TY - JOUR
T1 - Draft Sequences of the Radish (Raphanus sativus L.) Genome
AU - Hiroyasu, Kitashiba
AU - Feng, Li
AU - Hideki, Hirakawa
AU - Takahiro, Kawanabe
AU - Zhongwei, Zou
AU - Yoichi, Hasegawa
AU - Kaoru, Tonosaki
AU - Sachiko, Shirasawa
AU - Aki, Fukushima
AU - Shuji, Yokoi
AU - Takahata, Yoshihito
AU - Tomohiro, Kakizaki
AU - Masahiko, Ishida
AU - Shunsuke, Okamoto
AU - Koji, Sakamoto
AU - Kenta, Shirasawa
AU - Satoshi, Tabata
AU - Nishio, Takeshi
N1 - Publisher Copyright:
© The Author 2014.
PY - 2014/10/1
Y1 - 2014/10/1
N2 - Radish (Raphanussativus L., n = 9) is one of the major vegetables in Asia. Since thegenomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) fora radish inbred line, and 76,592 scaffolds of ≥300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified.
AB - Radish (Raphanussativus L., n = 9) is one of the major vegetables in Asia. Since thegenomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) fora radish inbred line, and 76,592 scaffolds of ≥300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified.
KW - Draft sequence
KW - High-density genetic map
KW - Radish
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U2 - 10.1093/dnares/dsu014
DO - 10.1093/dnares/dsu014
M3 - Article
C2 - 24848699
AN - SCOPUS:84922020423
VL - 21
SP - 481
EP - 490
JO - DNA Research
JF - DNA Research
SN - 1340-2838
IS - 5
ER -