scholarly journals Systematic analysis of JmjC gene family and stress­-response expression of KDM5 subfamily genes in Brassica napus

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11137
Author(s):  
Xinghui He ◽  
Qianwen Wang ◽  
Jiao Pan ◽  
Boyu Liu ◽  
Ying Ruan ◽  
...  
Keyword(s):  
High Temperature ◽  
Stress Response ◽  
Brassica Napus ◽  
Gene Duplication ◽  
Retention Rate ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Chromosomal Mapping ◽  
Oilseed Crop ◽  
Response Expression

Background Jumonji C (JmjC) proteins exert critical roles in plant development and stress response through the removal of lysine methylation from histones. Brassica napus, which originated from spontaneous hybridization by Brassica rapa and Brassica oleracea, is the most important oilseed crop after soybean. In JmjC proteins of Brassica species, the structure and function and its relationship with the parents and model plant Arabidopsis thaliana remain uncharacterized. Systematic identification and analysis for JmjC family in Brassica crops can facilitate the future functional characterization and oilseed crops improvement. Methods Basing on the conserved JmjC domain, JmjC homologs from the three Brassica species, B. rapa (AA), B. oleracea (CC) and B. napus, were identified from the Brassica database. Some methods, such as phylogenic analysis, chromosomal mapping, HMMER searching, gene structure display and Logos analysis, were used to characterize relationships of the JmjC homologs. Synonymous and nonsynonymous nucleotide substitutions were used to infer the information of gene duplication among homologs. Then, the expression levels of BnKDM5 subfamily genes were checked under abiotic stress by qRT-PCR. Results Sixty-five JmjC genes were identified from B. napus genome, 29 from B. rapa, and 23 from B. oleracea. These genes were grouped into seven clades based on the phylogenetic analysis, and their catalytic activities of demethylation were predicted. The average retention rate of B. napus JmjC genes (B. napus JmjC gene from B. rapa (93.1%) and B. oleracea (82.6%)) exceeded whole genome level. JmjC sequences demonstrated high conservation in domain origination, chromosomal location, intron/exon number and catalytic sites. The gene duplication events were confirmed among the homologs. Many of the BrKDM5 subfamily genes showed higher expression under drought and NaCl treatments, but only a few genes were involved in high temperature stress. Conclusions This study provides the first genome-wide characterization of JmjC genes in Brassica species. The BnJmjC exhibits higher conservation during the formation process of allotetraploid than the average retention rates of the whole B. napus genome. Furthermore, expression profiles of many genes indicated that BnKDM5 subfamily genes are involved in stress response to salt, drought and high temperature.

scholarly journals Systematic analysis of JmjC gene family of Brassica napus and KDM5 subfamily involved in abiotic stress response

2019 ◽  
Author(s):  
Xinghui He ◽  
Jiao Pan ◽  
Boyu Liu ◽  
Chengfang Tan ◽  
Ying Ruan ◽  
...  
Keyword(s):  
Stress Response ◽  
Brassica Napus ◽  
Stress Responses ◽  
Retention Rate ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Homologous Gene ◽  
Oilseed Crop

Abstract Background: Jumonji C (JmjC) proteins play an important role in plant development and stress response through the removal of lysine methylation from histones. Brassica napus, which originated from spontaneous hybridization between Brassica rapa and Brassica oleracea, is the most important oilseed crop after soybean, but evolutionary relationships and functions of JmjC proteins remain unclear. Results: 65 JmjC genes were identified from B. napus genome, 29 from B. rapa, and 23 from B. oleracea. These genes were grouped into seven clades according to conserved sequences, and their catalytic activities of demethylation were predicted. Group-KDM4/JHDM3 for H3K4/9/27/36, Group-KDM5A/B for H3K4, Group-JmjC domain-only A/B for H3K27/36, Group-KDM3/JHDM2 for H3K9, and Group-JMJD6 may be for arginine demethylases. B. napus inherited most of its JmjC genes from its parents. The average retention rate of B. napus JmjC gene from B. rapa (93.1%) and B. oleracea (82.6%) exceeded that of all homologous gene pairs (83.7%) across the whole B. napus genome. Thirteen new or duplicated JmjC genes have emerged in B. napus. Sequence similarity and domain organization analyses suggest that the functions of these genes might be diversified. Furthermore, KDM5 genes were examined under stress conditions due to H3K4 demethylation. Expression profiles indicated that the genes from B. napus are possibly involved in various stress responses. Conclusion: This study provides the first genome-wide characterization of JmjC genes in Brassica species. Its JmjC genes potentially have diverse functions, and its KDM5 genes might be involved in stress response. The results of this study facilitate the future functional characterization of the demethylation of JmjC family in Brassica crops.

