Genome-Wide Identification and Characterization of the PERK Gene Family in Gossypium hirsutum Reveals Gene Duplication and Functional Divergence

Qanmber, Ghulam; Liu, Ji; Yu, Daoqian; Liu, Zhao; Lu, Lili; Mo, Huijuan; Ma, Shuya; Wang, Zhi; Yang, Zuoren

doi:10.3390/ijms20071750

“…S6B-D). These results demonstrated that the PERK gene pairs shared between B. rapa and B. nigra, B. oleracea, and A. thaliana had undergone strong purifying selection with limited functional divergence after whole-genome duplication (13)(14)(15)(16)(17)).…”

Section: Gene Duplication Synteny and Ka/ks Analysesmentioning

confidence: 94%

“…The first PERK gene was identified in Brassica napus, which is rapidly induced by wounding, ubiquitously expressed in the stem, petals and pistils and controls root and stem branching [13,14]. Recent work addressing the PERK family of Gossypium hirsutum has revealed the expression patterns of these genes in response to various abiotic stresses and hormonal homeostasis [15]. In addition to these functions, PERKs are thought to act as sensors/receptors to monitor changes in the cell wall during its expansion [1,12].…”

mentioning

confidence: 99%

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Genome-wide analysis of proline-rich extension-like receptor protein kinase (PERK) in Brassica rapa and its association with the pollen development

Chen

¹

,

Wang

²

,

Wang

³

et al. 2020

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Background: Proline-rich extension-like receptor protein kinases (PERKs) are an important class of receptor kinases located in the plasma membrane, most of which play a vital role in pollen development. Results: Our study identified 25 putative PERK genes from the whole Brassica rapa genome (AA). Phylogenetic analysis of PERK protein sequences from 16 Brassicaceae species divided them into four subfamilies. The biophysical properties of the BrPERKs were investigated. Gene duplication and synteny analyses and the calculation of Ka/Ks values suggested that all 80 orthologous/paralogous gene pairs between B. rapa and A. thaliana, B. nigra and B. oleracea have experienced strong purifying selection. RNA-Seq data and qRT-PCR analyses showed that several BrPERK genes were expressed in different tissues, while some BrPERKs exhibited high expression levels only in buds. Furthermore, comparative transcriptome analyses from six male-sterile lines of B. rapa indicated that 7 BrPERK genes were downregulated in all six male-sterile lines. Meanwhile, the interaction networks of the BrPERK genes were constructed and 13 PERK coexpressed genes were identified, most of which were downregulated in the male sterile buds. Conclusion: Combined with interaction networks, coexpression and qRT-PCR analyses, these results demonstrated that two BrPERK genes, Bra001723.1 and Bra037558.1 (the orthologs of AtPERK6 (AT3G18810)), were downregulated beginning in the meiosis II period of male sterile lines and involved in anther development. Overall, this comprehensive analysis of some BrPERK genes elucidated their roles in male sterility.

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“…The AtGGPPS genes were used as queries to identify the (NAU, version 1.1), and G. hirsutum (NAU, version 1.1) as described in previous study [37]. The Arabidopsis, cotton (G. arboreum, G. hirsutum, G. barbadense and G. raimondii) and other plant species databases were downloaded from TAIR 10 (http://www.…”

Section: Sequence Identificationmentioning

confidence: 99%

Genome-wide characterization and expression analysis of geranylgeranyl diphosphate synthase genes in cotton (Gossypium spp.) in plant development and abiotic stresses

Ali

¹

,

Qanmber

²

,

Wei

³

et al. 2020

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Background: GGPP (geranylgeranyl diphosphate) is produced in the isoprenoid pathway and mediates the function of various plant metabolites, which is synthesized by GGPPS (GGPP synthases) in plants. GGPPS characterization has not been performed in any plant species except Arabidopsis thaliana. Here, we performed a complete computational and bioinformatics analysis of GGPPS and detected their transcription expression pattern in Gossypium hirsutum for the first time so that to explore their evolutionary relationship and potential functions. Finally, we unravelled evolutionary relationship, conserved sequence logos, gene duplication and potential involvement in plant development and abiotic stresses tolerance of GGPPS genes in G. hirsutum and other plant species. Results: A total of 159 GGPPS genes from 18 plant species were identified and evolutionary analysis divided these GGPPS genes into five groups to indicate their divergence from a common ancestor. Further, GGPPS family genes were conserved during evolution and underwent segmental duplication. The identified 25 GhGGPPS genes showed diverse expression pattern particularly in ovule and fiber development indicating their vital and divers roles in the fiber development. Additionally, GhGGPPS genes exhibited wide range of responses when subjected to abiotic (heat, cold, NaCl and PEG) stresses and hormonal (BL, GA, IAA, SA and MeJA) treatments, indicating their potential roles in various biotic and abiotic stresses tolerance. Conclusions: The GGPPS genes are evolutionary conserved and might be involve in different developmental stages and stress response. Some potential key genes (e.g. GhGGPP4, GhGGPP9, and GhGGPP15) were suggested for further study and provided valuable source for cotton breeding to improve fiber quality and resistant to various stresses.

