scholarly journals Functional examination of lncRNAs in allotetraploid Gossypium hirsutum

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Luyao Wang ◽  
Jin Han ◽  
Kening Lu ◽  
Menglin Li ◽  
Mengtao Gao ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Expression Patterns ◽  
Leaf Tissue ◽  
Evolutionary Model ◽  
Cotton Leaf ◽  
Functional Screening ◽  
Virus Induced Gene Silencing ◽  
Individual Gene ◽  
Cotton Species ◽  
Allotetraploid Cotton

Abstract Background An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. The function of the lncRNAs activated in allotetraploid cotton remain largely unknown. Results We employed transcriptome analysis to examine the relationship between the lncRNAs and mRNAs of protein coding genes (PCGs) in cotton leaf tissue under abiotic stresses. LncRNA expression was preferentially associated with that of the flanking PCGs. Selected highly-expressed lncRNA candidates (n = 111) were subjected to a functional screening pilot test in which virus-induced gene silencing was integrated with abiotic stress treatment. From this low-throughput screen, we obtained candidate lncRNAs relating to plant height and tolerance to drought and other abiotic stresses. Conclusions Low-throughput screen is an effective method to find functional lncRNA for further study. LncRNAs were more active in abiotic stresses than PCG expression, especially temperature stress. LncRNA XLOC107738 may take a cis-regulatory role in response to environmental stimuli. The degree to which lncRNAs are constitutively expressed may impact expression patterns and functions on the individual gene level rather than in genome-wide aggregate.

The Functional Examination of Conserved and Non-conserved lncRNA in Allotetraploid Gossypium hirsutum

2020 ◽  
Author(s):  
Xueying Guan ◽  
Luyao Wang ◽  
Jin Han ◽  
Kening Lu ◽  
Menglin Li ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Evolutionary Model ◽  
Functional Screening ◽  
Virus Induced Gene Silencing ◽  
Protein Coding ◽  
Polyploid Evolution ◽  
Protein Coding Genes ◽  
Cotton Species ◽  
Conservation Level ◽  
Allotetraploid Cotton

Abstract Background The relationship between the lncRNA conservation level and its function is controversial. One of the technique barrier to address this question is how to define the conserved non-coding genes across species.Results We developed an evolutionary model using diploid and allotetraploid cotton species to identify 80% of the non-coding transcripts unique to the allotetraploid cotton in comparison with its diploid ancestors. This led us to define conserved lncRNA and non-conserved lncRNA based on their conservation throughout polyploid evolution. LncRNA expression was preferentially associated with the flanking protein-coding genes, indicating a regulatory role in cis in response to environmental stimuli. However, the conserved and non-conserved lncRNAs showed no difference in their levels of association with the expression of the flanking protein-coding genes. The 111 selected highly expressed conserved and non-conserved lncRNA candidates were subjected to a virus-induced gene silencing operation that was integrated with abiotic stress treatments. From the low-throughput, functional screening pilot test, we obtained candidate lncRNAs related to plant height, tolerance to drought and other abiotic stresses. Conclusions The conservation level of the lncRNAs may impact on their expression patterns and functions as individual case rather than in genome wide.

scholarly journals Genome-wide identification and expression analysis of PUB genes in cotton

2020 ◽  
Author(s):  
Xuke Lu ◽  
Na Shu ◽  
Delong Wang ◽  
Junjuan Wang ◽  
Xiugui Chen ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Structure Evolution ◽  
Homologous Gene ◽  
Segmental Duplications ◽  
Gene Pairs ◽  
Genome Wide ◽  
Cotton Species ◽  
Tandem Duplications

Abstract Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stress, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and is a necessity when studying the mechanism of stress tolerance in cotton. Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely distributed in cells, but primarily in the nucleus. The PUBs in cotton were divided into six subfamilies (A-F) on the basis of phylogenetic analysis, and the intron/exon structure was comparatively conserved within each subfamily. Location analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs shared in A2 and D5 were found; however no tandem duplication region in A2 or D5 was found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, the At subgenome and the Dt subgenome of allotetraploid cotton, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. Conclusion: This study reports the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in response to abiotic stresses (including those induced by salt, drought, hot and cold) to varying degrees.

