Brief Note Natural hybridization between Gossypium mustelinum and exotic allotetraploid cotton species

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.

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Characterization and Stress Response of the JmjC Domain-Containing Histone Demethylase Gene Family in the Allotetraploid Cotton Species Gossypium hirsutum

Plants ◽

10.3390/plants9111617 ◽

2020 ◽

Vol 9 (11) ◽

pp. 1617

Author(s):

Jie Zhang ◽

Junping Feng ◽

Wei Liu ◽

Zhongying Ren ◽

Junjie Zhao ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Response ◽

Gossypium Hirsutum ◽

Gene Family ◽

Function Analysis ◽

Histone Demethylase ◽

Abiotic Stress Response ◽

Cotton Species ◽

Jmjc Domain ◽

Allotetraploid Cotton

Histone modification is an important epigenetic modification that controls gene transcriptional regulation in eukaryotes. Histone methylation is accomplished by histone methyltransferase and can occur on two amino acid residues, arginine and lysine. JumonjiC (JmjC) domain-containing histone demethylase regulates gene transcription and chromatin structure by changing the methylation state of the lysine residue site and plays an important role in plant growth and development. In this study, we carried out genome-wide identification and comprehensive analysis of JmjC genes in the allotetraploid cotton species Gossypium hirsutum. In total, 50 JmjC genes were identified and in G. hirsutum, and 25 JmjC genes were identified in its two diploid progenitors, G. arboreum and G. raimondii, respectively. Phylogenetic analysis divided these JmjC genes into five subfamilies. A collinearity analysis of the two subgenomes of G. hirsutum and the genomes of G. arboreum and G. raimondii uncovered a one-to-one relationship between homologous genes of the JmjC gene family. Most homologs in the JmjC gene family between A and D subgenomes of G. hirsutum have similar exon-intron structures, which indicated that JmjC family genes were conserved after the polyploidization. All G. hirsutumJmjC genes were found to have a typical JmjC domain, and some genes also possess other special domains important for their function. Analysis of promoter regions revealed that cis-acting elements, such as those related to hormone and abiotic stress response, were enriched in G. hirsutum JmjC genes. According to a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, most G. hirsutumJmjC genes had high abundance expression at developmental stages of fibers, suggesting that they might participate in cotton fiber development. In addition, some G. hirsutumJmjC genes were found to have different degrees of response to cold or osmotic stress, thus indicating their potential role in these types of abiotic stress response. Our results provide useful information for understanding the evolutionary history and biological function of JmjC genes in cotton.

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Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars

10.21203/rs.2.15897/v2 ◽

2019 ◽

Author(s):

Marianna de Oliveira Moura ◽

Anna Karoline S Fausto ◽

Amanda Fanelli ◽

Fernanda A de F Guedes ◽

Tatiane da F Silva ◽

...

Keyword(s):

Virus Infection ◽

Biotic Stress ◽

Expression Profiles ◽

In Silico Analysis ◽

Defense Responses ◽

Genome Wide ◽

Cotton Species ◽

Herbivore Attack ◽

Almost All ◽

Allotetraploid Cotton

Abstract Background Dicer-like proteins (DCLs) are fundamental players in RNA-silencing mechanisms acting in gene regulation via miRNAs and in antiviral protection in plants, in addition to being related to other biotic and abiotic stresses. Despite be identified in some crops, cotton DCLs weren't characterized until now. Here we characterize the DCLs of three cotton species and analyzed their expression profiles during biotic stress. Results We identified 11 DCLs in the allotetraploid cotton Gossypium hirsutum and 7 and 6 in the diploid G. arboreum and G. raimondii, respectively. Among some DCL duplication observed in these genomes, we observe the presence of an extra DCL3 in the three cotton species, not found in others eudicots until now. All the DCL types identified by in silico analysis in the allotetraploid cotton genome were able to generate transcripts, as observed by gene expression analysis in distinct tissues. Based on the importance of DCLs for plant virus defense, responses of cotton DCLs to virus infection and/or herbivore attack using two commercial cotton cultivars (cv.), one susceptible (Fibermax 966) and another resistant (Delta Opal) to polerovirus CLRDV infection were analyzed. Both cvs. responded differently to virus infection. At the initial stages, 24dpi, the resistant cv. showed strong induction of DCL2a and b, while the susceptible cv. showed a down-regulation of these genes, wherever DCL4 expression was highly induced. Herbivore attack did not induce contrasting profiles between cotton DCLs transcripts in either cotton cv. Conclusions The allotetraploide cotton G. hirsutum has almost all DCLs found in their diploid relative and duplication of DCL2 and DCL3 were found in the three species. All the four classes of DCL respond to aphid attack and virus infection in G. hirsutum, however, remarkable differences in DCL initial responses against the virus itself may be responsible for the virus susceptible and/or resistant phenotype of the contrasting cotton cv. studied.

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Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars

BMC Plant Biology ◽

10.1186/s12870-019-2112-4 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Marianna O. Moura ◽

Anna Karoline S. Fausto ◽

Amanda Fanelli ◽

Fernanda A. de F. Guedes ◽

Tatiane da F. Silva ◽

...