scholarly journals Systematic analysis of CCCH zinc finger family in Brassica napus showed that BnRR-TZFs are involved in stress resistance

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Boyi Pi ◽  
Jiao Pan ◽  
Mu Xiao ◽  
Xinchang Hu ◽  
Lei Zhang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Zinc Finger ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Natural Hybridization ◽  
Oilseed Crop ◽  
Systematic Analysis ◽  
Gene Pairs ◽  
Ccch Zinc Finger ◽  
Duplication Events

Abstract Background CCCH zinc finger family is one of the largest transcription factor families related to multiple biotic and abiotic stresses. Brassica napus L., an allotetraploid oilseed crop formed by natural hybridization between two diploid progenitors, Brassica rapa and Brassica oleracea. A systematic identification of rapeseed CCCH family genes is missing and their functional characterization is still in infancy. Results In this study, 155 CCCH genes, 81 from its parent B. rapa and 74 from B. oleracea, were identified and divided into 15 subfamilies in B. napus. Organization and syntenic analysis explained the distribution and collinearity relationship of CCCH genes, the selection pressure and evolution of duplication gene pairs in B. napus genome. 44 diploid duplication gene pairs and 4 triple duplication gene groups were found in B. napus of CCCH family and the segmental duplication is attributed to most CCCH gene duplication events in B. napus. Nine types of CCCH motifs exist in B. napus CCCH family members, and motif C-X7/8-C-X5-C-X3-H is the most common and a new conserved CCH motif (C-X5-C-X3-H) has been identified. In addition, abundant stress-related cis-elements exist in promoters of 27 subfamily IX (RR-TZF) genes and their expression profiles indicated that RR-TZF genes could be involved in responses to hormone and abiotic stress. Conclusions The results provided a foundation to understand the basic characterization and genes evolution of CCCH gene family in B. napus, and provided potential targets for genetic engineering in Brassicaceae crops in pursuit of stress-tolerant traits.

scholarly journals Genome-wide analysis and functional characterization of the DELLA gene family associated with stress tolerance in B. napus

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Rehman Sarwar ◽  
Ting Jiang ◽  
Peng Ding ◽  
Yue Gao ◽  
Xiaoli Tan ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Stress Tolerance ◽  
Stress Responses ◽  
Genomic Structure ◽  
Expression Patterns ◽  
Light Stress ◽  
Functional Characterization ◽  
Chromosomal Mapping ◽  
Della Proteins

Abstract Background Brassica napus is an essential crop for oil and livestock feed. Eventually, this crop's economic interest is at the most risk due to anthropogenic climate change. DELLA proteins constitute a significant repressor of plant growth to facilitate survival under constant stress conditions. DELLA proteins lack DNA binding domain but can interact with various transcription factors or transcription regulators of different hormonal families. Significant progress has been made on Arabidopsis and cereal plants. However, no comprehensive study regarding DELLA proteins has been delineated in rapeseed. Results In our study, we have identified 10 BnaDELLA genes. All of the BnaDELLA genes are closely related to five AtDELLA genes, suggesting a relative function and structure. Gene duplication and synteny relationship among Brassica. napus, Arabidopsis. thaliana, Brassica rapa, Brassica oleracea, and Brassica nigra genomes were also predicted to provide valuable insights into the BnaDELLA gene family evolutionary characteristics. Chromosomal mapping revealed the uneven distribution of BnaDELLA genes on eight chromosomes, and site-specific selection assessment proposes BnaDELLA genes purifying selection. The motifs composition in all BnaDELLA genes is inconsistent; however, every BnaDELLA gene contains 12 highly conserved motifs, encoding DELLA and GRAS domains. The two known miRNAs (bna-miR6029 and bna-miR603) targets BnaC07RGA and BnaA09GAI, were also predicted. Furthermore, quantitative real-time PCR (qRT-PCR) analysis has exhibited the BnaDELLA genes diverse expression patterns in the root, mature-silique, leaf, flower, flower-bud, stem, shoot-apex, and seed. Additionally, cis-acting element prediction shows that all BnaDELLA genes contain light, stress, and hormone-responsive elements on their promoters. The gene ontology (GO) enrichment report indicated that the BnaDELLA gene family might regulate stress responses. Combine with transcriptomic data used in this study, we detected the distinct expression patterns of BnaDELLA genes under biotic and abiotic stresses. Conclusion In this study, we investigate evolution feature, genomic structure, miRNAs targets, and expression pattern of the BnaDELLA gene family in B. napus, which enrich our understanding of BnaDELLA genes in B. napus and suggests modulating individual BnaDELLA expression is a promising way to intensify rapeseed stress tolerance and harvest index.

