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Research Article
Dawn Luthe
The Pennsylvania State University, Plant Science, State College, PA, U.S.A
Corresponding Author
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Background: Jasmonates (JAs) are important for plants to coordinate growth, reproduction, and defense responses. In JA signaling, jasmonate ZIM-domain (JAZ) proteins serve as master regulators at the initial stage of herbivores attacks. Although discovered in many plant species, little in-depth characterization of JAZ gene expression has been reported in the agronomically important crop, maize (Zea mays L.).
Results: In this study 16 JAZ genes from the maize genome were identified and classified. Phylogenetic analyses were performed from maize, rice, sorghum, Brachypodium, and Arabidopsis using deduced protein sequences, total six clades were proposed and conservation was observed in each group, such as similar gene exon/intron structures. Synteny analysis across four monocots indicated these JAZ gene families had a common ancestor, and duplication events in maize genome may drive the expansion of JAZ gene family, including genome-wide duplication (GWD), transposon, and/or tandem duplication. Strong purifying selection acted on all JAZ genes except those in group 4, which were under neutral selection. Further, we cloned three paralogous JAZ gene pairs from two maize inbreds differing in JA levels and insect resistance, and gene polymorphisms were observed between two inbreds.
Conclusions: Here we analyzed the composition and evolution of JAZ genes in maize with three other monocot plants. Extensive phylogenetic and synteny analysis revealed the expansion and selection fate of maize JAZ. This is the first study comparing the difference between two inbreds, and we propose genotype-specific JAZ gene expression might be present in maize plants. Since genetic redundancy in JAZ gene family hampers our understanding of their role in response to specific elicitors, we hope this research could be pertinent to elucidating the defensive responses in plants.
Keywords
Maize, Insect resistance, Jasmonate-ZIM domain, Phylogenetic analysis, Selection
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This is a list of supplementary files associated with this preprint. Click to download.
- SupplementalFigure15.pdf
Supplemental Fig. 1 Exon/intron structure of the corresponding OsJAZ gene. Intron phase numbers were indications of the intron position within a codon: 0, intron not located within a codon (or located between two codons); 1, located between the first and second bases of a codon; 2, located between the second and third bases of a codon Supplemental Fig. 2 Exon/intron structure of the corresponding SbJAZ gene. Intron phase numbers were indications of the intron position within a codon: 0, intron not located within a codon (or located between two codons); 1, located between the first and second bases of a codon; 2, located between the second and third bases of a codon Supplemental Fig. 3 Exon/intron structure of the corresponding BdJAZ gene. Intron phase numbers were indications of the intron position within a codon: 0, intron not located within a codon (or located between two codons); 1, located between the first and second bases of a codon; 2, located between the second and third bases of a codon Supplemental Fig. 4 Sequences logo of the (a) TIFY domain, (b) Jas domain, and (c) N-terminal CMID domains from four grass JAZ genes Supplemental Fig. 5 Distribution of conserved motifs in JAZ proteins. (a) Conserved motifs from maize JAZ proteins. (b) Conserved motifs from JAZ groups 1, 3, and 4 in maize, rice, sorghum, Brachypodium, and Arabidopsis. The conserved motifs with non-overlapping sites (p-value>0.0001) were shown in colored boxes generated by MEME server. TIFY, Jas, and N-terminal CMID motifs were represented in motif 1, 2, and 3, respectively
- SupplementalTable18.xlsx
Supplemental Table 1 List of members of JAZ family in this study Supplemental Table 2 Rice JAZ family Supplemental Table 3 Sorghum JAZ family Supplemental Table 4 Brachypodium JAZ family Supplemental Table 5 Search results from plant repeats database Supplemental Table 6 Primers used in JAZ gDNA cloning Supplemental Table 7 Primers used in JAZ cDNA cloning Supplemental Table 8 Primers used in JAZ PCR of oat-maize addition lines
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This is a preprint, 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
Dawn Luthe
The Pennsylvania State University, Plant Science, State College, PA, U.S.A
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
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Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
Version 1
Posted 21 Jan, 2021
No community comments so far
Editorial decision: Major revision
On 05 Feb, 2021
Reviews received
Received 25 Jan, 2021
Reviewers agreed
On 21 Jan, 2021
Reviewers invited
Invitations sent on 21 Jan, 2021
Editor assigned
On 21 Jan, 2021
Editor invited
On 20 Jan, 2021
Submission checks complete
On 20 Jan, 2021
First submitted
On 09 Jan, 2021
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background: Jasmonates (JAs) are important for plants to coordinate growth, reproduction, and defense responses. In JA signaling, jasmonate ZIM-domain (JAZ) proteins serve as master regulators at the initial stage of herbivores attacks. Although discovered in many plant species, little in-depth characterization of JAZ gene expression has been reported in the agronomically important crop, maize (Zea mays L.).