Keyword(s):

Virus Infection ◽

Biotic Stress ◽

Time Course ◽

Expression Profiles ◽

In Silico Analysis ◽

Inoculation Site ◽

Cotton Species ◽

Herbivore Attack ◽

Almost All ◽

Allotetraploid Cotton

Abstract Background Dicer-like proteins (DCLs) are essential players in RNA-silencing mechanisms, acting in gene regulation via miRNAs and in antiviral protection in plants and have also been associated to other biotic and abiotic stresses. To the best of our knowledge, despite being identified in some crops, cotton DCLs haven’t been characterized until now. In this work, we characterized the DCLs of three cotton species and analyzed their expression profiles during biotic stress. Results As main results, 11 DCLs in the allotetraploid cotton Gossypium hirsutum, 7 and 6 in the diploid G. arboreum and G. raimondii, were identified, respectively. Among some DCLs duplications observed in these genomes, the presence of an extra DCL3 in the three cotton species were detected, which haven’t been found in others eudicots. All the DCL types identified by in silico analysis in the allotetraploid cotton genome were able to generate transcripts, as observed by gene expression analysis in distinct tissues. Based on the importance of DCLs for plant defense against virus, responses of cotton DCLs to virus infection and/or herbivore attack using two commercial cotton cultivars (cv.), one susceptible (FM966) and another resistant (DO) to polerovirus CLRDV infection, were analyzed. Both cvs. Responded differently to virus infection. At the inoculation site, the resistant cv. showed strong induction of DCL2a and b, while the susceptible cv. showed a down-regulation of these genes, wherever DCL4 expression was highly induced. A time course of DCL expression in aerial parts far from inoculation site along infection showed that DCL2b and DCL4 were repressed 24 h after infection in the susceptible cotton. As CLRDV is aphid-transmitted, herbivore attack was also checked. Opposite expression pattern of DCL2a and b and DCL4 was observed for R and S cottons, showing that aphid feeding alone may induce DCL modulation. Conclusions Almost all the DCLs of the allotetraploide G. hirsutum cotton were found in their relative diploids. Duplications of DCL2 and DCL3 were found in the three species. All four classes of DCL responded to aphid attack and virus infection in G. hirsutum. DCLs initial responses against the virus itself and/or herbivore attack may be contributing towards virus resistance.

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

Cells ◽

10.3390/cells8050412 ◽

2019 ◽

Vol 8 (5) ◽

pp. 412 ◽

Cited By ~ 2

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.

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Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species

Molecular Plant ◽

10.1016/j.molp.2020.07.006 ◽

2020 ◽

Vol 13 (9) ◽

pp. 1238-1240

Author(s):

Peng He ◽

Yuzhou Zhang ◽

Guanghui Xiao

Keyword(s):

Genome Evolution ◽

Cotton Species ◽

Allotetraploid Cotton

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Divergent improvement of two cultivated allotetraploid cotton species

Plant Biotechnology Journal ◽

10.1111/pbi.13547 ◽

2021 ◽

Author(s):

Lei Fang ◽

Ting Zhao ◽

Yan Hu ◽

Zhanfeng Si ◽

Xiefei Zhu ◽

...

Keyword(s):

Cotton Species ◽

Allotetraploid Cotton

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Comprehensive Identification and Expression Analysis of CRY Gene Family in Gossypium

10.21203/rs.3.rs-1165543/v1 ◽

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.

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Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars

10.21203/rs.2.15897/v1 ◽

2019 ◽

Author(s):

Marianna de Oliveira Moura ◽

Anna Karoline S Fausto ◽

Amanda Fanelli ◽

Fernanda A de F Guedes ◽

Tatiane da F Silva ◽

...

Keyword(s):

Virus Infection ◽

Biotic Stress ◽

Expression Profiles ◽

In Silico Analysis ◽

Defense Responses ◽

Genome Wide ◽

Cotton Species ◽

Herbivore Attack ◽

Almost All ◽

Allotetraploid Cotton

Abstract Background Dicer-like proteins (DCLs) are fundamental players in RNA-silencing mechanisms acting in gene regulation via miRNAs and in antiviral protection in plants, in addition to being related to other biotic and abiotic stresses. Despite be identified in some crops, cotton DCLs weren't characterized until now. Here we characterize the DCLs of three cotton species and analyzed their expression profiles during biotic stress. Results We identified 11 DCLs in the allotetraploid cotton Gossypium hirsutum and 7 and 6 in the diploid G. arboreum and G. raimondii, respectively. Among some DCL duplication observed in these genomes, we observe the presence of an extra DCL3 in the three cotton species, not found in others eudicots until now. All the DCL types identified by in silico analysis in the allotetraploid cotton genome were able to generate transcripts, as observed by gene expression analysis in distinct tissues. Based on the importance of DCLs for plant virus defense, responses of cotton DCLs to virus infection and/or herbivore attack using two commercial cotton cultivars (cv.), one susceptible (Fibermax 966) and another resistant (Delta Opal) to polerovirus CLRDV infection were analyzed. Both cvs. responded differently to virus infection. At the initial stages, 24dpi, the resistant cv. showed strong induction of DCL2a and b, while the susceptible cv. showed a down-regulation of these genes, wherever DCL4 expression was highly induced. Herbivore attack did not induce contrasting profiles between cotton DCLs transcripts in either cotton cv. Conclusions The allotetraploide cotton G. hirsutum has almost all DCLs found in their diploid relative and duplication of DCL2 and DCL3 were found in the three species. All the four classes of DCL respond to aphid attack and virus infection in G. hirsutum, however, remarkable differences in DCL initial responses against the virus itself may be responsible for the virus susceptible and/or resistant phenotype of the contrasting cotton cv. studied.

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

10.21203/rs.3.rs-88142/v1 ◽

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.

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