scholarly journals Next-generation sequencing: a powerful tool for the discovery of molecular markers in breast ductal carcinomain situ

2013 ◽  
Vol 13 (2) ◽  
pp. 151-165 ◽  
Author(s):  
Hitchintan Kaur ◽  
Shihong Mao ◽  
Seema Shah ◽  
David H Gorski ◽  
Stephen A Krawetz ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Ductal Carcinomain Situ ◽  
Carcinomain Situ ◽  
Generation Sequencing

Molecular marker information from de novo assembled transcriptomes of chilli pepper (Capsicum annuum L.) varieties based on next-generation sequencing technology

2014 ◽  
Vol 12 (S1) ◽  
pp. S83-S86 ◽  
Author(s):  
Yul-Kyun Ahn ◽  
Swati Tripathi ◽  
Young-Il Cho ◽  
Jeong-Ho Kim ◽  
Hye-Eun Lee ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Sequence Variant ◽  
Nucleotide Polymorphisms ◽  
Next Generation ◽  
Chilli Pepper ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

Development of soybean aphid genomic SSR markers using next generation sequencing

Genome ◽  
2011 ◽  
Vol 54 (5) ◽  
pp. 360-367 ◽  
Author(s):  
Tae-Hwan Jun ◽  
Andrew P. Michel ◽  
M.A. Rouf Mian
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
Ssr Markers ◽  
The United States ◽  
Soybean Aphid ◽  
Genomic Sequences ◽  
Next Generation ◽  
Soybean Aphids ◽  
Genomic Ssr ◽  
Generation Sequencing

Simple sequence repeats (SSRs) or microsatellites are very useful molecular markers, owing to their locus-specific codominant and multiallelic nature, high abundance in the genome, and high rates of transferability across species. The soybean aphid ( Aphis glycines Matsumura) has become the most damaging insect pest of soybean ( Glycine max (L.) Merr.) in North America, since it was first found in the Midwest of the United States in 2000. Biotypes of the soybean aphid capable of colonizing newly developed aphid-resistant soybean cultivars have been recently discovered. Genetic resources, including molecular markers, to study soybean aphids are severely lacking. Recently developed next generation sequencing platforms offer opportunities for high-throughput and inexpensive genome sequencing and rapid marker development. The objectives of this study were (i) to develop and characterize genomic SSR markers from soybean aphid genomic sequences generated by next generation sequencing technology and (ii) to evaluate the utility of the SSRs for genetic diversity or relationship analyses. In total 128 SSR primer pairs were designed from sequences generated by Illumina GAII from a reduced representation library of A. glycines. Nearly 94% (120) of the primer pairs amplified SSR alleles of expected size and 24 SSR loci were polymorphic among three aphid samples from three populations. The polymorphic SSRs were successfully used to differentiate among 24 soybean aphids from Ohio and South Dakota. Sequencing of PCR products of two SSR markers from four aphid samples revealed that the allelic polymorphism was due to variation in the SSR repeats among the aphids. These markers should be particularly useful for genetic differentiation among aphids collected from soybean fields at different localities and regions. These SSR markers provide the soybean aphid research community with the first set of PCR-based codominant markers developed from the genomic sequences of A. glycines.

scholarly journals Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing

2015 ◽  
Vol 35 (4) ◽  
Author(s):  
Zübeyir Devran ◽  
Erdem Kahveci ◽  
Ercan Özkaynak ◽  
David J. Studholme ◽  
Mahmut Tör
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Development of molecular markers for invasive alien plants in Korea: a case study of a toxic weed, Cenchrus longispinus L., based on next generation sequencing data

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7965
Author(s):  
JongYoung Hyun ◽  
Hoang Dang Khoa Do ◽  
Joonhyung Jung ◽  
Joo-Hwan Kim
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
Genomic Data ◽  
Alien Plants ◽  
Next Generation Sequencing Data ◽  
Phylogenomic Analysis ◽  
Next Generation ◽  
Invasive Alien Plants ◽  
Chloroplast Genomes ◽  
Generation Sequencing

Background Genomic data play an important role in plant research because of its implications in studying genomic evolution, phylogeny, and developing molecular markers. Although the information of invasive alien plants was collected, the genomic data of those species have not been intensively studied. Methods We employ the next generation sequencing and PCR methods to explore the genomic data as well as to develop and test the molecular markers. Results In this study, we characterize the chloroplast genomes (cpDNA) of Cenchrus longispinus and C. echinatus, of which the lengths are 137,144 and 137,131 bp, respectively. These two newly sequenced genomes include 78 protein-coding genes, 30 tRNA, and four rRNA. There are 56 simple single repeats and 17 forward repeats in the chloroplast genome of C. longispinus. Most of the repeats locate in non-coding regions. However, repeats can be found in infA, ndhD, ndhH, ndhK, psbC, rpl22, rpoC2, rps14, trnA-UGC, trnC-GCA, trnF-GAA, trnQ-UUG, trnS-UGA, trnS-GCU, and ycf15. The phylogenomic analysis revealed the monophyly of Cenchrus but not Panicum species in tribe Paniceae. The single nucleotide polymorphism sites in atpB, matK, and ndhD were successfully used for developing molecular markers to distinguish C. longispinus and related taxa. The simple PCR protocol for using the newly developed molecular markers was also provided.

scholarly journals Next-generation sequencing reveals clinically actionable molecular markers in myeloid sarcoma

Leukemia ◽  
2015 ◽  
Vol 29 (10) ◽  
pp. 2113-2116 ◽  
Author(s):  
Z Li ◽  
F Stölzel ◽  
K Onel ◽  
M Sukhanova ◽  
M K Mirza ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
Myeloid Sarcoma ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Development of novel SSR molecular markers using a Next-Generation Sequencing approach (ddRADseq) in Stetsonia coryne (Cactaceae)

2021 ◽  
Vol 93 (suppl 3) ◽  
Author(s):  
ANGELA VERÓNICA GUTIÉRREZ ◽  
CARLA VALERIA FILIPPI ◽  
NATALIA CRISTINA AGUIRRE ◽  
ANDREA FABIANA PUEBLA ◽  
CINTIA VANESA ACUÑA ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing
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