scholarly journals Genome-wide characterization and expression profiling of B3 superfamily during flower induction stage in pineapple (Ananas comosus L.)

2020 ◽  
Author(s):  
Cheng Cheng Ruan ◽  
Zhe Chen ◽  
Fu Chu Hu ◽  
Xiang He Wang ◽  
Li Jun Guo ◽  
...  
Keyword(s):  
Development Process ◽  
Purifying Selection ◽  
Ananas Comosus ◽  
Flower Bud ◽  
Genome Wide ◽  
Localization Analysis ◽  
Ethephon Treatment ◽  
High Level ◽  
Differentiation Period ◽  
Induction Stage

AbstractThe B3 superfamily is a plant-specific family, which involves in growth and development process. By now, the identification of B3 superfamily in pineapple (Ananas comosus) has not reported. In this study, 57 B3 genes were identified and further phylogenetically classified into five subfamilies, all genes contained B3 domain. Chromosomal localization analysis revealed that 54 of 57 AcB3 genes were located on 21 chromosomes.Collinearity analysis indicated that the segmental duplication was the main event in the evolution of B3 gene superfamily and most of them were under purifying selection. Moreover, there were 7 and 39 pairs of orthologous B3s were identified between pineapple and Arabidopsis or rice, respectively, which indicated the closer genetic relationship between pineapple and rice. Most genes had cis-element of abscisic acid, ethylene, MeJA, light, and abiotic stress. qRT-PCR showed that the expression level of most AcB3 genes were up-regulated within 1 d after ethephon treatment and expressed high level in flower bud differentiation period in stem apex. This study provide a comprehensive understanding of AcB3s and a basis for future molecular studies of ethephon induced pineapple flowering.

scholarly journals Genome-wide characterization and expression profiling of B3 superfamily during ethylene-induced flowering in pineapple (Ananas comosus L.)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cheng Cheng Ruan ◽  
Zhe Chen ◽  
Fu Chu Hu ◽  
Wei Fan ◽  
Xiang He Wang ◽  
...  
Keyword(s):  
Development Process ◽  
Chromosomal Localization ◽  
Purifying Selection ◽  
Ananas Comosus ◽  
Pcr Analysis ◽  
Flower Bud ◽  
Genome Wide ◽  
Localization Analysis ◽  
Ethephon Treatment ◽  
Differentiation Period

Abstract Background The B3 superfamily (B3s) represents a class of large plant-specific transcription factors, which play diverse roles in plant growth and development process including flowering induction. However, identification and functional surveys of B3 superfamily have not been reported in ethylene-induced pineapple flowering (Ananas comosus). Results 57 B3 genes containing B3 domain were identified and phylogenetically classified into five subfamilies. Chromosomal localization analysis revealed that 54 of 57 AcB3s were located on 21 Linkage Groups (LG). Collinearity analysis demonstrated that the segmental duplication was the main event in the evolution of B3 gene superfamily, and most of them were under purifying selection. The analysis of cis-element composition suggested that most of these genes may have function in response to abscisic acid, ethylene, MeJA, light, and abiotic stress. qRT-PCR analysis of 40 AcB3s containing ethylene responsive elements exhibited that the expression levels of 35 genes were up-regulated within 1 d after ethephon treatment and some were highly expressed in flower bud differentiation period in stem apex, such as Aco012003, Aco019552 and Aco014401. Conclusion This study provides a basic information of AcB3s and clues for involvement of some AcB3s in ethylene-induced flowering in pineapple.

scholarly journals Genome-wide characterization and expression analysis of the heat shock transcription factor family in pumpkin (Cucurbita moschata)

2020 ◽  
Author(s):  
Changwei Shen ◽  
Jingping Yuan
Keyword(s):  
Heat Shock ◽  
Stress Hormones ◽  
Purifying Selection ◽  
Cucurbita Moschata ◽  
Plant Tolerance ◽  
Biotic Stresses ◽  
Genome Wide ◽  
Localization Analysis ◽  
Duplication Events ◽  
High Level

Abstract Background: Crop quality and yield are affected by abiotic and biotic stresses, and heat shock transcription factors (Hsfs) are considered to play important roles in regulating plant tolerance under various stresses. To investigate the response of Cucurbita moschata to abiotic stress, we analyzed the genome of C. moschata.Results: In this research, a total of 36 C. moschata Hsf (CmHsf) members were identified and classified into three subfamilies (I, II, and III) according to their amino acid sequence identity. The Hsfs of the same subfamily usually exhibit a similar gene structure (intron-exon distribution) and conserved domains (DNA-binding and other functional domains). Chromosome localization analysis showed that the 36 CmHsfs were unevenly distributed on 18 of the 21 chromosomes (except for Cm_Chr00, Cm_Chr08 and Cm_Chr20), among which 18 genes formed 9 duplicated gene pairs that have undergone segmental duplication events. The Ka/Ks ratio showed that the duplicated CmHsfs have mainly experienced strong purifying selection. High-level synteny was observed between C. moschata and other Cucurbitaceae species.Conclusions: The expression profile of CmHsfs in the roots, stems, cotyledons and true leaves revealed that the CmHsfs exhibit tissue specificity. The analysis of cis-acting elements and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that some key CmHsfs were activated by cold stress, heat stress, hormones and salicylic acid. This study lays the foundation for revealing the role of CmHsfs in resistance to various stresses, which is of great significance for the selection of stress-tolerant C. moschata.