scholarly journals Genome-wide identification and characterization of NF-Y gene family in peanut (Arachis hypogaea L.)

2019 ◽  
Author(s):  
Qian Wan ◽  
Lu Luo ◽  
Xiurong Zhang ◽  
Yuying Lv ◽  
Suqing Zhu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Response ◽  
Gene Duplication ◽  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Salt Stress Response

Abstract Background Nuclear factor Y (NF-Y) gene family consists of NF-YA, NF-YB and NF-YC subfamilies. Many members of NF-Y family have been involved in plant development processes, phytohormone signaling and tolerance to stresses in Arabidopsis and other plant species. However, little attention has been given in peanut. Results A total of 33 AhNF-Y genes (AhNF-Ys) were identified and distributed on 16 chromosomes. A phylogenetic analysis indicated that NF-Y genes prossessed highly conservatism in different plants. Gene duplication analyze indicated that only segmental duplication were detected. The abiotic stress-related regulatory elements analysis showed that AhNF-Ys, except for AhNF-YB6, contained at least one abiotic stress response element. With RNA-seq data, the tissue/organ-specific expression and differential expression profiling under salt stress were analyzed, indicating that six selected AhNF-Y gene may play potential roles in the regulation of salt stress response. qRT-PCR results suggested that these AhNF-Y genes also responded to osmotic, ABA (Abscisic Acid) and SA (Salicylic acid) stresses. Conclusions In this study, thirty three AhNF-Y genes were identified in cultivated peanut and the phylogeny, gene structures, motif composition, chromosomal location, gene duplication, stress-related regulatory elements, and expression patterns were also examined. These results may contribute to functional characterization of AhNF-Y genes in further research.

scholarly journals Effects of long-term high-temperature stress on reproductive growth and seed development in development in Brassica napus

2021 ◽  
Author(s):  
Kateřina Mácová ◽  
Unnikannan Prabhullachandran ◽  
Ioannis Spyroglou ◽  
Marie Štefková ◽  
Aleš Pěnčík ◽  
...  
Keyword(s):  
High Temperature ◽  
Brassica Napus ◽  
Embryo Development ◽  
High Temperatures ◽  
Seed Yield ◽  
Seed Quality ◽  
Abortion Rate ◽  
Preharvest Sprouting ◽  
Oilseed Crop ◽  
Oil Composition

AbstractBrassica napus is the second most important oilseed crop worldwide. Increasing average temperatures and extreme weather have a severe impact on rapeseed yield. We determined the response of three cultivars to different temperature regimes (21/18 °C, 28/18 °C and 34/18 °C), focusing on the plant appearance, seed yield, seed quality, seed viability, and embryo development. Our microscopic observations identified that embryo development is affected by high temperatures. We noticed an acceleration of its development, in addition to pattern defects. Reduced fertilization rate, increased abortion rate, and preharvest sprouting would be responsible for the low seed yield at the high-temperature regime. Hormone profiling indicates that reduced auxin levels in young seeds may cause the observed embryo pattern defects. Moreover, reduced seed dormancy may result from low ABA and IAA levels in mature seeds. Glucosinolates and oil composition measurements suggest reduced seed quality. These identified cues help understand seed thermomorphogenesis and pave the way to the development of thermoresilient rapeseed plants.HighlightBrassica napus flowering plants’ growth at high temperatures accelerates embryo development, causing a high seed abortion rate and reduced seed quality. Temperature-reduced ABA levels cause premature seed sprouting.

