenting Wu ◽  
Haixuan Lv ◽  
...  
Keyword(s):  
Polyacrylamide Gel Electrophoresis ◽  
Momordica Charantia ◽  
Bitter Gourd ◽  
Group Method ◽  
Whole Genome ◽  
Sequencing Data ◽  
African Countries ◽  
Arithmetic Means ◽  
Relationship Analysis ◽  
Indel Markers

Abstract Bitter gourd (Momordica charantia L.) is one of the most important vegetable crops in many Asian and African countries. Here, InDel markers developed by comparing whole genome re-sequencing data were used to analyze the genetic diversity of a bitter gourd germplasm sample from various geographical origins. To verify the reliability of the set of InDel markers identified, 220 pairs of InDel primers were designed. The primers were preliminarily detected by 8% polyacrylamide gel electrophoresis, and 25 pairs of primers with better polymorphism were screened. Using the 25 primer combinations, the 53 bitter gourd accessions were effectively distinguished and the InDel fingerprint of DNA was constructed. Concomitantly, the degree of purity of different crosses was determined based on the differences in specific bands among genotypes. The unweighted pair-group method with arithmetic means showed that the 53 bitter gourd materials may be divided into three groups, with a similarity coefficient of 0.645 as the threshold. Therefore, this study can provide many InDel markers for genotypic identification, genetic relationship analysis, and genetic map construction of bitter gourd.

Development and evaluation of InDel markers in cotton based on whole-genome re-sequencing data

2019 ◽  
Vol 45 (2) ◽  
pp. 196
Author(s):  
Mi WU ◽  
Nian WANG ◽  
Chao SHEN ◽  
Cong HUANG ◽  
Tian-Wang WEN ◽  
...  
Keyword(s):  
Whole Genome ◽  
Sequencing Data ◽  
Indel Markers

scholarly journals Development and Application of Novel InDel Markers in Flax (Linum usitatissimum L.) Through Whole-Genome Re-Sequencing

2021 ◽  
Author(s):  
Hui Jiang ◽  
Gen Pan ◽  
Touming Liu ◽  
Li Chang ◽  
Siqi Huang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Snp Markers ◽  
Diversity Analysis ◽  
Whole Genome ◽  
Chromosome 2 ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Genetic Diversity Analysis ◽  
Indel Markers

Abstract Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87 − 3 and 84 − 3) with the flax reference genome. The length of InDels ranged from 1–277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and chromosome 2 (1505) showed the highest number of InDels among flax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using 32 pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535 and lus10025284) tightly linked to InDel-26 or InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the markers into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.

scholarly journals Improvement of the technique of SNP-typing of Vibrio cholerae strains on the basis of the analysis of the primary data of whole genome sequencing

2021 ◽  
Vol 97 (6) ◽  
pp. 587-593
Author(s):  
A. S. Vodopianov ◽  
R. V. Pisanov ◽  
S. O. Vodopianov ◽  
I. P. Oleynikov
Keyword(s):  
Cluster Analysis ◽  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Vibrio Cholerae ◽  
Genome Sequencing ◽  
Primary Data ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Snp Typing

Aim. To improve the method of the quality assessment of single nucleotide polymorphisms, which are used for SNP-typing, based on the analysis of their distribution in the primary data of whole genome sequencing (reads).Materials and methods. Data of the whole genome sequencing of 56 Vibrio cholerae strains obtained using different types of sequencers were used. The software was developed using Java programming language. Cluster analysis and construction of the dendrogram were performed with the author's software using the UPGMA method.Results and discussion. The «instability» of detection the number of SNP in the genome of cholera causative agent was shown. The method of selection of the SNP list for phylogenetic analysis based on the analysis of the primary data of whole genome sequencing (reads), has been developed. The method of using «control genomes» for cluster analysis of whole genome sequencing data has been proposed.Conclusion. The list of 3198 «stable SNP» for phylogenetic analysis has been composed. Genetic affinity between the non-toxigenic strains that contain the tcpA gene (ctxAB–tcpA+) and preCTX-strains of V. cholerae was shown.

Sign in / Sign up

Export Citation Format

Share Document