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

2019 ◽  
Author(s):  
Xuke Lu ◽  
Na Shu ◽  
Delong Wang ◽  
Junjuan Wang ◽  
Xiugui Chen ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Abiotic Stresses ◽  
Function Analysis ◽  
Structure Evolution ◽  
Homologous Gene ◽  
Segmental Duplications ◽  
Gene Pairs ◽  
Genome Wide ◽  
Cotton Species ◽  
Tandem Duplications

Abstract 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.

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

2019 ◽  
Author(s):  
Xuke Lu ◽  
Na Shu ◽  
Delong Wang ◽  
Junjuan Wang ◽  
Xiugui Chen ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Abiotic Stresses ◽  
Function Analysis ◽  
Structure Evolution ◽  
Homologous Gene ◽  
Segmental Duplications ◽  
Gene Pairs ◽  
Genome Wide ◽  
Cotton Species ◽  
Tandem Duplications

Abstract 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.

scholarly journals Genome-wide Identification and Expression Analysis of the GRAS Transcription Factor Family and its Response to Abiotic Stress in Sorghum [Sorghum bicolor (L.) Moench]

2021 ◽  
Author(s):  
Yu Fan ◽  
Jun Yan ◽  
Dili Lai ◽  
Hao Yang ◽  
Guoxing Xue ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Sorghum Bicolor ◽  
Plant Development ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Segmental Duplications ◽  
Systematic Analysis ◽  
Genome Wide ◽  
Duplication Events ◽  
Gibberellin Content

Abstract Background: GRAS is a very important family of transcription factors that are unique to plants, playing important roles in plant development and their response to abiotic stress. Since the sequencing of the sorghum genome, a large number of genetic studies based on this genomic information have been carried out. Nevertheless, no detailed identification or genome-wide analysis of GRAS family genes in Sorghum bicolor has been published.Results: A total of 81 SbGRAS genes were identified based on the S. bicolor genome. They were named SbGRAS01 to SbGRAS81 and grouped into 13 subfamilies (LISCL, DLT, OS19, SCL4/7, PAT1, SHR, SCL3, HAM-1, SCR, DELLA, HAM-2, LAS and OS4). SbGRAS genes are not evenly distributed on the chromosomes, and we found tandem duplication events and segmental duplications of SbGRAS genes on S. bicolor chromosomes. According to the results of the gene and motif composition, SbGRAS members located in the same group contained analogous intron/exon and motif organizations. By quantitative (q) RT-PCR, we quantified the expression of SbGRAS members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage. We also measured gibberellin content under the different abiotic stresses.Conclusions: We identified 81 SbGRAS genes and further analyzed their structural composition, and evolution and expression patterns of SbGRAS proteins. The latter analysis indicated that SbGRAS is important in the course of plant development and its response to abiotic stress. Collectively, this systematic analysis lays the foundation for further study of the functional characteristics of GRAS genes of S. bicolor.

scholarly journals Comprehensive Analysis of Autophagy-Related Genes in Sweet Orange (Citrus sinensis) Highlights Their Roles in Response to Abiotic Stresses

2020 ◽  
Vol 21 (8) ◽  
pp. 2699 ◽  
Author(s):  
Xing-Zheng Fu ◽  
Xue Zhou ◽  
Yuan-Yuan Xu ◽  
Qiu-Ling Hui ◽  
Chang-Pin Chun ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Citrus Sinensis ◽  
Sweet Orange ◽  
Expression Patterns ◽  
Bioinformatic Analysis ◽  
Degradation Pathway ◽  
Segmental Duplications ◽  
Intracellular Degradation ◽  
Genome Wide ◽  
A Genome

Autophagy is a highly conserved intracellular degradation pathway that breaks down damaged macromolecules and/or organelles. It is involved in plant development and senescence, as well as in biotic and abiotic stresses. However, the autophagy process and related genes are largely unknown in citrus. In this study, we identified 35 autophagy-related genes (CsATGs—autophagy-related genes (ATGs) of Citrus sinensis, Cs) in a genome-wide manner from sweet orange (Citrus sinensis). Bioinformatic analysis showed that these CsATGs were highly similar to Arabidopsis ATGs in both sequence and phylogeny. All the CsATGs were randomly distributed on nine known (28 genes) and one unknown (7 genes) chromosomes. Ten CsATGs were predicted to be segmental duplications. Expression patterns suggested that most of the CsATG were significantly up- or down-regulated in response to drought; cold; heat; salt; mannitol; and excess manganese, copper, and cadmium stresses. In addition, two ATG18 members, CsATG18a and CsATG18b, were cloned from sweet orange and ectopically expressed in Arabidopsis. The CsATG18a and CsATG18b transgenic plants showed enhanced tolerance to osmotic stress, salt, as well as drought (CsATG18a) or cold (CsATG18b), compared to wild-type plants. These results highlight the essential roles of CsATG genes in abiotic stresses.

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.

scholarly journals Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xin Wang ◽  
Ming-Hua Wu ◽  
Dong Xiao ◽  
Ruo-Lan Huang ◽  
Jie Zhan ◽  
...  
Keyword(s):  
Stress Responses ◽  
Segmental Duplication ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Segmental Duplications ◽  
Evolutionary Analysis ◽  
Gene Pairs ◽  
Al Stress ◽  
Peanut Genome

Abstract Background As an important cash crop, the yield of peanut is influenced by soil acidification and pathogen infection. Receptor-like protein kinases play important roles in plant growth, development and stress responses. However, little is known about the number, location, structure, molecular phylogeny, and expression of RLKs in peanut, and no comprehensive analysis of RLKs in the Al stress response in peanuts have been reported. Results A total of 1311 AhRLKs were identified from the peanut genome. The AhLRR-RLKs and AhLecRLKs were further divided into 24 and 35 subfamilies, respectively. The AhRLKs were randomly distributed across all 20 chromosomes in the peanut. Among these AhRLKs, 9.53% and 61.78% originated from tandem duplications and segmental duplications, respectively. The ka/ks ratios of 96.97% (96/99) of tandem duplication gene pairs and 98.78% (646/654) of segmental duplication gene pairs were less than 1. Among the tested tandem duplication clusters, there were 28 gene conversion events. Moreover, all total of 90 Al-responsive AhRLKs were identified by mining transcriptome data, and they were divided into 7 groups. Most of the Al-responsive AhRLKs that clustered together had similar motifs and evolutionarily conserved structures. The gene expression patterns of these genes in different tissues were further analysed, and tissue-specifically expressed genes, including 14 root-specific Al-responsive AhRLKs were found. In addition, all 90 Al-responsive AhRLKs which were distributed unevenly in the subfamilies of AhRLKs, showed different expression patterns between the two peanut varieties (Al-sensitive and Al-tolerant) under Al stress. Conclusions In this study, we analysed the RLK gene family in the peanut genome. Segmental duplication events were the main driving force for AhRLK evolution, and most AhRLKs subject to purifying selection. A total of 90 genes were identified as Al-responsive AhRLKs, and the classification, conserved motifs, structures, tissue expression patterns and predicted functions of Al-responsive AhRLKs were further analysed and discussed, revealing their putative roles. This study provides a better understanding of the structures and functions of AhRLKs and Al-responsive AhRLKs.

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