Difference between revisions of "IC4R009-Genome-2014-24578372"

Revision as of 15:51, 26 June 2016

Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice

The researchers describe deep whole-genome sequencing of the aus rice cultivar Kasalath by using the advanced next-generation sequencing (NGS) technologies to gain a better understanding of the sequence and structural changes among highly differentiated cultivars.
the reference Nipponbare sequence is particularly useful for evolutionary and functional studies, its use for extensive analysis of genome diversity remains limited because of considerable inter- and intra-species and even intrasubspecies chromosomal rearrangements, such as insertionsanddeletions,duplications,inversions,translocations, and transpositions.

Total genomic DNA of Kasalath was extracted from young leaves of a singleplant by using the cetyltrimethylammonium bromide method
The researchers constructed DNA libraries with insert sizes of 800–1500 bp according to standard manufacturer’s protocols (http://www.454.com/; Basel, Switzerland) to generate long-read sequencesbyusing Roche454 pyrosequencing technology (GS-FLX Titanium and GS-FLXþ platforms) as described previously.
The researchers also constructed libraries with insert sizes of 250–400 bp according to the manufacturer’s instructions (Illumina, San Diego, CA, USA) to produce short single or paired-end reads on the Illumina GAIIx or HiSeq 2000 platforms.

Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan *Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
Department of Bioscience, Faculty of Applied Bioscience,Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan.

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 ==The Background of This Project==
 *The researchers describe deep whole-genome sequencing of the aus rice cultivar Kasalath by using the advanced next-generation sequencing (NGS) technologies to gain a better understanding of the sequence and structural changes among highly differentiated cultivars.
+*the reference Nipponbare sequence is particularly useful for evolutionary and functional studies, its use for extensive analysis of genome diversity remains limited because of considerable inter- and intra-species and even intrasubspecies chromosomal rearrangements, such as insertionsanddeletions,duplications,inversions,translocations, and transpositions.
 ==Plant Culture & Treatment==