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Research Article
Shuxun Yu
Cotton Research Institute
Corresponding Author
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Background: B-BOX (BBX) proteins are zinc-finger transcription factors with one or two BBX domains and sometimes a CCT domain. These proteins play an essential role in regulating plant growth and development, as well as in resisting abiotic stress. So far, the BBX gene family has been widely studied in other crops. However, no one has systematically studied the BBX gene in cotton.
Results: In the present study, 17, 18, 37 and 33 BBX genes were detected in Gossypium arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively, via genome-wide identification. Phylogenetic analysis showed that all BBX genes were divided into 5 main categories. The protein motifs and exon/intron structures indicated that each group of BBX genes was highly conserved. Collinearity analysis revealed that the amplification of BBX gene family in Gossypium spp. was mainly through segmental replication. Nonsynonymous (Ka)/ synonymous (Ks) substitution ratios indicated that the BBX gene family had undergone purification selection throughout the long-term natural selection process. Moreover, transcriptomic data showed that some GhBBX genes were highly expressed in floral organs. Transcriptome data analysis and qRT-PCR verification showed that different GhBBX genes had different biological functions in flower bud differentiation, abiotic stress and stress response.
Conclusions: Our comprehensive analysis of BBX in G. hirsutum provides a basis for further study on the molecular role of GhBBXs in regulating flowering and cotton resistance to abiotic stress.
Keywords
G. hirsutum, BBX, flower bud differentiation, phytohormone, stress response
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No competing interests reported.
This is a list of supplementary files associated with this preprint. Click to download.
- TableS1qPCRprimer.xlsx
Additional file 1: Table S1. Primer pairs used in the qRT-PCR analysis.
- TableS2basicinformation.xlsx
Additional file 2: Table S2. Detailed physicochemical characteristics and Gene location of BBX proteins of A. thaliana, G. arboreum, G. raimondii, G. hirsutum and G. barbadense. The pI and MW were computed by ExPASy website. Subcellular localizations of BBX proteins were predicted by CELLO version 2.5 server. Gene locus information for BBXs in G. arboreum, G. raimondii, G. hirsutum and G. barbadense. was obtained from gene annotation.
- TableS3genepair.xlsx
Additional file 3: Table S3 | Ka/Ks ratios and duplicate types of gene pairs between the A and D subgenomes of allotetraploid cottons and their corresponding ancestral A and D diploid genomes, respectively. The homologous gene pairs were identified by the results of BLAST and collinearity analysis. When both Ka and Ks were equal to 0, Ka /Ks was considered equal to 1. When only Ks was equal to 0, it was marked as Ka>>Ks. WGD or segmental means that the gene might arise from whole-genome duplication or segmental duplication.
- TableS4numberofciselements.xlsx
Additional file 4: Table S4 | Statistical results of phytohormone and stress response cis-acting elements in the promoter segments of BBXs. These cis-acting elements were identified using PlantCARE software with the upstream 2000-bp sequences of cotton BBXs.
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CURRENT STATUS: Under Review
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Reviewers agreed
On 05 Feb, 2021
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Editor invited
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A new preprint design is coming!
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This preprint is under consideration at BMC Genomics. 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
Shuxun Yu
Cotton Research Institute
Corresponding Author
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: Under Review
Version 1
Posted 16 Feb, 2021
No community comments so far
Editorial decision: Major revision
On 05 Mar, 2021
Reviews received
Received 02 Mar, 2021
Reviewers agreed
On 09 Feb, 2021
Reviewers agreed
On 05 Feb, 2021
Reviewers invited
Invitations sent on 04 Feb, 2021
Editor assigned
On 04 Feb, 2021
Editor invited
On 04 Feb, 2021
Submission checks complete
On 04 Feb, 2021
First submitted
On 01 Feb, 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
Background: B-BOX (BBX) proteins are zinc-finger transcription factors with one or two BBX domains and sometimes a CCT domain. These proteins play an essential role in regulating plant growth and development, as well as in resisting abiotic stress. So far, the BBX gene family has been widely studied in other crops. However, no one has systematically studied the BBX gene in cotton.
Results: In the present study, 17, 18, 37 and 33 BBX genes were detected in Gossypium arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively, via genome-wide identification. Phylogenetic analysis showed that all BBX genes were divided into 5 main categories. The protein motifs and exon/intron structures indicated that each group of BBX genes was highly conserved. Collinearity analysis revealed that the amplification of BBX gene family in Gossypium spp. was mainly through segmental replication. Nonsynonymous (Ka)/ synonymous (Ks) substitution ratios indicated that the BBX gene family had undergone purification selection throughout the long-term natural selection process. Moreover, transcriptomic data showed that some GhBBX genes were highly expressed in floral organs. Transcriptome data analysis and qRT-PCR verification showed that different GhBBX genes had different biological functions in flower bud differentiation, abiotic stress and stress response.
Conclusions: Our comprehensive analysis of BBX in G. hirsutum provides a basis for further study on the molecular role of GhBBXs in regulating flowering and cotton resistance to abiotic stress.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
No competing interests reported.
This is a list of supplementary files associated with this preprint. Click to download.
- TableS1qPCRprimer.xlsx
Additional file 1: Table S1. Primer pairs used in the qRT-PCR analysis.
- TableS2basicinformation.xlsx
Additional file 2: Table S2. Detailed physicochemical characteristics and Gene location of BBX proteins of A. thaliana, G. arboreum, G. raimondii, G. hirsutum and G. barbadense. The pI and MW were computed by ExPASy website. Subcellular localizations of BBX proteins were predicted by CELLO version 2.5 server. Gene locus information for BBXs in G. arboreum, G. raimondii, G. hirsutum and G. barbadense. was obtained from gene annotation.
- TableS3genepair.xlsx
Additional file 3: Table S3 | Ka/Ks ratios and duplicate types of gene pairs between the A and D subgenomes of allotetraploid cottons and their corresponding ancestral A and D diploid genomes, respectively. The homologous gene pairs were identified by the results of BLAST and collinearity analysis. When both Ka and Ks were equal to 0, Ka /Ks was considered equal to 1. When only Ks was equal to 0, it was marked as Ka>>Ks. WGD or segmental means that the gene might arise from whole-genome duplication or segmental duplication.
- TableS4numberofciselements.xlsx
Additional file 4: Table S4 | Statistical results of phytohormone and stress response cis-acting elements in the promoter segments of BBXs. These cis-acting elements were identified using PlantCARE software with the upstream 2000-bp sequences of cotton BBXs.
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