scholarly journals Genome-wide identification and expression analysis of PUB genes in cotton

2020 ◽  
Author(s):  
Xuke Lu ◽  
Na Shu ◽  
Delong Wang ◽  
Junjuan Wang ◽  
Xiugui Chen ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Structure Evolution ◽  
Homologous Gene ◽  
Segmental Duplications ◽  
Gene Pairs ◽  
Genome Wide ◽  
Cotton Species ◽  
Tandem Duplications

Abstract Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stress, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and is a necessity when studying the mechanism of stress tolerance in cotton. Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely distributed in cells, but primarily in the nucleus. The PUBs in cotton were divided into six subfamilies (A-F) on the basis of phylogenetic analysis, and the intron/exon structure was comparatively conserved within each subfamily. Location analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs shared in A2 and D5 were found; however no tandem duplication region in A2 or D5 was found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, the At subgenome and the Dt subgenome of allotetraploid cotton, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. Conclusion: This study reports the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in response to abiotic stresses (including those genes induced by salt, drought, hot and cold) to varying degrees.

scholarly journals Genome-wide identification and expression analysis of PUB genes in cotton

2020 ◽  
Author(s):  
Xuke Lu ◽  
Na Shu ◽  
Delong Wang ◽  
Junjuan Wang ◽  
Xiugui Chen ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Structure Evolution ◽  
Homologous Gene ◽  
Segmental Duplications ◽  
Gene Pairs ◽  
Genome Wide ◽  
Cotton Species ◽  
Tandem Duplications

Abstract Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stresses, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and a necessity when studying the mechanisms of stress- tolerance in cotton.Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely localized in cells, but primarily in the nucleus. The PUBs in cotton were classified into six subfamilies (A-F) on the basis of phylogenetic analysis, which was testified by the analysis of conserved motifs and exon-intron structures. Chromosomal localization analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment analysis, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs in A2 and D5 were found; however no tandem duplications in A2 or D5 were found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, At sub-genome and Dt sub-genome of G. hirsutum, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. Conclusion: This study reported the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in the response to abiotic stresses (including salt, drought, hot and cold) to varying degrees.

scholarly journals Evolutionary Conservation and Divergence of Genes Encoding 3-Hydroxy-3-methylglutaryl Coenzyme A Synthase in the Allotetraploid Cotton Species Gossypium hirsutum

Cells ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 412 ◽  
Author(s):  
Wei Liu ◽  
Zhiqiang Zhang ◽  
Wei Zhu ◽  
Zhongying Ren ◽  
Lin Jia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gossypium Hirsutum ◽  
Plant Species ◽  
Coenzyme A ◽  
Mevalonate Pathway ◽  
Expression Patterns ◽  
Duplicated Genes ◽  
Ancestral Gene ◽  
Cotton Species ◽  
Allotetraploid Cotton

Polyploidization is important for the speciation and subsequent evolution of many plant species. Analyses of the duplicated genes produced via polyploidization events may clarify the origin and evolution of gene families. During terpene biosynthesis, 3-hydroxy-3-methylglutaryl coenzyme A synthase (HMGS) functions as a key enzyme in the mevalonate pathway. In this study, we first identified a total of 53 HMGS genes in 23 land plant species, while no HMGS genes were detected in three green algae species. The phylogenetic analysis suggested that plant HMGS genes may have originated from a common ancestral gene before clustering in different branches during the divergence of plant lineages. Then, we detected six HMGS genes in the allotetraploid cotton species (Gossypium hirsutum), which was twice that of the two diploid cotton species (Gossypium raimondii and Gossypium arboreum). The comparison of gene structures and phylogenetic analysis of HMGS genes revealed conserved evolution during polyploidization in Gossypium. Moreover, the expression patterns indicated that six GhHMGS genes were expressed in all tested tissues, with most genes considerably expressed in the roots, and they were responsive to various phytohormone treatments and abiotic stresses. The sequence and expression divergence of duplicated genes in G. hirsutum implied the sub-functionalization of GhHMGS1A and GhHMGS1D as well as GhHMGS3A and GhHMGS3D, whereas it implied the pseudogenization of GhHMGS2A and GhHMGS2D. Collectively, our study unraveled the evolutionary history of HMGS genes in green plants and from diploid to allotetraploid in cotton and illustrated the different evolutionary fates of duplicated HMGS genes resulting from polyploidization.

