Would an RRS by any other name sound as RAD

作者: Erin O Campbell , Bryan M T Brunet , Julian R Dupuis , Felix A H Sperling

DOI: 10.1101/283085

关键词:

摘要: Sampling markers throughout a genome with restriction enzymes emerged in the 2000s as reduced representation shotgun sequencing (RRS). Rapid advances technology have since spurred modifications of RRS, giving rise to many derivatives unique names, such RADseq. But naming conventions often been more creative than consistent, unclear criteria for recognition method resulting proliferation names characterized by ambiguity. We conducted literature review assess methodological and etymological relationships among 36 enzyme-based methods, well rates correct referencing commonly-used methods. identify several instances convergence or misattribution literature, note that published modified only minor elements parent protocols. urge greater restraint derivative strike better balance between clarity, scientific innovation, attribution.

参考文章(51)
Hans Recknagel, Arne Jacobs, Pawel Herzyk, Kathryn R. Elmer, Double-digest RAD sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with nonmodel organisms. Molecular Ecology Resources. ,vol. 15, pp. 1316- 1329 ,(2015) , 10.1111/1755-0998.12406
Erwin L. van Dijk, Yan Jaszczyszyn, Claude Thermes, Library preparation methods for next-generation sequencing: Tone down the bias Experimental Cell Research. ,vol. 322, pp. 12- 20 ,(2014) , 10.1016/J.YEXCR.2014.01.008
Qiang Chen, Yufang Ma, Yumei Yang, Zhenliang Chen, Rongrong Liao, Xiaoxian Xie, Zhen Wang, Pengfei He, Yingying Tu, Xiangzhe Zhang, Changsuo Yang, Hongjie Yang, Fuqing Yu, Youmin Zheng, Zhiwu Zhang, Qishan Wang, Yuchun Pan, Genotyping by genome reducing and sequencing for outbred animals. PLOS ONE. ,vol. 8, ,(2013) , 10.1371/JOURNAL.PONE.0067500
Xiaowen Sun, Dongyuan Liu, Xiaofeng Zhang, Wenbin Li, Hui Liu, Weiguo Hong, Chuanbei Jiang, Ning Guan, Chouxian Ma, Huaping Zeng, Chunhua Xu, Jun Song, Long Huang, Chunmei Wang, Junjie Shi, Rui Wang, Xianhu Zheng, Cuiyun Lu, Xiaowu Wang, Hongkun Zheng, SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing PLoS ONE. ,vol. 8, pp. e58700- ,(2013) , 10.1371/JOURNAL.PONE.0058700
Robert J. Toonen, Jonathan B. Puritz, Zac H. Forsman, Jonathan L. Whitney, Iria Fernandez-Silva, Kimberly R. Andrews, Christopher E. Bird, ezRAD: a simplified method for genomic genotyping in non-model organisms PeerJ. ,vol. 1, ,(2013) , 10.7717/PEERJ.203
Shi Wang, Eli Meyer, John K McKay, Mikhail V Matz, 2b-RAD: a simple and flexible method for genome-wide genotyping Nature Methods. ,vol. 9, pp. 808- 810 ,(2012) , 10.1038/NMETH.2023
Humira Sonah, Maxime Bastien, Elmer Iquira, Aurélie Tardivel, Gaétan Légaré, Brian Boyle, Éric Normandeau, Jérôme Laroche, Stéphane Larose, Martine Jean, François Belzile, An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLOS ONE. ,vol. 8, ,(2013) , 10.1371/JOURNAL.PONE.0054603
Carly F. Graham, Travis C. Glenn, Andrew G. McArthur, Douglas R. Boreham, Troy Kieran, Stacey Lance, Richard G. Manzon, Jessica A. Martino, Todd Pierson, Sean M. Rogers, Joanna Y. Wilson, Christopher M. Somers, Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq). Molecular Ecology Resources. ,vol. 15, pp. 1304- 1315 ,(2015) , 10.1111/1755-0998.12404
Hoa T. Truong, A. Marcos Ramos, Feyruz Yalcin, Marjo de Ruiter, Hein J. A. van der Poel, Koen H. J. Huvenaars, René C. J. Hogers, Leonora. J. G. van Enckevort, Antoine Janssen, Nathalie J. van Orsouw, Michiel J. T. van Eijk, Sequence-Based Genotyping for Marker Discovery and Co-Dominant Scoring in Germplasm and Populations PLoS ONE. ,vol. 7, pp. e37565- ,(2012) , 10.1371/JOURNAL.PONE.0037565