Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Tae-Jin YangRod A Wing

Abstract

Rice is an important crop and a model system for monocot genomics, and is a target for whole genome sequencing by the International Rice Genome Sequencing Project (IRGSP). The IRGSP is using a clone by clone approach to sequence rice based on minimum tiles of BAC or PAC clones. For chromosomes 10 and 3 we are using an integrated physical map based on two fingerprinted and end-sequenced BAC libraries to identifying a minimum tiling path of clones. In this study we constructed and tested two rice genomic libraries with an average insert size of 10 kb (10-kb library) to support the gap closure and finishing phases of the rice genome sequencing project. The HaeIII library contains 166,752 clones covering approximately 4.6x rice genome equivalents with an average insert size of 10.5 kb. The Sau3AI library contains 138,960 clones covering 4.2x genome equivalents with an average insert size of 11.6 kb. Both libraries were gridded in duplicate onto 11 high-density filters in a 5 x 5 pattern to facilitate screening by hybridization. The libraries contain an unbiased coverage of the rice genome with less than 5% contamination by clones containing organelle DNA or no insert. An efficient method was developed, consisting of pooled overgo h...Continue Reading

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Citations

Jun 21, 2005·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Tae-Jin YangRod A Wing
Nov 2, 2005·Molecular Genetics and Genomics : MGG·Chia-Hsiung ChengTeh-Yuan Chow
Dec 8, 2006·Nucleic Acids Research·Kavitha MadishettyTimothy J Close
Apr 14, 2012·Journal of Biomedicine & Biotechnology·Ruvini Ariyadasa, Nils Stein
Jul 9, 2004·Journal of Genetics·Akhilesh K TyagiSulabha Sharma
Dec 2, 2015·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Jonghoon LeeTae-Jin Yang

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