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Barbara Gilmore, Nahla Bassil, April Nyberg, Brian Knaus, Don Smith, Danny L. Barney, and Kim Hummer

labor-intensive and ultimately yields low numbers of SSRs. Next generation sequencing (NGS) platforms termed “next generation” or “massively parallel” were recently developed. These platforms are changing genomic discovery in plants, delivering large

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Michael Dossett, Jill M. Bushakra, Barbara Gilmore, Carol A. Koch, Chaim Kempler, Chad E. Finn, and Nahla V. Bassil

next-generation, sequencing technology has been a boon to the development of molecular markers and genomic resources for many plant species. Perhaps nowhere has this benefit been realized more than in the study of nonmodel organisms for which research

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Misaki Ishibashi, Takeshi Nabe, Yoko Nitta, and Yuichi Uno

analysis, has been greatly accelerated by RNA sequencing (RNA-seq) with the advent of next-generation sequencing (NGS) technologies. Selection of suitable methods for isolating and purifying RNA is thus dependent on the type of downstream assay(s) that will

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Gehendra Bhattarai and Shawn A. Mehlenbacher

from binary data for 192 simple sequence repeat markers. Discussion The high throughput and low cost of next-generation sequencing allows plant genomes to be sequenced and SSR markers to be developed efficiently as a by-product of genome sequencing. In

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Michael J. Havey and Yul-Kyun Ahn

). Individual colonies were picked using blue-white selection, plasmids purified, and 2500 random inserts were Sanger sequenced from the 5′ end as previously described ( Kuhl et al., 2004 ). For next-generation sequencing, plasmids were purified through CsCl

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Zehuang Zhang, Qihua Lin, and Qiuzhen Zhong

phenomenon was not clear. In recent years, transcriptome sequencing technology using RNA-seq, which is based on next-generation sequencing, has been widely used in a range of research fields and can provide a quick and convenient method to establish the basic

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Min Wang, Wenrui Liu, Biao Jiang, Qingwu Peng, Xiaoming He, Zhaojun Liang, and Yu’e Lin

to powdery mildew were identified by combining BSA and SLAF-Seq ( Zhang et al., 2015 ). Furthermore, a major QTL controlling early flowering in cucumber was discovered using next-generation sequencing ( Lu et al., 2014 ). Therefore, in our study, we

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Daofeng Liu, Jing Ma, Jianfeng Yang, Tien V. Nguyen, Huamin Liu, Renwei Huang, Shunzhao Sui, and Mingyang Li

/indels were identified from the transcriptomic database. Next-generation transcriptome sequencing leads to superior resources for the development of such markers not only because of the vast amount of sequence information from which markers can be identified

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Barbara S. Gilmore, Nahla V. Bassil, Danny L. Barney, Brian J. Knaus, and Kim E. Hummer

species of little economic importance (reviewed in Zalapa et al., 2012 ). For example, DNA sequencing using next-generation sequencing technology (Ilumina platform ® ; Ilumina, San Diego, CA) allowed development of polymorphic SSR markers for alaska

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Zhiyong Wang, Paul Raymer, and Zhenbang Chen

transcriptome sequencing for species without reference sequences ( Hearnden et al., 2007 ). Mulkey et al. (2014) developed 215 primer pairs of S. secundatum using an Illumina Genome Analyzer. The most common SSR methods for isolation using next generation