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Research article
Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance
Su Ryun Choi
Chungnam National University College of Agriculture and Life Sciences
Corresponding Author
ORCiD: https://orcid.org/0000-0002-1401-9875
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This work is licensed under a CC BY 4.0 License. Read Full License
Background: The nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several species, the evolution, structure, expression, and function of these genes remain unknown in radish (Raphanus sativus L.). A recently released draft R. sativus L. reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish.
Results: A total of 225 NBS-encoding genes were identified in the radish genome based on the essential NB-ARC domain through HMM search and Pfam database, with 202 mapped onto nine chromosomes and the remaining 23 localized on different scaffolds. According to a gene structure analysis, we identified 99 NBS-LRR-type genes and 126 partial NBS-encoding genes. Additionally, 80 and 19 genes respectively encoded an N-terminal Toll/interleukin-like domain and a coiled-coil domain. Furthermore, 72% of the 202 NBS-encoding genes were grouped in 48 clusters distributed in 24 crucifer blocks on chromosomes. The U block on chromosomes R02, R04, and R08 had the most NBS-encoding genes (48), followed by the R (24), D (23), E (23), and F (17) blocks. These clusters were mostly homogeneous, containing NBS-encoding genes derived from a recent common ancestor. Tandem (15 events) and segmental (20 events) duplications were revealed in the NBS family. Comparative evolutionary analyses of orthologous genes among Arabidopsis thaliana, Brassica rapa, and Brassica oleracea reflected the importance of the NBS-LRR gene family during evolution. Moreover, examinations of cis-elements identified 70 major elements involved in responses to methyl jasmonate, abscisic acid, auxin, and salicylic acid. According to RNA-seq expression analyses, 75 NBS-encoding genes contributed to the resistance of radish to Fusarium wilt. A quantitative real-time PCR analysis revealed that RsTNL03 (Rs093020) and RsTNL09 (Rs042580) expression positively regulates radish resistance to Fusarium oxysporum, in contrast to the negative regulatory role for RsTNL06 (Rs053740).
Conclusions: The NBS-encoding gene structures, tandem and segmental duplications, synteny, and expression profiles in radish were elucidated for the first time and compared with those of other Brassicaceae family members (A. thaliana, B. oleracea, and B. rapa) to clarify the evolution of the NBS gene family. These results may be useful for functionally characterizing NBS-encoding genes in radish.
Keywords
Raphanus sativus L., NBS-encoding gene, gene duplication, evolution, synteny, Fusarium oxysporum
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This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1.xlsx
Additional file 1: Table S1: Information regarding the radish NBS-LRR genes Additional file 1: Table S2: Clusters of radish NBS-LRR genes Additional file 1: Table S3: Predicted promoter elements of NBS-encoding genes in the radish genome Additional file 1: Table S4: Analysis and distribution of conserved motifs in radish CNL and TNL proteins Additional file 1: Table S5: MEME analysis of the CNL and TNL proteins Additional file 1: Table S6: Tandem arrays of the radish NBS-LRR genes Additional file 1: Table S7: Segmentally duplicated radish NBS-LRR genes Additional file 1: Table S8: Ka/Ks values for the segmentally duplicated genes in the radish genome Additional file 1: Table S9: Segmentally duplicated NBS-LRR genes in the radish/A. thaliana, radish/B. oleracea, and radish/B. rapa genomes Additional file 1: Table S10: Common segmentally duplicated NBS-LRR genes in the radish/A. thaliana, radish/B. oleracea, and radish/B. rapa genomes Additional file 1: Table S11: Ka/Ks values between radish and three related plant species Additional file 1: Table S12: The information for gene structure and domain change of radish/A. thaliana, radish/B. oleracea, and radish/B. rapa genomes Additional file 1: Table S13: The resistance of radish lines to F. oxysporum f. sp. Raphani 59 Additional file 1: Table S14: The summary of the RNA-Seq database Additional file 1: Table S15: Details regarding the qRT-PCR primers Additional file 1: Table S16: The transcriptome data of the radish lines after inoculated with F. oxysporum f. sp. Raphani 59
- Additionalfile2Fig.1.tif
Additional file 2: Fig. 1 Distribution of TNL, CNL, and partial genes. Distributions for each class are presented across the radish chromosomes. RUS, scaffold summary. Bars are divided into CNL genes (orange), TNL genes (blue), and partial genes (green)
- Additionalfile3Fig.2.tif
Additional file 3: Fig. 2: Phylogenetic tree representing the relationships among radish NBS-encoding genes. Different colored arcs represent the different groups (or subgroups) of NBS-encoding genes.
