See the published version of this preprint at BMC Genomics.
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Methodology article
Bo Zheng
Corresponding Author
ORCiD: https://orcid.org/0000-0002-5337-5477
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CLE genes is challenging because of their low sequence similarity.
Results: We developed a machine learning-aided method for predicting CLE genes by using a CLE motif-specific residual score matrix and a novel clustering method based on the Euclidean distance of 12 amino acid residues from the CLE motif in a site-weight dependent manner. In total, 2156 CLE candidates—including 627 novel candidates—were predicted from 69 plant species. The results from our CLE motif-based clustering are consistent with previous reports using the entire pre-propeptide. Characterization of CLE candidates provided systematic statistics on protein lengths, signal peptides, relative motif positions, amino acid compositions of different parts of the CLE precursor proteins, and decisive factors of CLE prediction. The approach taken here provides information on the evolution of the CLE gene family and provides evidence that the CLE and IDA/IDL genes share a common ancestor.
Conclusions: Our new approach is applicable to SSPs or other proteins with short conserved domains and hence, provides a useful tool for gene prediction, classification and evolutionary analysis.
Keywords
Peptide hormone, CLE, Machine learning, Euclidean distance, Gene prediction, Gene clustering, Evolution
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This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1.pdf
Additional file 1: Figure S1. Amino acid composition of all proteins, all small proteins, CLE precursors, CLE signal peptides, CLE variable regions and CLE motifs in 69 species.
- Additionalfile2.pdf
Additional file 2: Figure S2. Comparison of three amino acid substitution matrices for evaluating CLE motif scores.
- Additionalfile3.pdf
Additional file 3: Figure S3. Amino acid usage frequency of CLE motifs.
- Additionalfile4.pdf
Additional file 4: Figure S4. Weblogo representation of CLE motifs in each group or subgroup of the CLE gene family in plants.
- Additionalfile5.pdf
Additional file 5: Figure S5. Number and proportion of CLE genes in the genomes of 69 plant species.
- Additionalfile6.pdf
Additional file 6: Figure S6. Top ten most frequently used CLE motifs in 69 species.
- Additionalfile7.pdf
Additional file 7: Figure S7. Statistical analysis of the lengths of the C-terminal tails of CLE candidates.
- Additionalfile8.pdf
Additional file 8: Figure S8. Statistical analysis of protein lengths, SignalP scores, motif positions and CLE motif scores of CLE candidates from 69 species.
- Additionalfile9.pdf
Additional file 9: Figure S9. Distribution of protein lengths of CLE precursors in the range of 50-150 amino acid residues.
- Additionalfile10.pdf
Additional file 10: Figure S10. Gene structure of CLE candidates regulated by alternative splicing in A. thaliana and Z. mays.
- Additionalfile11.pdf
Additional file 11: Figure S11. K-type and W-type CLE candidates in plants.
- Additionalfile12.xls
Additional file 12: Table S1. Predicted CLE candidates in 69 plant species
- Additionalfile13.xls
Additional file 13: Table S2. Comparison of group information on Arabidopsis CLE genes from the literature and from this study.
- Additionalfile14.xls
Additional file 14: Table S3. Comparison of E-values for evaluating the grouping of CLE motifs from Goad et al. [7] and from the site-weight based method described in this study.
- Additionalfile15.xls
Additional file 15: Table S4. Number of types of CLE motifs in 69 plant species.
- Additionalfile16.xls
Additional file 16: Table S5. CLE candidates in algae and bryophytes.
- Additionalfile17.xls
Additional file 17: Table S6. Top 10 most frequently used CLE motifs in monocots and dicots.
- Additionalfile18.xls
Additional file 18: Table S7. Number of CLE genes lying above the CLE motif scores of the corresponding quantiles.
- Additionalfile19.xls
Additional file 19: Table S8. Number of CLE genes lying above the threshold of the SignalP score.
- Additionalfile20.xls
Additional file 20: Table S9. CLE motifs used for finding the optimal amino acid substitution matrix.
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CURRENT STATUS: Published
View the published article at BMC Genomics.
Version 3
Posted 12 Oct, 2020
No community comments so far
Submission checks complete
On 01 Oct, 2020
Editorial decision: Accept
On 29 Sep, 2020
No comments provided
Review #1 received
Received 16 Sep, 2020
Reviewer #1 agreed
On 15 Sep, 2020
Editor assigned
On 14 Sep, 2020
Reviewers invited
Invitations sent on 14 Sep, 2020
Submission checks complete
On 13 Sep, 2020
Editor invited
On 13 Sep, 2020
No comments provided
Editorial decision: Minor revision
On 21 Aug, 2020
Review #2 received
Received 17 Aug, 2020
Reviewer #2 agreed
On 03 Aug, 2020
Review #1 received
Received 08 Jun, 2020
Reviewer #1 agreed
On 09 Feb, 2020
Reviewers invited
Invitations sent on 06 Feb, 2020
Editor assigned
On 14 Jan, 2020
Submission checks complete
On 13 Jan, 2020
Editor invited
On 13 Jan, 2020
First submitted
On 11 Jan, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
Learn more about our company.