scholarly journals Genome-wide identification and expression analysis of PUB genes in cotton

2020 ◽  
Author(s):  
Xuke Lu ◽  
Na Shu ◽  
Delong Wang ◽  
Junjuan Wang ◽  
Xiugui Chen ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Structure Evolution ◽  
Homologous Gene ◽  
Segmental Duplications ◽  
Gene Pairs ◽  
Genome Wide ◽  
Cotton Species ◽  
Tandem Duplications

Abstract Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stresses, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and a necessity when studying the mechanisms of stress- tolerance in cotton. Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely localized in cells, but primarily in the nucleus. The PUBs in cotton were classified into six subfamilies (A-F) on the basis of phylogenetic analysis, which was testified by the analysis of conserved motifs and exon-intron structures. Chromosomal localization analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment analysis, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs in A2 and D5 were found; however no tandem duplications in A2 or D5 were found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, At sub-genome and Dt sub-genome of G. hirsutum, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. Conclusion: This study reported the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in the response to abiotic stresses (including salt, drought, hot and cold) to varying degrees.

scholarly journals Comprehensive Identification and Expression Analysis of CRY Gene Family in Gossypium

2022 ◽  
Author(s):  
Chaochen Huang ◽  
Pengbo Li ◽  
Junfeng Cao ◽  
Zishou Zheng ◽  
Jinquan Huang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Expression Patterns ◽  
Diploid Species ◽  
Cry Genes ◽  
Gene Expressions ◽  
Element Analysis ◽  
Cry Gene ◽  
Cotton Species ◽  
Allotetraploid Cotton

Abstract Background: The cryptochromes (CRY) comprise a specific blue light receptor for plants and animals, which play crucial roles in physiological processes of plant growth, development, and stress tolerance. Results: In the present work, a systematical analysis of CRY gene family from five allotetraploid cotton species, G. hirsutum, G. barbadense, G. tomentosum, G. mustelinum and G. darwinii together with seven diploid species. There were 18, 17, 17, 17, and 17 CRYs identified in G. hirsutum, G. barbadense, G. tomentosum, G. mustelinum and G. darwinii, respectively, whereas five to nine CRY genes were identified in the diploid species. Phylogenetic analysis of the protein-coding sequences revealed that CRY genes from the allotetraploids G. hirsutum and G. barbadense, three diploid cotton species (G. raimondii, G. herbaceum, and G. arboreum), and Arabidopsis thaliana could be classified into seven clades. Synteny analysis suggested that the homoeolog of G. hirsutum Gh_A02G0384 has undergone an evolutionary loss event in the other four allotetraploid cotton species. Cis-element analysis predicated the possible functions of CRY genes in G. hirsutum. Public RNA-seq data were investigated to analyze the expression patterns of G. hirsutum CRY genes in various tissues as well as gene expressions under abiotic stress treatments. Conclusion: These results indicated the possible functions of G. hirsutum CRY genes in differential tissues as well as in response to abiotic stress during the cotton plants life cycle.

scholarly journals Genome-wide identification and expression analysis of PUB genes in cotton

2020 ◽  
Author(s):  
Xuke Lu ◽  
Na Shu ◽  
Delong Wang ◽  
Junjuan Wang ◽  
Xiugui Chen ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Structure Evolution ◽  
Homologous Gene ◽  
Segmental Duplications ◽  
Gene Pairs ◽  
Genome Wide ◽  
Cotton Species ◽  
Tandem Duplications

Abstract Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stresses, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and a necessity when studying the mechanisms of stress- tolerance in cotton.Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely localized in cells, but primarily in the nucleus. The PUBs in cotton were classified into six subfamilies (A-F) on the basis of phylogenetic analysis, which was testified by the analysis of conserved motifs and exon-intron structures. Chromosomal localization analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment analysis, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs in A2 and D5 were found; however no tandem duplications in A2 or D5 were found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, At sub-genome and Dt sub-genome of G. hirsutum, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. Conclusions: This study reported the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in the response to abiotic stresses (including salt, drought, hot and cold) to varying degrees.