- Additionalfile4Fig.3.tif
Additional file 4: Fig. 3: Relative expression levels of RsCNL and RsTNL radish genes. The ‘YR4’ (resistant) and ‘YR18’ (susceptible) lines are represented by white and gray bars, respectively. The y-axis represents the relative gene expression levels, whereas the time-points (0, 1, 3, 6, 9, and 12 DAI) are presented on the x-axis.
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This preprint is under consideration at BMC Plant Biology. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance
Su Ryun Choi
Chungnam National University College of Agriculture and Life Sciences
Corresponding Author
ORCiD: https://orcid.org/0000-0002-1401-9875
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
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Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 5
Posted 23 Dec, 2020
No community comments so far
Editor assigned
On 08 Dec, 2020
Submission checks complete
On 08 Dec, 2020
Editor invited
On 08 Dec, 2020
No comments provided
Editor assigned
On 02 Dec, 2020
Submission checks complete
On 02 Dec, 2020
Editor invited
On 02 Dec, 2020
No comments provided
Submission checks complete
On 21 Nov, 2020
Editorial decision: Minor revision
On 18 Nov, 2020
No comments provided
Review #1 received
Received 01 Nov, 2020
Reviewer #1 agreed
On 26 Oct, 2020
Reviewer #2 agreed
On 26 Oct, 2020
Editor assigned
On 25 Oct, 2020
Reviewers invited
Invitations sent on 25 Oct, 2020
Submission checks complete
On 24 Oct, 2020
Editor invited
On 24 Oct, 2020
No comments provided
Editorial decision: Major revision
On 17 Sep, 2020
Review #2 received
Received 03 Sep, 2020
Review #1 received
Received 27 Aug, 2020
Reviewer #3 agreed
On 15 Aug, 2020
Reviewer #2 agreed
On 13 Aug, 2020
Reviewer #1 agreed
On 11 Aug, 2020
Reviewers invited
Invitations sent on 10 Aug, 2020
Editor invited
On 31 Jul, 2020
Editor assigned
On 27 Jul, 2020
Submission checks complete
On 26 Jul, 2020
First submitted
On 24 Jul, 2020
Metrics
Comments: 0
PDF Downloads: ...
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License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: The nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several species, the evolution, structure, expression, and function of these genes remain unknown in radish (Raphanus sativus L.). A recently released draft R. sativus L. reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish.
Results: A total of 225 NBS-encoding genes were identified in the radish genome based on the essential NB-ARC domain through HMM search and Pfam database, with 202 mapped onto nine chromosomes and the remaining 23 localized on different scaffolds. According to a gene structure analysis, we identified 99 NBS-LRR-type genes and 126 partial NBS-encoding genes. Additionally, 80 and 19 genes respectively encoded an N-terminal Toll/interleukin-like domain and a coiled-coil domain. Furthermore, 72% of the 202 NBS-encoding genes were grouped in 48 clusters distributed in 24 crucifer blocks on chromosomes. The U block on chromosomes R02, R04, and R08 had the most NBS-encoding genes (48), followed by the R (24), D (23), E (23), and F (17) blocks. These clusters were mostly homogeneous, containing NBS-encoding genes derived from a recent common ancestor. Tandem (15 events) and segmental (20 events) duplications were revealed in the NBS family. Comparative evolutionary analyses of orthologous genes among Arabidopsis thaliana, Brassica rapa, and Brassica oleracea reflected the importance of the NBS-LRR gene family during evolution. Moreover, examinations of cis-elements identified 70 major elements involved in responses to methyl jasmonate, abscisic acid, auxin, and salicylic acid. According to RNA-seq expression analyses, 75 NBS-encoding genes contributed to the resistance of radish to Fusarium wilt. A quantitative real-time PCR analysis revealed that RsTNL03 (Rs093020) and RsTNL09 (Rs042580) expression positively regulates radish resistance to Fusarium oxysporum, in contrast to the negative regulatory role for RsTNL06 (Rs053740).
Conclusions: The NBS-encoding gene structures, tandem and segmental duplications, synteny, and expression profiles in radish were elucidated for the first time and compared with those of other Brassicaceae family members (A. thaliana, B. oleracea, and B. rapa) to clarify the evolution of the NBS gene family. These results may be useful for functionally characterizing NBS-encoding genes in radish.
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