scholarly journals Whole genome sequence resource for Fusarium oxysporum f. sp. capsici 14003, the causative agent of pepper wilt

Plant Disease ◽  
2020 ◽  
Author(s):  
Yongxin Shu ◽  
Mei Luo ◽  
Zhangyong Dong
Keyword(s):  
Fusarium Oxysporum ◽  
Genome Sequence ◽  
Plant Diseases ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Genome Wide ◽  
A Genome ◽  
And Control ◽  
Common Plant

Pepper wilt, caused by the fungal pathogen Fusarium oxysporum f. sp. capsici, is one of the most common plant diseases worldwide. In this study, we obtained the whole genome sequence of the highly virulent Fusarium oxysporum f. sp. capsici strain 14003 sequenced using the Illumina Hiseq 2000 platform. In total, 3.87 million paired-end reads were obtained and assembled into 796 scaffolds with a genome-wide length of 47.6 Mb. In addition, we filtered genes that may be related to specific virulence factors and performed a comparative analysis between the genome of strain 14003 and the sequenced genomes of 36 isolates. The genome-sequencing results for strain 14003 will enhance the theoretical basis for pepper wilt prevention and control.

A genome-wide resource of intron spanning primers compatible for quantitative PCR and intron length polymorphism in rice

2019 ◽  
Vol 79 (02) ◽  
Author(s):  
Humira Sonah ◽  
Hasthi Ram ◽  
Bikram Pratap Singh ◽  
Jawaharlal Katara ◽  
Radha Chopra ◽  
...  
Keyword(s):  
Quantitative Pcr ◽  
Genome Sequence ◽  
Sequence Variation ◽  
Whole Genome Sequence ◽  
Pcr Analysis ◽  
Sequence Information ◽  
Whole Genome ◽  
Intron Length Polymorphism ◽  
Genome Wide ◽  
A Genome

Whole genome sequence availability in rice has provided several advantages for genomics as well as other omics assisted applications. Genome-wide molecular markers are one of such availability that has exceptional importance in modern plant breeding. In the present study, a resource of intron-spanning primers (ISPs) was developed using whole genome sequence information of two rice subspecies, japonica (cv. Nipponbare) and indica (cv. 93-11). The ISPs were designed in a way that the PCR using a cDNA template will yield 60 to 100 base pair size amplicon ideal for the quantitative PCR analysis. Whereas, PCR using genomic DNA will amplify the introns, which are more prone to sequence variation. The sequence variation in the intron serves as an excellent marker resource. The application of ISPs was demonstrated by characterizing 12 diverse rice cultivars. A total of eight out of ten ISPs were found to be polymorphic. The resource will be helpful for the rice molecular biologist and breeder community.

scholarly journals Linkage disequilibrium maps for European and African populations constructed from whole genome sequence data

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Alejandra Vergara-Lope ◽  
M. Reza Jabalameli ◽  
Clare Horscroft ◽  
Sarah Ennis ◽  
Andrew Collins ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Genome Sequence ◽  
Sequence Data ◽  
Association Studies ◽  
Large Population ◽  
Whole Genome Sequence ◽  
European Ancestry ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Genome Wide

Abstract Quantification of linkage disequilibrium (LD) patterns in the human genome is essential for genome-wide association studies, selection signature mapping and studies of recombination. Whole genome sequence (WGS) data provides optimal source data for this quantification as it is free from biases introduced by the design of array genotyping platforms. The Malécot-Morton model of LD allows the creation of a cumulative map for each choromosome, analogous to an LD form of a linkage map. Here we report LD maps generated from WGS data for a large population of European ancestry, as well as populations of Baganda, Ethiopian and Zulu ancestry. We achieve high average genetic marker densities of 2.3–4.6/kb. These maps show good agreement with prior, low resolution maps and are consistent between populations. Files are provided in BED format to allow researchers to readily utilise this resource.

scholarly journals Imputation to whole-genome sequence using multiple pig populations and its use in genome-wide association studies

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Sanne van den Berg ◽  
Jérémie Vandenplas ◽  
Fred A. van Eeuwijk ◽  
Aniek C. Bouwman ◽  
Marcos S. Lopes ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Association Studies ◽  
Genome Wide Association ◽  
Whole Genome Sequence ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Genome Wide

scholarly journals Genome Sequence Resource of ‘Candidatus Liberibacter asiaticus’ strain 9PA From Brazil

Plant Disease ◽  
2021 ◽  
Vol 105 (1) ◽  
pp. 199-201
Author(s):  
P. A. Silva ◽  
J. Huang ◽  
N. A. Wulff ◽  
Z. Zheng ◽  
R. Krugner ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sweet Orange ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Candidatus Liberibacter Asiaticus ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Citrus Huanglongbing ◽  
Liberibacter Asiaticus ◽  
And Control

‘Candidatus Liberibacter asiaticus’, an unculturable α-proteobacterium, is associated with citrus huanglongbing (HLB), a devastating disease threatening citrus production in Brazil and worldwide. In this study, a draft whole-genome sequence of ‘Ca. L. asiaticus’ strain 9PA from a sweet orange (cultivar Pera) tree collected in São Paulo State, Brazil, is reported. The 9PA genome is 1,231,881 bp, including two prophages, with G+C content of 36.7%. This is the first report of a whole-genome sequence of ‘Ca. L. asiaticus’ from Brazil or South America. The 9PA genome sequence will enrich ‘Ca. L. asiaticus’ genome resources and facilitate HLB research and control in Brazil and the world.

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