scholarly journals Roles of the 14-3-3 gene family in cotton flowering

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Na Sang ◽  
Hui Liu ◽  
Bin Ma ◽  
Xianzhong Huang ◽  
Lu Zhuo ◽  
...  
Keyword(s):  
Gene Family ◽  
Protein Interactions ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Bimolecular Fluorescence Complementation ◽  
Structural Motif ◽  
Virus Induced Gene Silencing ◽  
Protein Protein Interactions ◽  
Basic Leucine Zipper ◽  
Genome Wide

Abstract Background In plants, 14-3-3 proteins, also called GENERAL REGULATORY FACTORs (GRFs), encoded by a large multigene family, are involved in protein–protein interactions and play crucial roles in various physiological processes. No genome-wide analysis of the GRF gene family has been performed in cotton, and their functions in flowering are largely unknown. Results In this study, 17, 17, 31, and 17 GRF genes were identified in Gossypium herbaceum, G. arboreum, G. hirsutum, and G. raimondii, respectively, by genome-wide analyses and were designated as GheGRFs, GaGRFs, GhGRFs, and GrGRFs, respectively. A phylogenetic analysis revealed that these proteins were divided into ε and non-ε groups. Gene structural, motif composition, synteny, and duplicated gene analyses of the identified GRF genes provided insights into the evolution of this family in cotton. GhGRF genes exhibited diverse expression patterns in different tissues. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhGRFs interacted with the cotton FLOWERING LOCUS T homologue GhFT in the cytoplasm and nucleus, while they interacted with the basic leucine zipper transcription factor GhFD only in the nucleus. Virus-induced gene silencing in G. hirsutum and transgenic studies in Arabidopsis demonstrated that GhGRF3/6/9/15 repressed flowering and that GhGRF14 promoted flowering. Conclusions Here, 82 GRF genes were identified in cotton, and their gene and protein features, classification, evolution, and expression patterns were comprehensively and systematically investigated. The GhGRF3/6/9/15 interacted with GhFT and GhFD to form florigen activation complexs that inhibited flowering. However, GhGRF14 interacted with GhFT and GhFD to form florigen activation complex that promoted flowering. The results provide a foundation for further studies on the regulatory mechanisms of flowering.

scholarly journals Identification and Characterization of Abiotic Stress Responsive CBL-CIPK Family Genes in Medicago

2021 ◽  
Vol 22 (9) ◽  
pp. 4634
Author(s):  
Wenxuan Du ◽  
Junfeng Yang ◽  
Lin Ma ◽  
Qian Su ◽  
Yongzhen Pang
Keyword(s):  
Abiotic Stress ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Interacting Protein ◽  
Forage Crop ◽  
Cis Acting ◽  
Protein Motifs ◽  
Plant Signal Transduction ◽  
Identification And Characterization

The calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) play important roles in plant signal transduction and response to abiotic stress. Plants of Medicago genus contain many important forages, and their growth is often affected by a variety of abiotic stresses. However, studies on the CBL and CIPK family member and their function are rare in Medicago. In this study, a total of 23 CBL and 58 CIPK genes were identified from the genome of Medicago sativa as an important forage crop, and Medicaog truncatula as the model plant. Phylogenetic analysis suggested that these CBL and CIPK genes could be classified into five and seven groups, respectively. Moreover, these genes/proteins showed diverse exon-intron organizations, architectures of conserved protein motifs. Many stress-related cis-acting elements were found in their promoter region. In addition, transcriptional analyses showed that these CBL and CIPK genes exhibited distinct expression patterns in various tissues, and in response to drought, salt, and abscisic acid treatments. In particular, the expression levels of MtCIPK2 (MsCIPK3), MtCIPK17 (MsCIPK11), and MtCIPK18 (MsCIPK12) were significantly increased under PEG, NaCl, and ABA treatments. Collectively, our study suggested that CBL and CIPK genes play crucial roles in response to various abiotic stresses in Medicago.

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