Identification and function analysis of drought-specific small RNAs in Gossypium hirsutum L.

Lu, Xuke; Yin, Zujun; Wang, Junjuan; Chen, Xiugui; Wang, Delong; Wang, Shuai; Guo, Lixue; Fan, Weili; Chen, Chao; Wang, Xiaoge; Cui, Ruifeng; Zhang, Binglei; Han, Mingge; Yang, Xiaomin; Ye, Wuwei

doi:10.1016/j.plantsci.2018.11.015

Cited by 15 publications

(11 citation statements)

References 44 publications

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“…After the treatment, plant leaves were harvested and frozen with liquid nitrogen for use. For the agrobacteriummediated transformation, we referred the method used by Lu et al [41].…”

Section: Planting Of Cotton and Nicotiana Benthamiana Seedlingsmentioning

confidence: 99%

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

Shu²,

Wang

et al. 2020

BMC Genomics

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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 (D 5), G. arboreum (A 2), G. hirsutum (AD 1) 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 D 5 , 2 tandem duplications and 25 segmental duplications in A 2 , and 143 homologous gene pairs in A 2 and D 5 were found; however no tandem duplications in A 2 or D 5 were found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intrasubgenome 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.

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“…After the treatment, plant leaves were harvested and frozen with liquid nitrogen for use. For the agrobacteriummediated transformation, we referred the method used by Lu et al [41].…”

Section: Planting Of Cotton and Nicotiana Benthamiana Seedlingsmentioning

confidence: 99%

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

Shu²,

Wang

et al. 2020

BMC Genomics

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“…Uniform seedlings were chosen and transplanted into sand pots (10 plants in each pot) in the greenhouse (14 h/day, 30°C and 10 h/night, 24°C) at the Institute of Cotton Research of CAAS. For the agrobacterium-mediated transformation, we referred the method used by Lu et al [26].…”

Section: Cotton and Arabidopsis Thalianamentioning

confidence: 99%

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

Shu²,

Wang

et al. 2019

Preprint

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Background: U-box gene is gene of ubiquitin ligase, which contain U-box domain. Plant U-box gene (PUB) plays an important role in the response to stresses, but less reports about PUBs in cotton were issued. Therefore research of PUBs in cotton will be of great importance and necessity to study the mechanism of tolerance-resistance of the cotton. Results: In this study, we identified 93, 96, 185 and 208 PUBs from the three sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. arbadense (AD2), respectively. Subcellular localization analysis showed that the PUBs in cotton were distributed in various parts of the cells, mainly in the nucleus. The PUBs in cotton were divided into six subfamilies (A-F) by phylogenetic analysis, and intron/exon structure was comparatively conserved within the subfamily. Location analysis showed cotton PUBs were unevenly anchored on all the chromosomes varying from 1 to 14. It was found that there are 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 between A2 and D5, through multiple sequence alignment, but that the tandem duplication region of A2 or D5 was not found. It was also found that, there were 105, 14 and 17 homologous gene pairs in intra-subgenome of At and Dt, At subgenome, Dt subgenome of allotetraploid cotton, respectively. Among the PUBs family, totally 106, 116, 85 and 81 homologous gene pairs were found in A2-At, A2-Dt, D5-At and D5-Dt. Function analysis of GhPUB85A and GhPUB45D showed they positively responded the abiotic stresses, but the expression patterns were different. Besides, although the expressions of these two homologous genes were similar, their contributions were different when responding to stresses, showing different response differences to abiotic stresses and function division of two subgenomes of G. hirsutum. Conclusion: This study provided the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs was highly conserved in evolutionary history of cotton. All PUB genes were involved in response to abiotic stresses at varying degrees.

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“…There have been many reports on the molecular mechanisms induced by drought stress in leguminous forage ( Li et al, 2017 ; Zhang et al, 2018 , 2019 ), but few on M. ruthenica . Moreover, a number of miRNAs have been identified to be associated with responses to drought stress in several species, such as Arabidopsis thaliana ( Liu et al, 2008 ), tomato ( Liu et al, 2018 ), Oryza sativa ( Chen and Li, 2018 ; Nadarajah and Kumar, 2019 ), and Gossypium hirsutum ( Lu et al, 2019 ). Here, we integrated transcriptome, miRNAome, and degradome results to identify drought-response genes and miRNAs in M. ruthenica , and find potential regulatory patterns of miRNA-target pairs.…”

Section: Introductionmentioning

confidence: 99%

Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica

et al. 2021

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Drought is a major limiting factor in foraging grass yield and quality. Medicago ruthenica (M. ruthenica) is a high-quality forage legume with drought resistance, cold tolerance, and strong adaptability. In this study, we integrated transcriptome, small RNA, and degradome sequencing in identifying drought response genes, microRNAs (miRNAs), and key miRNA-target pairs in M. ruthenica under drought and rewatering treatment conditions. A total of 3,905 genes and 50 miRNAs (45 conserved and 5 novel miRNAs) were significantly differentially expressed in three test conditions (CK: control, DS: plants under drought stress, and RW: plants rewatering after drought stress). The degradome sequencing (AllenScore < 4) analysis revealed that 104 miRNAs (11 novel and 93 conserved miRNAs) were identified with 263 target transcripts, forming 296 miRNA-target pairs in three libraries. There were 38 differentially expressed targets from 16 miRNAs in DS vs. CK, 31 from 11 miRNAs in DS vs. RW, and 6 from 3 miRNAs in RW vs. CK; 21, 18, and 3 miRNA-target gene pairs showed reverse expression patterns in DS vs. CK, DS vs. RW, and RW vs. CK comparison groups, respectively. These findings provide valuable information for further functional characterization of genes and miRNAs in response to abiotic stress, in general, and drought stress in M. ruthenica, and potentially contribute to drought resistance breeding of forage in the future.

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Identification and function analysis of drought-specific small RNAs in Gossypium hirsutum L.

Cited by 15 publications

References 44 publications

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

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

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

Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica

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