Dataset Information

Draft sequences of the radish (Raphanus sativus L.) genome.

ABSTRACT: Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes 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) for a 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.

SUBMITTER: Kitashiba H

PROVIDER: S-EPMC4195494 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

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Draft sequences of the radish (Raphanus sativus L.) genome.

Kitashiba Hiroyasu H Li Feng F Hirakawa Hideki H Kawanabe Takahiro T Zou Zhongwei Z Hasegawa Yoichi Y Tonosaki Kaoru K Shirasawa Sachiko S Fukushima Aki A Yokoi Shuji S Takahata Yoshihito Y Kakizaki Tomohiro T Ishida Masahiko M Okamoto Shunsuke S Sakamoto Koji K Shirasawa Kenta K Tabata Satoshi S Nishio Takeshi T

DNA research : an international journal for rapid publication of reports on genes and genomes 20140516 5

Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes 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) for a radish inbred line, and 76,592 scaffolds of ≥ 300 bp were con ...[more]

PMID: 24848699

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Project description:Radish (Raphanus sativus L., 2n?=?2x?=?18) is a major root vegetable crop especially in eastern Asia. Radish root contains various nutritions which play an important role in strengthening immunity. Repetitive elements are primary components of the genomic sequence and the most important factors in genome size variations in higher eukaryotes. To date, studies about repetitive elements of radish are still limited. To better understand genome structure of radish, we undertook a study to evaluate the proportion of repetitive elements and their distribution in radish.We conducted genome-wide characterization of repetitive elements in radish with low coverage genome sequencing followed by similarity-based cluster analysis. Results showed that about 31% of the genome was composed of repetitive sequences. Satellite repeats were the most dominating elements of the genome. The distribution pattern of three satellite repeat sequences (CL1, CL25, and CL43) on radish chromosomes was characterized using fluorescence in situ hybridization (FISH). CL1 was predominantly located at the centromeric region of all chromosomes, CL25 located at the subtelomeric region, and CL43 was a telomeric satellite. FISH signals of two satellite repeats, CL1 and CL25, together with 5S rDNA and 45S rDNA, provide useful cytogenetic markers to identify each individual somatic metaphase chromosome. The centromere-specific histone H3 (CENH3) has been used as a marker to identify centromere DNA sequences. One putative CENH3 (RsCENH3) was characterized and cloned from radish. Its deduced amino acid sequence shares high similarities to those of the CENH3s in Brassica species. An antibody against B. rapa CENH3, specifically stained radish centromeres. Immunostaining and chromatin immunoprecipitation (ChIP) tests with anti-BrCENH3 antibody demonstrated that both the centromere-specific retrotransposon (CR-Radish) and satellite repeat (CL1) are directly associated with RsCENH3 in radish.Proportions of repetitive elements in radish were estimated and satellite repeats were the most dominating elements. Fine karyotyping analysis was established which allow us to easily identify each individual somatic metaphase chromosome. Immunofluorescence- and ChIP-based assays demonstrated the functional significance of satellite and centromere-specific retrotransposon at centromeres. Our study provides a valuable basis for future genomic studies in radish.

Project description:Floral induction that initiates bolting and flowering is crucial for reproductive fitness in radishes. CONSTANS-like (CO-like, COL) genes play an important role in the circadian clock, which ensures regular development through complicated time-keeping mechanisms. However, the specific biological and functional roles of each COL transcription factor gene in the radish remain unknown. In this study, we performed a genome-wide identification of COL genes in the radish genome of three cultivars including 'Aokubi', 'kazusa' and 'WK10039', and we analyzed their exon-intron structure, gene phylogeny and synteny, and expression levels in different tissues. The bioinformatics analysis identified 20 COL transcription factors in the radish genome, which were divided into three subgroups (Group I to Group III). RsaCOL-09 and RsaCOL-12 might be tandem duplicated genes, whereas the others may have resulted from segmental duplication. The Ka/Ks ratio indicated that all the COL genes in radish, Arabidopsis, Brassica rapa, Brassica oleracea, Capsella rubella and rice were under purifying selection. We identified 6 orthologous and 19 co-orthologous COL gene pairs between the radish and Arabidopsis, and we constructed an interaction network among these gene pairs. The expression values for each COL gene during vegetable and flower development showed that the majority of Group I members had similar expression patterns. In general, the expression of radish COL genes in Groups I and III decreased during development, whereas the expression of radish COL genes in Group II first increased and then decreased. Substantial numbers of radish COL genes were differentially expressed after vernalization treatment. The expression levels of RsaCOL-02 and RsaCOL-04 were significantly increased during vernalization treatment, while the expression of RsaCOL-10 was significantly decreased. These outcomes provide insights for improving the genetic control of bolting and flowering in radish and other root vegetable crops, and they facilitate genetic improvements to radish yields and quality.

Project description:Radish (Raphanus sativus L.) belongs to the family Brassicaceae, and is an economically important root crop grown worldwide. Flowering is necessary for plant propagation, but it is also an important agronomic trait influencing R. sativus fleshy taproot yield and quality in the case of an imbalance between vegetative and reproductive growth. There is currently a lack of detailed information regarding the pathways regulating the flowering genes or their evolution in R. sativus. The release of the R. sativus genome sequence provides an opportunity to identify and characterize the flowering genes using a comparative genomics approach.We identified 254 R. sativus flowering genes based on sequence similarities and analyses of syntenic regions. The genes were unevenly distributed on the various chromosomes. Furthermore, we discovered the existence of R. sativus core function genes in the flowering regulatory network, which revealed that basic flowering pathways are relatively conserved between Arabidopsis thaliana and R. sativus. Additional comparisons with Brassica oleracea and Brassica rapa indicated that the retained flowering genes differed among species after genome triplication events. The R. sativus flowering genes were preferentially retained, especially those associated with gibberellin signaling and metabolism. Moreover, analyses of selection pressures suggested that the genes in vernalization and autonomous pathways were more variable than the genes in other R. sativus flowering pathways.Our results revealed that the core flowering genes are conserved between R. sativus and A. thaliana to a certain extent. Moreover, the copy number variation and functional differentiation of the homologous genes in R. sativus increased the complexity of the flowering regulatory networks after genome polyploidization. Our study provides an integrated framework for the R. sativus flowering pathways and insights into the evolutionary relationships between R. sativus flowering genes and the genes from A. thaliana and close relatives.

Dataset Information

Draft sequences of the radish (Raphanus sativus L.) genome.

Publications

Draft sequences of the radish (Raphanus sativus L.) genome.

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