Peer Review #3 of "Genome-wide identification of the PEBP genes in pears and the putative role of PbFT in flower bud differentiation (v0.3)"

Abstract 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.

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Genome-wide identification of the PEBP genes in pears and the putative role of PbFT in flower bud differentiation

PeerJ ◽

10.7717/peerj.8928 ◽

2020 ◽

Vol 8 ◽

pp. e8928

Author(s):

Shuliang Zhao ◽

Yarui Wei ◽

Hongguang Pang ◽

Jianfeng Xu ◽

Yingli Li ◽

...

Keyword(s):

Expression Patterns ◽

Day Length ◽

Promoter Regions ◽

Flower Bud ◽

Genome Wide ◽

Flower Bud Differentiation ◽

Vegetative And Reproductive Growth ◽

And Function ◽

Phosphatidylethanolamine Binding Protein

Although Phosphatidylethanolamine-binding protein (PEBP) genes have been identified in several plants, little is known about PEBP genes in pears. In this study, a total of 24 PEBP genes were identified, in which 10, 5 and 9 were from Pyrus bretschneideri genome, Pyrus communis genome and Pyrus betuleafolia genome, respectively. Subsequently, gene structure, phylogenetic relationship, chromosomal localization, promoter regions, collinearity and expression were determined with these PEBP genes. It was found that only PbFT from PEBP genes of P. bretschneideri was relatively highly expressed in leaves during flower bud differentiation. Whereas, expression patterns of TFL1 homologues, gene23124 and gene16540, were different from PbFT in buds. The expression pattern and the treatment of reduction day-length indicated that the expression of PbFT in leaves were regulated by day-length and circadian clock. Additionally, the phenotype of transgenic Arabidopsis suggested that PbFT played a role in not only promoting flower bud differentiation, but also regulating the balance between vegetative and reproductive growth. These results may provide important information for further understanding of the evolution and function of PEBP genes in pears.

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Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton

BMC Genomics ◽

10.1186/s12864-020-07069-w ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Jingjing Zhang ◽

Aimin Wu ◽

Hengling Wei ◽

Pengbo Hao ◽

Qi Zhang ◽

...

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Expression Patterns ◽

Histone Deacetylation ◽

Systematic Research ◽

Motif Analysis ◽

Flower Bud ◽

Early Maturity ◽

Genome Wide ◽

Flower Bud Differentiation

Abstract Background Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is reported that RPD3 genes play crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on the RPD3/HDA1 gene family in cotton. Results In this study, genome-wide analysis identified 9, 9, 18, and 18 RPD3 genes in Gossypium raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. This gene family was divided into 4 subfamilies through phylogenetic analysis. The exon-intron structure and conserved motif analysis revealed high conservation in each branch of the cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the RPD3 gene family in cotton. There was at least one presumed cis-element related to plant hormones in the promoter regions of all GhRPD3 genes, especially MeJA- and ABA-responsive elements, which have more members than other hormone-relevant elements. The expression patterns showed that most GhRPD3 genes had relatively high expression levels in floral organs and performed higher expression in early-maturity cotton compared with late-maturity cotton during flower bud differentiation. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA or ABA. Conclusions Our findings reveal that GhRPD3 genes may be involved in flower bud differentiation and resistance to abiotic stresses, which provides a basis for further functional verification of GhRPD3 genes in cotton development and a foundation for breeding better early-maturity cotton cultivars in the future.

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Genome-wide association study reveals putative role of gga-miR-15a in controlling feed conversion ratio in layer chickens

BMC Genomics ◽

10.1186/s12864-017-4092-9 ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 8

Author(s):

Jingwei Yuan ◽

Sirui Chen ◽

Fengying Shi ◽

Guiqin Wu ◽

Aiqiao Liu ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Conversion Ratio ◽

Feed Conversion Ratio ◽

Genome Wide Association ◽

Feed Conversion ◽

Putative Role ◽

Genome Wide ◽

Layer Chickens

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Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton

10.21203/rs.2.19331/v1 ◽

2019 ◽

Author(s):

Jingjing Zhang ◽

Aimin Wu ◽

Hengling Wei ◽

Pengbo Hao ◽

Qi Zhang ◽

...

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Expression Patterns ◽

Histone Deacetylation ◽

Functional Verification ◽

Systematic Research ◽

Flower Bud ◽

Early Maturity ◽

Genome Wide ◽

Flower Bud Differentiation

Abstract Background: Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. As the superfamily of HDACs, RPD3/HDA1-type HDACs were most studied and reported that RPD3 genes played crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on RPD3/HDA1 gene family in cotton. Results: In this research, 9, 9, 18 and 18 RPD3 genes were determined by genome-wide analysis in Gossypium raimondii, G. arboreum, G. hirsutum and G. barbadense, respectively. This gene family was divided into 4 subfamilies through phylogenetic analysis. The exon-intron structure and conserved motifs analysis exhibited high conservation in each branch of cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the GhRPD3 gene family. There was at least one presumed cis-element related to plant hormone existing in the promoter regions of all the GhRPD3 genes, especially MeJA and ABA responsive elements, owning more members than other hormone-relevant elements. Characterizations of expression patterns showed that most GhRPD3 genes performed relative high expression in floral organs and possessed the higher expression in early-maturity cotton compared with the late-maturity cotton during flower bud differentiation period. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA and ABA. Conclusions: Our findings revealed that GhRPD3 genes might be involved in flower bud differentiation and resistance to abiotic stresses, which provided a basis for further functional verification of GhRPD3 genes in cotton development and a foundation for breeding better early-maturity cotton cultivars in the future.

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