A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
See the published version of this preprint at BMC Genomics.
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
Methodology article
Bo Zheng
Corresponding Author
ORCiD: https://orcid.org/0000-0002-5337-5477
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
Version 3
Posted 12 Oct, 2020
No community comments so far
Submission checks complete
On 01 Oct, 2020
Editorial decision: Accept
On 29 Sep, 2020
No comments provided
Review #1 received
Received 16 Sep, 2020
Reviewer #1 agreed
On 15 Sep, 2020
Editor assigned
On 14 Sep, 2020
Reviewers invited
Invitations sent on 14 Sep, 2020
Submission checks complete
On 13 Sep, 2020
Editor invited
On 13 Sep, 2020
No comments provided
Editorial decision: Minor revision
On 21 Aug, 2020
Review #2 received
Received 17 Aug, 2020
Reviewer #2 agreed
On 03 Aug, 2020
Review #1 received
Received 08 Jun, 2020
Reviewer #1 agreed
On 09 Feb, 2020
Reviewers invited
Invitations sent on 06 Feb, 2020
Editor assigned
On 14 Jan, 2020
Submission checks complete
On 13 Jan, 2020
Editor invited
On 13 Jan, 2020
First submitted
On 11 Jan, 2020
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: The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CLE genes is challenging because of their low sequence similarity.
Results: We developed a machine learning-aided method for predicting CLE genes by using a CLE motif-specific residual score matrix and a novel clustering method based on the Euclidean distance of 12 amino acid residues from the CLE motif in a site-weight dependent manner. In total, 2156 CLE candidates—including 627 novel candidates—were predicted from 69 plant species. The results from our CLE motif-based clustering are consistent with previous reports using the entire pre-propeptide. Characterization of CLE candidates provided systematic statistics on protein lengths, signal peptides, relative motif positions, amino acid compositions of different parts of the CLE precursor proteins, and decisive factors of CLE prediction. The approach taken here provides information on the evolution of the CLE gene family and provides evidence that the CLE and IDA/IDL genes share a common ancestor.
Conclusions: Our new approach is applicable to SSPs or other proteins with short conserved domains and hence, provides a useful tool for gene prediction, classification and evolutionary analysis.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1.pdf
Additional file 1: Figure S1. Amino acid composition of all proteins, all small proteins, CLE precursors, CLE signal peptides, CLE variable regions and CLE motifs in 69 species.
- Additionalfile2.pdf
Additional file 2: Figure S2. Comparison of three amino acid substitution matrices for evaluating CLE motif scores.
- Additionalfile3.pdf
Additional file 3: Figure S3. Amino acid usage frequency of CLE motifs.
- Additionalfile4.pdf
Additional file 4: Figure S4. Weblogo representation of CLE motifs in each group or subgroup of the CLE gene family in plants.
- Additionalfile5.pdf
Additional file 5: Figure S5. Number and proportion of CLE genes in the genomes of 69 plant species.
- Additionalfile6.pdf
Additional file 6: Figure S6. Top ten most frequently used CLE motifs in 69 species.
- Additionalfile7.pdf
Additional file 7: Figure S7. Statistical analysis of the lengths of the C-terminal tails of CLE candidates.
- Additionalfile8.pdf
Additional file 8: Figure S8. Statistical analysis of protein lengths, SignalP scores, motif positions and CLE motif scores of CLE candidates from 69 species.
- Additionalfile9.pdf
Additional file 9: Figure S9. Distribution of protein lengths of CLE precursors in the range of 50-150 amino acid residues.
- Additionalfile10.pdf
Additional file 10: Figure S10. Gene structure of CLE candidates regulated by alternative splicing in A. thaliana and Z. mays.
- Additionalfile11.pdf
Additional file 11: Figure S11. K-type and W-type CLE candidates in plants.
- Additionalfile12.xls
Additional file 12: Table S1. Predicted CLE candidates in 69 plant species
- Additionalfile13.xls
Additional file 13: Table S2. Comparison of group information on Arabidopsis CLE genes from the literature and from this study.
- Additionalfile14.xls
Additional file 14: Table S3. Comparison of E-values for evaluating the grouping of CLE motifs from Goad et al. [7] and from the site-weight based method described in this study.
- Additionalfile15.xls
Additional file 15: Table S4. Number of types of CLE motifs in 69 plant species.
- Additionalfile16.xls
Additional file 16: Table S5. CLE candidates in algae and bryophytes.
- Additionalfile17.xls
Additional file 17: Table S6. Top 10 most frequently used CLE motifs in monocots and dicots.
- Additionalfile18.xls
Additional file 18: Table S7. Number of CLE genes lying above the CLE motif scores of the corresponding quantiles.
- Additionalfile19.xls
Additional file 19: Table S8. Number of CLE genes lying above the threshold of the SignalP score.
- Additionalfile20.xls
Additional file 20: Table S9. CLE motifs used for finding the optimal amino acid substitution matrix.
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