Results: In this study 16 JAZ genes from the maize genome were identified and classified. Phylogenetic analyses were performed from maize, rice, sorghum, Brachypodium, and Arabidopsis using deduced protein sequences, total six clades were proposed and conservation was observed in each group, such as similar gene exon/intron structures. Synteny analysis across four monocots indicated these JAZ gene families had a common ancestor, and duplication events in maize genome may drive the expansion of JAZ gene family, including genome-wide duplication (GWD), transposon, and/or tandem duplication. Strong purifying selection acted on all JAZ genes except those in group 4, which were under neutral selection. Further, we cloned three paralogous JAZ gene pairs from two maize inbreds differing in JA levels and insect resistance, and gene polymorphisms were observed between two inbreds.
Conclusions: Here we analyzed the composition and evolution of JAZ genes in maize with three other monocot plants. Extensive phylogenetic and synteny analysis revealed the expansion and selection fate of maize JAZ. This is the first study comparing the difference between two inbreds, and we propose genotype-specific JAZ gene expression might be present in maize plants. Since genetic redundancy in JAZ gene family hampers our understanding of their role in response to specific elicitors, we hope this research could be pertinent to elucidating the defensive responses in plants.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
- SupplementalFigure15.pdf
Supplemental Fig. 1 Exon/intron structure of the corresponding OsJAZ gene. Intron phase numbers were indications of the intron position within a codon: 0, intron not located within a codon (or located between two codons); 1, located between the first and second bases of a codon; 2, located between the second and third bases of a codon Supplemental Fig. 2 Exon/intron structure of the corresponding SbJAZ gene. Intron phase numbers were indications of the intron position within a codon: 0, intron not located within a codon (or located between two codons); 1, located between the first and second bases of a codon; 2, located between the second and third bases of a codon Supplemental Fig. 3 Exon/intron structure of the corresponding BdJAZ gene. Intron phase numbers were indications of the intron position within a codon: 0, intron not located within a codon (or located between two codons); 1, located between the first and second bases of a codon; 2, located between the second and third bases of a codon Supplemental Fig. 4 Sequences logo of the (a) TIFY domain, (b) Jas domain, and (c) N-terminal CMID domains from four grass JAZ genes Supplemental Fig. 5 Distribution of conserved motifs in JAZ proteins. (a) Conserved motifs from maize JAZ proteins. (b) Conserved motifs from JAZ groups 1, 3, and 4 in maize, rice, sorghum, Brachypodium, and Arabidopsis. The conserved motifs with non-overlapping sites (p-value>0.0001) were shown in colored boxes generated by MEME server. TIFY, Jas, and N-terminal CMID motifs were represented in motif 1, 2, and 3, respectively
- SupplementalTable18.xlsx
Supplemental Table 1 List of members of JAZ family in this study Supplemental Table 2 Rice JAZ family Supplemental Table 3 Sorghum JAZ family Supplemental Table 4 Brachypodium JAZ family Supplemental Table 5 Search results from plant repeats database Supplemental Table 6 Primers used in JAZ gDNA cloning Supplemental Table 7 Primers used in JAZ cDNA cloning Supplemental Table 8 Primers used in JAZ PCR of oat-maize addition lines
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