BENCHMARKS Overall, good control of DNA shearing
allows flexible coordination between library insert length and read length to maximize the efficiency of mate-pair sequencing. This coordination has a large impact on the proportion of reads recognized as true mates and their contribution to scaffolding that depends on read lengths, in addition to the cost of sequencing reagents. Most importantly, we propose a new cost-saving scheme for library preparation (allowing for approximately 1/3 the current cost) that does not require the purchase of additional commercial products or laborious preparation of self-made items (as described in Reference 10), except for the tagment buffer. The mate-pair reads from this
study have been deposited in the NCBI Sequence Read Archive (SRA) under BioProject ID PRJDB3317. The genome sequences of the Madagascar ground gecko after scaffolding will be released in a designated database, after sequencing more reads and rebuilding scaffolds, which will be announced on our laboratory web site (
www.clst.riken. jp/phylo/
imate.html).
Author contributions
K.T., C.T., K.I., O.N., and S.K. conceived the original idea of the study. K.T. carried out the experiments, and S.K., O.N., and K.T. analyzed the data. K.T., C.T., K.I., O.N., and S.K. edited the manuscript. S.K. supervised the project.
Acknowledgments
We thank all other members of GRAS, the sequencing core of RIKEN Kobe Institute in the Biosystem Dynamics Group, RIKEN CLST, for insightful discussion as well as Eriko Kajikawa, Shinichi Aizawa, Yasuhide Furuta, and Hiroshi Kiyonari in the Biosystem Dynamics Group, RIKEN CLST, for the supply of animal materials. Our gratitude extends to Helen Gunter, Yuichiro Hara, Sean Keeley, and Mitsutaka Kadota for critical reading of the manuscript.
Competing interests The authors declare no competing interests.
References
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N.Nath, J.L. Froula,A. Clum, T. Zhang, J. Cheng,A.C. Copeland, et al. 2012. Generation of long insert pairs using a Cre-loxP inverse PCR approach. PLoS ONE 7:e29437.
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Received 28 October 2014; accepted 24 February 2015.
Address correspondence to Shigehiro Kuraku, Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Japan. E-mail: shigehiro.
kuraku@riken.jp
To purchase reprints of this article, contact:
biotechniques@fosterprinting.com
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