Development of Whole Genome Sequence-based Novel SSR Markers in Astragalus membranaceus (Fisch.)

2021 ◽  
Vol 29 (6) ◽  
pp. 418-424
Author(s):  
Mok Hur ◽  
Yurry Um ◽  
Yi Lee ◽  
Yoon Jeong Lee ◽  
Sung Cheol Koo ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Astragalus Membranaceus ◽  
Whole Genome

scholarly journals Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gehendra Bhattarai ◽  
Ainong Shi ◽  
Devi R. Kandel ◽  
Nora Solís-Gracia ◽  
Jorge Alberto da Silva ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genome Sequence ◽  
Reference Genome ◽  
Whole Genome Sequence ◽  
Large Set ◽  
Whole Genome ◽  
Genome Sequences ◽  
Sequence Comparisons ◽  
Ssr Loci ◽  
Simple Sequence

AbstractThe availability of well-assembled genome sequences and reduced sequencing costs have enabled the resequencing of many additional accessions in several crops, thus facilitating the rapid discovery and development of simple sequence repeat (SSR) markers. Although the genome sequence of inbred spinach line Sp75 is available, previous efforts have resulted in a limited number of useful SSR markers. Identification of additional polymorphic SSR markers will support genetics and breeding research in spinach. This study aimed to use the available genomic resources to mine and catalog a large number of polymorphic SSR markers. A search for SSR loci on six chromosome sequences of spinach line Sp75 using GMATA identified a total of 42,155 loci with repeat motifs of two to six nucleotides in the Sp75 reference genome. Whole-genome sequences (30x) of additional 21 accessions were aligned against the chromosome sequences of the reference genome and in silico genotyped using the HipSTR program by comparing and counting repeat numbers variation across the SSR loci among the accessions. The HipSTR program generated SSR genotype data were filtered for monomorphic and high missing loci, and a final set of the 5986 polymorphic SSR loci were identified. The polymorphic SSR loci were present at a density of 12.9 SSRs/Mb and were physically mapped. Out of 36 randomly selected SSR loci for validation, two failed to amplify, while the remaining were all polymorphic in a set of 48 spinach accessions from 34 countries. Genetic diversity analysis performed using the SSRs allele score data on the 48 spinach accessions showed three main population groups. This strategy to mine and develop polymorphic SSR markers by a comparative analysis of the genome sequences of multiple accessions and computational genotyping of the candidate SSR loci eliminates the need for laborious experimental screening. Our approach increased the efficiency of discovering a large set of novel polymorphic SSR markers, as demonstrated in this report.

scholarly journals Development of Genome-wide Simple Sequence Repeat Markers from Whole-genome Sequence of Mungbean (Vigna radiata)

2021 ◽  
Author(s):  
Kanimoli Mathivathana Mayalagu ◽  
Karthikeyan Adhimoolam ◽  
Jagadeeshselvam Nallathambi ◽  
Veera Ranjani Rajagopalan ◽  
Madhumitha Balasubramanian ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genome Sequence ◽  
Genomic Sequence ◽  
Model Organism ◽  
Cost Effective ◽  
Whole Genome Sequence ◽  
Human Consumption ◽  
Whole Genome ◽  
Ssr Primers ◽  
Simple Sequence

Background: Mungbean is an important pulse crop and it is mainly cultivated in Asia for human consumption. Its small genome and diploid nature make it a well-suited model organism among legume crops. Thus, cost-effective, reliable and highly polymorphic molecular markers distributing the whole genome are needed for diversity, mapping and functional genomics studies in this model species. Methods: The whole-genome sequence of mungbean was obtained and used as a source of identification of simple sequence repeats (SSR). The sequence reads were aligned and SSRs detection was performed using the Phobos plugin tandem repeat finder in the Geneious software program. A total of 12 mungbean genotypes were selected to validate the newly developed SSR markers. Result: In the present study, a total of 12, 49,774 and 11, 86, 386 perfect and imperfect SSR repeats were identified from the mungbean genome. The tri-repeats were the most abundant (26.10%), followed by hexa (20.82%), penta (20.45%), tetra (17.65%) and di-repeats (14.95%). We designed 1330 SSR primers based on the genomic sequence of flanking perfect SSRs (Di and tri-repeats). Among them, 50 SSR primers uniformly distributed across the 11 mungbean chromosomes were selected and used to validate 12 mungbean genotypes. The newly developed genomic SSR markers generated in the present study are a valuable genomic resource for the mungbean breeding programs.

Whole-Genome Sequence Characterization of Primary Auxin-Responsive Aux/IAA Gene Family in Sorghum (Sorghum bicolor L.)

2010 ◽  
Vol 36 (4) ◽  
pp. 688-694
Author(s):  
Yi-Jun WANG ◽  
Yan-Ping LÜ ◽  
Qin XIE ◽  
De-Xiang DENG ◽  
Yun-Long BIAN
Keyword(s):  
Sorghum Bicolor ◽  
Gene Family ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequence Characterization ◽  
I Gene

Whole-Genome Sequence Isolation, Chromosome Location, and Characteriza-tion of Primary Auxin-ResponsiveAux/IAAGene Family inAegilops tauschii

2014 ◽  
Vol 40 (12) ◽  
pp. 2059
Author(s):  
Lin-Yi QIAO ◽  
Xin LI ◽  
Zhi-Jian CHANG ◽  
Xiao-Jun ZHANG ◽  
Hai-Xian ZHAN ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Chromosome Location

scholarly journals Whole genome sequence of Corynebacterium kroppenstedtii isolated from a case of recurrent granulomatous mastitis

IDCases ◽  
2020 ◽  
pp. e01034
Author(s):  
Charlie Tan ◽  
Fang-I Lu ◽  
Patryk Aftanas ◽  
Kara Tsang ◽  
Samira Mubareka ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Granulomatous Mastitis

TIGER: inferring DNA replication timing from whole-genome sequence data

2021 ◽  
Author(s):  
Amnon Koren ◽  
Dashiell J Massey ◽  
Alexa N Bracci
Keyword(s):  
Dna Replication ◽  
Genome Sequence ◽  
Genomic Dna ◽  
Sequence Data ◽  
Replication Timing ◽  
Whole Genome Sequence ◽  
Supplementary Information ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Dna Replication Timing

Abstract Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and Implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online

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