scholarly journals Genome-Wide Characterization of Adaptation and Speciation in Tiger Swallowtail Butterflies Using De Novo Transcriptome Assemblies

2013 ◽  
Vol 5 (6) ◽  
pp. 1233-1245 ◽  
Author(s):  
Wei Zhang ◽  
Krushnamegh Kunte ◽  
Marcus R. Kronforst
Keyword(s):  
De Novo ◽  
De Novo Transcriptome ◽  
Genome Wide ◽  
Swallowtail Butterflies ◽  
Tiger Swallowtail

scholarly journals De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 41 ◽  
Author(s):  
Luca Venturini ◽  
Alberto Ferrarini ◽  
Sara Zenoni ◽  
Giovanni Battista Tornielli ◽  
Marianna Fasoli ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
De Novo ◽  
De Novo Transcriptome ◽  
Varietal Diversity

scholarly journals Development and Characterization of SSR Markers in the Gossypium Barbadense Genome

2021 ◽  
Author(s):  
Wenjuan ZHONG ◽  
Can YUAN ◽  
Zhengjie CHEN ◽  
Yonghang ZHOU ◽  
Siwei Chen ◽  
...  
Keyword(s):  
Ssr Markers ◽  
De Novo ◽  
Low Cost ◽  
Fiber Quality ◽  
Gossypium Barbadense ◽  
Pcr Analysis ◽  
Genetic Studies ◽  
Genome Wide ◽  
User Friendly

Abstract BackgroundThe fiber quality and resistance traits of Gossypium barbadense are considerably better than that of other Gossypium species. Simple sequence repeats (SSRs) are user friendly, low cost markers widely used in genetic studies. However, most SSRs have been developed from G. hirsutum, G. arboreum, and G. raimondii; no genome-wide SSRs have been developed from G. barbadense.The de novo sequences of G. barbadense cv. Xinhai21 were utilized to develop SSR markers and scanned to detect SSRs using the MIcroSAtellite (http://pgrc.ipk-gatersleben.de/misa/) identification tool. And then in silico PCR analysis was conducted to evaluate these primers polymorphism in five Gossypium species.ResultsIn total, 85,582 SSRs were identified with different motifs. 153,560 primer pairs were successfully designed for 73,419 SSRs. In silico analysis, we found that 8,466 primer pairs of 3,288 SSRs yielded one product (monomorphic) simultaneously in five Gossypium species. two Gossypium species (30 G. hirsutum and 27 G. barbadense accessions) were successfully separated by 300 primer pairs with the polymorphism information content (PIC) ranging from 0.00 to 0.93. ConclusionThese newly developed SSR markers will be helpful for the construction of genetic linkage maps, genetic diversity analyses, QTL mapping, and molecular breeding of Gossypium species.

De novo transcriptome characterization of Lilium ‘Sorbonne’ and key enzymes related to the flavonoid biosynthesis

2014 ◽  
Vol 290 (1) ◽  
pp. 399-412 ◽  
Author(s):  
Ming-fang Zhang ◽  
Ling-min Jiang ◽  
Dong-mei Zhang ◽  
Gui-xia Jia
Keyword(s):  
De Novo ◽  
Flavonoid Biosynthesis ◽  
De Novo Transcriptome ◽  
Key Enzymes

scholarly journals Topologically Dependent Abundance of Spontaneous DNA Damage in Single Human Cells

2019 ◽  
Author(s):  
Qiangyuan Zhu ◽  
Yichi Niu ◽  
Michael Gundry ◽  
Kuanwei Sheng ◽  
Muchun Niu ◽  
...  
Keyword(s):  
Dna Damage ◽  
Single Cell ◽  
Genome Stability ◽  
De Novo ◽  
Single Cells ◽  
Human Cells ◽  
Single Nucleotide Variants ◽  
Genome Wide ◽  
First Time

AbstractIn the studies of single-cell genomics, the large endeavor has been focused on the detection of the permanent changes in the genome. On the other hand, spontaneous DNA damage frequently occurs and results in transient single-stranded changes to the genome until they are repaired. So far, successful profiling of these dynamic changes has not been demonstrated by single-cell whole-genome amplification methods. Here we reported a novel single-cell WGA method: Linearly Produced Semiamplicon based Split Amplification Reaction (LPSSAR), which allows, for the first time, the genome-wide detection of the DNA damage associated single nucleotide variants (dSNVs) in single human cells. The sequence-based detection of dSNVs allows the direct characterization of the major damage signature that occurred in human cells. In the analysis of the abundance of dSNVs along the genome, we observed two modules of dSNV abundance, instead of a homogeneous abundance of dSNVs. Interestingly, we found that the two modules are associated with the A/B topological compartments of the genome. This result suggests that the genome topology directly influences genome stability. Furthermore, with the detection of a large number of dSNVs in single cells, we showed that only under a stringent filtering condition, can we distinguish the de novo mutations from the dSNVs and achieve a reliable estimation of the total level of de novo mutations in a single cell.

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