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

Revision as of 16:04, 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.

The researchers sequenced the whole genome of Kasalath rice by using two NGS platforms, Illumina (GAIIx and HiSeq2000) for short

reads and Roche 454 (GS FLX Titanium and GS FLXþ Titanium) for long reads.

The researchers performed de novo assembly and chromosomal mapping of the NGS read seq sequences.
The researchers carried out the transcriptome analysis with RNA-Seq data obtained from young leaves and panicles of Kasalath by using the GAIIx for annotation of expressed sequences.
Comparative analysis oftheKasalathsequenceandthoseofotherricecultivars confirmed its value as a new reference genome to facilitate future evolutionary and functional genomic studies in rice.

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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 ==Plant Culture & Treatment==
-*Total genomic DNA of Kasalath was extracted from young leaves of a singleplant by using the cetyltrimethylammonium bromide method
+*The researchers sequenced the whole genome of Kasalath rice by using two NGS platforms, Illumina (GAIIx and HiSeq2000) for short
-*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.
+reads and Roche 454 (GS FLX Titanium and GS FLXþ Titanium) for long reads.
-*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.
+*The researchers performed de novo assembly and chromosomal mapping of the NGS read seq sequences.
+*The researchers carried out the transcriptome analysis with RNA-Seq data obtained from young leaves and panicles of Kasalath by using the GAIIx for annotation of expressed sequences.
+*Comparative analysis oftheKasalathsequenceandthoseofotherricecultivars confirmed its value as a new reference genome to facilitate future evolutionary and functional genomic studies in rice.
 ==Research Findings==