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“…The GGPPS genes in other species were identified by using Arabidopsis GGPPS genes sequences (Lange and Ghassemian, 2003) as queries for other 16 described in previous study [37]. The Arabidopsis, cotton (G. arboreum, G. hirsutum and G. raimondii) and other plant species databases were downloaded from TAIR 10 (http://www.arabidopsis.org), COTTONGEN (https://www.cottongen.org/) and Phytozome v11 (https://phytozome.jgi.%20doe.gov/pz/portal.html) respectively and GGPPS protein sequences were confirmed by SMART [38] and Interproscan 63.0 [39] (http://www.ebi.ac.uk/InterProScan/).…”

Section: Sequence Identificationmentioning

confidence: 99%

Genome-wide characterization and expression analysis of geranyl geranyl diphosphate synthase genes of cotton (Gossypium spp.) in plant development and abiotic stresses

Ali

¹

,

Qanmber

²

,

Wei

³

et al. 2020

Preprint

Self Cite

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Background: GGPP (geranyl geranyl diphosphate) is produced in the isoprenoid pathway and mediates the function of various plant metabolites, which is synthesized by GGPPS (GGPP synthases) in plants. GGPPS characterization has not been performed in any plant species except Arabidiosis thaliana. Here, we performed a complete computational and bioinformatics analysis of GGPPS and detected their transcription expression pattern in Gossypium hirsutum for the first time in order to explore their evolutionary relationship and potential functions. We unravel evolutionary relationship, conserved sequence logos, gene duplication and potential involvement in plant development and abiotic stresses tolerance of GGPPS genes in G. hirsutum.Results: A total of 134 GGPPS genes from 17 plant species were identified. Evolutionary analysis divided GGPPS genes into five groups and indicated their divergence from a common ancestor.Further, GGPPS family genes were conserved during evolution and underwent segmental duplication.25 GhGGPPS genes identified showed diverse expression pattern particularly in ovule and fiber development indicating their vital and divers roles in the fiber development. Additionally, GhGGPPS genes exhibited wide range of responses when subjected to abiotic (heat, cold, NaCl and PEG) and hormonal (BL, GA, IAA, SA and MeJA) stresses. Conclusions:Collectively, GGPPS genes are evolutionary conserved, may are involved in different development stages and stress signaling pathways, some potential key genes (e.g. GhGGPP4, GhGGPP9, GhGGPP15) were suggested and provide valuable source for cotton breeding in fiber quality and resistant to various stresses. BackgroundIsoprenoids represent the largest group of biologically active specialized metabolites in plants. Many Isoprenoids provides protection to plants from pathogens and herbivores [1]. Isoprenoids also have important functions in plant photosynthesis and respiration process and involve many hormonal pathways (abscisic acid, brassinosteroids, cytokinin, gibberellin, and strigolactones) important for development and growth regulation in plants [1][2][3][4].In isoprenoid pathway, prenyl diphosphate synthases are active with important isozymes for 4 isoprenoid metabolism, use isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) as substrates in the mevalonate (MVA) or methylerythritol (MEP) pathway. In general, they are represented by three enzymes such as geranyl diphosphate (GPP) synthase, farnesyldiphosphate (FPP) synthase and geranylgeranyl diphosphate (GGPP) synthase in plants [4].GGPPS is an essential enzyme among three isoprenoids for primary and secondary isoprenoid compounds synthesis such as chlorophylls, carotenoids and derivatives including different hormones (e.g. abscisic acid (ABA), strigolactones and gibberellins), and proteins (e.g. plastoquinones, ubiquinones, phylloquinones, tocopherols, diterpenoids, polyprenols, dolichols, and prenylated) [4].GGPPS catalyzes successive additions of IPP to DMAPP, GPP and FPP as a homodimer [5] an...

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Genome-Wide Identification and Characterization of the PERK Gene Family in Gossypium hirsutum Reveals Gene Duplication and Functional Divergence

Cited by 46 publications

References 91 publications

Genome-wide analysis of proline-rich extension-like receptor protein kinase (PERK) in Brassica rapa and its association with the pollen development

Genome-wide analysis of proline-rich extension-like receptor protein kinase (PERK) in Brassica rapa and its association with the pollen development

Genome-wide characterization and expression analysis of geranylgeranyl diphosphate synthase genes in cotton (Gossypium spp.) in plant development and abiotic stresses

Genome-wide characterization and expression analysis of geranyl geranyl diphosphate synthase genes of cotton (Gossypium spp.) in plant development and abiotic stresses

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