scholarly journals Genome-wide Characterization and Functional Analysis of the Heat Shock Transcription Factor Family in Pumpkin

2020 ◽  
Author(s):  
Changwei Shen ◽  
Jingping Yuan
Keyword(s):  
Heat Shock ◽  
Stress Hormones ◽  
Purifying Selection ◽  
Cucurbita Moschata ◽  
Plant Tolerance ◽  
Biotic Stresses ◽  
Genome Wide ◽  
Localization Analysis ◽  
Duplication Events ◽  
High Level

Abstract Background: Crop quality and yield are affected by abiotic and biotic stresses, and heat shock transcription factors (Hsfs) are considered to play important roles in regulating plant tolerance under various stresses. To investigate the response of pumpkin to abiotic stress, we analysed the genome of pumpkin. Results:In this research, a total of 36 Cucurbita moschata Hsf (CmHsf) members were identified and classified into three subfamilies (I, II, and III) according to their amino acid sequence identity. The Hsfs of the same subfamily usually exhibit a similar gene structure (intron-exon distribution) and conserved domains (DNA-binding and other functional domains). Chromosome localization analysis showed that the 36 CmHsfs were unevenly distributed on 18 of the 21 chromosomes (except for Cm_Chr00, Cm_Chr08 and Cm_Chr20), among which 18 genes formed 9 duplicated gene pairs that have undergone segmental duplication events. The Ka/Ks ratio showed that the duplicated CmHsfs have mainly experienced strong purifying selection. High-level synteny was observed between Cucurbita moschata and other Cucurbitaceae species. Conclusions: The expression profile of CmHsfs in the roots, stems, cotyledons and true leaves revealed that the CmHsfs exhibit tissue specificity. The analysis of cis-acting elements and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that some key CmHsf genes were activated by cold stress, heat stress, hormones and salicylic acid. This study lays the foundation for revealing the role of CmHsfs in resistance to various stresses, which is of great significance for the selection of stress-tolerant pumpkin varieties.

scholarly journals Genome-wide characterization and expression analysis of the heat shock transcription factor family in pumpkin (Cucurbita moschata)

2020 ◽  
Author(s):  
Changwei Shen ◽  
Jingping Yuan
Keyword(s):  
Heat Shock ◽  
Stress Hormones ◽  
Purifying Selection ◽  
Cucurbita Moschata ◽  
Plant Tolerance ◽  
Biotic Stresses ◽  
Genome Wide ◽  
Localization Analysis ◽  
Duplication Events ◽  
High Level

Abstract Background: Crop quality and yield are affected by abiotic and biotic stresses, and heat shock transcription factors (Hsfs) are considered to play important roles in regulating plant tolerance under various stresses. To investigate the response of Cucurbita moschata to abiotic stress, we analyzed the genome of C. moschata. Results: In this research, a total of 36 C. moschata Hsf (CmHsf) members were identified and classified into three subfamilies (I, II, and III) according to their amino acid sequence identity. The Hsfs of the same subfamily usually exhibit a similar gene structure (intron-exon distribution) and conserved domains (DNA-binding and other functional domains). Chromosome localization analysis showed that the 36 CmHsfs were unevenly distributed on 18 of the 21 chromosomes (except for Cm_Chr00, Cm_Chr08 and Cm_Chr20), among which 18 genes formed 9 duplicated gene pairs that have undergone segmental duplication events. The Ka/Ks ratio showed that the duplicated CmHsfs have mainly experienced strong purifying selection. High-level synteny was observed between C. moschata and other Cucurbitaceae species. Conclusions: The expression profile of CmHsfs in the roots, stems, cotyledons and true leaves revealed that the CmHsfs exhibit tissue specificity. The analysis of cis-acting elements and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that some key CmHsfs were activated by cold stress, heat stress, hormones and salicylic acid. This study lays the foundation for revealing the role of CmHsfs in resistance to various stresses, which is of great significance for the selection of stress-tolerant C. moschata.

scholarly journals Genome-wide characterization and expression analysis of the heat shock transcription factor family in pumpkin (Cucurbita moschata)

2020 ◽  
Author(s):  
Changwei Shen ◽  
Jingping Yuan
Keyword(s):  
Heat Shock ◽  
Stress Hormones ◽  
Purifying Selection ◽  
Cucurbita Moschata ◽  
Plant Tolerance ◽  
Biotic Stresses ◽  
Genome Wide ◽  
Localization Analysis ◽  
Duplication Events ◽  
High Level

