Whole genome sequencing data of Oryza sativa L. cv. Takanari

Oryza sativa L. ‘Takanari’ is one of the most productive indica cultivars [1,2]. Reciprocal chromosome segment substitution lines (CSSLs) derived from a cross between ‘Koshihikari’ and ‘Takanari’ are useful tools for the detection and precise mapping of target quantitative trait loci (QTL) in ‘Takanari’. Although the available Os-Nipponbare-Reference-IRGSP-1.0 reference genome is available and useful for evaluating genetic diversity among japonica cultivars, it is not always useful for evaluating genetic diversity harbored by indica cultivars such as ‘Takanari’. To reveal sequence variants in ‘Takanari’ and to exploit these variants in rice breeding programs, the whole genome of ‘Takanari’ was sequenced using a combination of Illumina HiSeq X Ten (20,983,495 reads and %GC 43) and PacBio (2,847,220 high-quality subreads). NGS data obtained have been deposited in the DNA Data Bank of Japan (DDBJ) under accession number DRA007557.


a b s t r a c t
Oryza sativa L. 'Takanari' is one of the most productive indica cultivars [1,2]. Reciprocal chromosome segment substitution lines (CSSLs) derived from a cross between 'Koshihikari' and 'Takanari' are useful tools for the detection and precise mapping of target quantitative trait loci (QTL) in 'Takanari'. Although the available Os-Nipponbare-Reference-IRGSP-1.0 reference genome is available and useful for evaluating genetic diversity among japonica cultivars, it is not always useful for evaluating genetic diversity harbored by indica cultivars such as 'Takanari'. To reveal sequence variants in 'Takanari' and to exploit these variants in rice breeding programs, the whole genome of 'Takanari' was sequenced using a combination of Illumina HiSeq X Ten (20,983,495 reads and %GC 43) and PacBio (2,847,220 high-quality subreads). NGS data obtained have been deposited in the DNA Data Bank of Japan (DDBJ) under accession number DRA007557.
© 2019 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).

Data
The rice cultivar 'Takanari' [1] is a semi-dwarf and high yielding variety developed in Japan [2]. 'Takanari' has a large sink size with a high spikelet number per panicle, high source ability and high carbohydrate translocation capacity [6].
Although short read sequencing has high accuracy and throughput, it is difficult to resolve repeat sequences and identify complex structural variations. Additional genomic techniques, such as longread sequencing [7], are required for detailed characterization of complex genomic regions in rice genomes [4]. This article reports publicly available whole-genome sequences of 'Takanari' with single molecule, real-time (SMRT) and short-read sequencing technologies. Using PacBio SMRT technology, we produced 25.6 Gb of long-read sequencing raw data with 68 Â coverage. Using Illumina paired-end whole-genome shotgun sequencing technology, we generated 6.3 Gb of short-read sequencing data from a 150 bp paired-end library with coverage of 16 Â coverage.
The whole-genome sequences reported in this study will be useful for the genetic improvement of rice, by allowing the genetics of the superior agronomic characteristics of 'Takanari' to be investigated.

Plant materials
In 2017, Oryza sativa L. 'Takanari' plants were cultivated in a growth chamber (SANYO MLR-351H) at the National Agriculture and Food Research Organization in Tsukuba, Ibaraki, Japan.

DNA extraction and quality control
Genomic DNA was extracted from the leaf blade of Oryza sativa L. 'Takanari' using Tiagen Plant Genomic DNA Kit (TIAGEN, China) following the manufacturer's instructions. Quality and quantity of DNA were checked by agarose gel electrophoresis and Qubit Fluorimeter (Thermo Fisher Scientific Inc., USA).

Library preparation and sequencing
The extracted genomic DNA was prepared using SMRTbellTM and TruSeq Nano DNA Library preparation methods. For the PacBio Sequel System, SMRTbell TM libraries were prepared following the manufacturer's protocol, Template Preparation and Sequencing Guide (2010e2014) (Pacific Biosciences of California, CA, USA). For HiSeq X Ten, the TruSeq Nano DNA Library was generated using Specifications Value of the data Genomic data of high-yielding cultivar 'Takanari' can be useful for identifying genes/quantitative trait loci (QTL) [3]. The data will help to resolve complex repetitive regions, long indels, and structural variants harbored by Oryza sativa L. [5]. The data is valuable for those working on crop improvement.
the Truseq Nano DNA HT Sample Preparation Kit (Illumina USA) following the manufacturer's recommendations.