Abstract Background: Crop quality and yield are affected by abiotic and biotic stresses, and heat shock transcription factors (Hsfs) are considered to play important roles in regulating plant tolerance under various stresses. To investigate the response of Cucurbita moschata to abiotic stress, we analyzed the genome of C. moschata. Results: In this research, a total of 36 C. moschata Hsf (CmHsf) members were identified and classified into three subfamilies (I, II, and III) according to their amino acid sequence identity. The Hsfs of the same subfamily usually exhibit a similar gene structure (intron-exon distribution) and conserved domains (DNA-binding and other functional domains). Chromosome localization analysis showed that the 36 CmHsfs were unevenly distributed on 18 of the 21 chromosomes (except for Cm_Chr00, Cm_Chr08 and Cm_Chr20), among which 18 genes formed 9 duplicated gene pairs that have undergone segmental duplication events. The Ka/Ks ratio showed that the duplicated CmHsfs have mainly experienced strong purifying selection. High-level synteny was observed between C. moschata and other Cucurbitaceae species. Conclusions: The expression profile of CmHsfs in the roots, stems, cotyledons and true leaves revealed that the CmHsfs exhibit tissue specificity. The analysis of cis-acting elements and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that some key CmHsfs were activated by cold stress, heat stress, hormones and salicylic acid. This study lays the foundation for revealing the role of CmHsfs in resistance to various stresses, which is of great significance for the selection of stress-tolerant C. moschata.

scholarly journals Genome-wide characterization and expression analysis of the heat shock transcription factor family in pumpkin (Cucurbita moschata)

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Changwei Shen ◽  
Jingping Yuan
Keyword(s):  
Heat Shock ◽  
Stress Hormones ◽  
Purifying Selection ◽  
Cucurbita Moschata ◽  
Plant Tolerance ◽  
Biotic Stresses ◽  
Genome Wide ◽  
Localization Analysis ◽  
Duplication Events ◽  
High Level

Abstract Background Crop quality and yield are affected by abiotic and biotic stresses, and heat shock transcription factors (Hsfs) are considered to play important roles in regulating plant tolerance under various stresses. To investigate the response of Cucurbita moschata to abiotic stress, we analyzed the genome of C. moschata. Results In this research, a total of 36 C. moschata Hsf (CmHsf) members were identified and classified into three subfamilies (I, II, and III) according to their amino acid sequence identity. The Hsfs of the same subfamily usually exhibit a similar gene structure (intron-exon distribution) and conserved domains (DNA-binding and other functional domains). Chromosome localization analysis showed that the 36 CmHsfs were unevenly distributed on 18 of the 21 chromosomes (except for Cm_Chr00, Cm_Chr08 and Cm_Chr20), among which 18 genes formed 9 duplicated gene pairs that have undergone segmental duplication events. The Ka/Ks ratio showed that the duplicated CmHsfs have mainly experienced strong purifying selection. High-level synteny was observed between C. moschata and other Cucurbitaceae species. Conclusions The expression profile of CmHsfs in the roots, stems, cotyledons and true leaves revealed that the CmHsfs exhibit tissue specificity. The analysis of cis-acting elements and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that some key CmHsfs were activated by cold stress, heat stress, hormones and salicylic acid. This study lays the foundation for revealing the role of CmHsfs in resistance to various stresses, which is of great significance for the selection of stress-tolerant C. moschata.

scholarly journals Genome-Wide Identification and Characterization of JAZ Protein Family in Two Petunia Progenitors

Plants ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 203 ◽  
Author(s):  
Shaoze Tian ◽  
Siyu Liu ◽  
Yu Wang ◽  
Kun Wang ◽  
Chaoqun Yin ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Purifying Selection ◽  
Protein Family ◽  
Pcr Analysis ◽  
Petunia Inflata ◽  
Flower Bud ◽  
Genome Wide ◽  
Meja Treatment ◽  
Jaz Proteins

Jasmonate ZIM-domain (JAZ) family proteins are the key repressors in the jasmonate signaling pathway and play crucial roles in plant development, defenses, and responses to stresses. However, our knowledge about the JAZ protein family in petunia is limited. This research respectively identified 12 and 16 JAZ proteins in two Petunia progenitors, Petunia axillaris and Petunia inflata. Phylogenetic analysis showed that the 28 proteins could be divided into four groups (Groups A–D) and further classified into six subgroups (A1, A2, B1, B3, C, and D1); members in the same subgroup shared some similarities in motif composition and sequence structure. The Ka/Ks ratios of seven paralogous pairs were less than one, suggesting the petunia JAZ family might have principally undergone purifying selection. Quantitative real-time PCR (qRT-PCR) analysis revealed that PaJAZ genes presented differential expression patterns during the development of flower bud and anther in petunia, and the expression of PaJAZ5, 9, 12 genes was generally up-regulated after MeJA treatment. Subcellular localization assays demonstrated that proteins PaJAZ5, 9, 12 were localized in nucleus. Yeast two hybrid (Y2H) elucidated most PaJAZ proteins (PaJAZ1-7, 9, 12) might interact with transcription factor MYC2. This study provides insights for further investigation of functional analysis in petunia JAZ family proteins.

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