scholarly journals MicroRNA-mRNA expression profiles and their potential role in cadmium stress response in Brassica napus

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Ying Fu ◽  
Annaliese S. Mason ◽  
Yaofeng Zhang ◽  
Baogang Lin ◽  
Meili Xiao ◽  
...  
Keyword(s):  
Stress Response ◽  
Brassica Napus ◽  
Mrna Expression ◽  
Contaminated Soils ◽  
Metal Tolerance ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Induced Response ◽  
Phenylpropanoid Metabolism ◽  
Cd Stress

Abstract Background Oilseed rape is an excellent candidate for phytoremediation of cadmium (Cd) contaminated soils given its advantages of high biomass, fast growth, moderate metal accumulation, ease of harvesting, and metal tolerance, but the cadmium response pathways in this species (Brassica napus) have yet to be fully elucidated. A combined analysis of miRNA and mRNA expression to infer Cd-induced regulation has not been reported in B. napus. Results We characterized concurrent changes in miRNA and mRNA profiles in the roots and shoots of B. napus seedlings after 10 days of 10 mg/L Cd2+ treatment. Cd treatment significantly affected the expression of 22 miRNAs belonging to 11 families in the root and 29 miRNAs belonging to 14 miRNA families in the shoot. Five miRNA families (MIR395, MIR397, MIR398, MIR408 and MIR858) and three novel miRNAs were differentially expressed in both tissues. A total of 399 differentially expressed genes (DEGs) in the root and 389 DEGs in the shoot were identified, with very little overlap between tissue types. Eight anti-regulation miRNA-mRNA interaction pairs in the root and eight in the shoot were identified in response to Cd and were involved in key plant stress response pathways: for example, four genes targeted by miR398 were involved in a pathway for detoxification of superoxide radicals. Cd stress significantly impacted the photosynthetic pathway. Transcription factor activation, antioxidant response pathways and secondary metabolic processes such as glutathione (GSH) and phenylpropanoid metabolism were identified as major components for Cd-induced response in both roots and shoots. Conclusions Combined miRNA and mRNA profiling revealed miRNAs, genes and pathways involved in Cd response which are potentially critical for adaptation to Cd stress in B. napus. Close crosstalk between several Cd-induced miRNAs and mRNAs was identified, shedding light on possible mechanisms for response to Cd stress in underground and aboveground tissues in B. napus. The pathways, genes, and miRNAs identified here will be valuable targets for future improvement of cadmium tolerance in B. napus.

scholarly journals Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qi Wu ◽  
Yiming Luo ◽  
Xiaoyong Wu ◽  
Xue Bai ◽  
Xueling Ye ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Functional Characterization ◽  
Chenopodium Quinoa ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Rna Seq ◽  
Short Day ◽  
Homologous Genes ◽  
The Relationship ◽  
Encoding Genes

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

scholarly journals Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huili Qiao ◽  
Jingya Wang ◽  
Yuanzhuo Wang ◽  
Juanjuan Yang ◽  
Bofan Wei ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Target Gene ◽  
Fat Body ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Differentially Expressed ◽  
Post Injection ◽  
Biological Processes ◽  
Potential Target ◽  
Non Coding Rnas

Abstract Background 20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects. Results RNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were constructed and sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42,797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of LNC_000560 and Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B. Conclusions This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model.

scholarly journals Comparison of gene expression in the red imported fire ant (Solenopsis invicta) under different temperature conditions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mohammad Vatanparast ◽  
Robert T. Puckett ◽  
Deuk-Soo Choi ◽  
Youngjin Park
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
High Temperature ◽  
Temperature Stress ◽  
Solenopsis Invicta ◽  
Expression Profiles ◽  
Fire Ant ◽  
Molecular Response ◽  
Red Imported Fire Ant ◽  
Imported Fire Ant

AbstractThe red imported fire ant (RIFA), Solenopsis invicta Buren is native to South America and is known as a global problematic invasive species. This study focused on the molecular response of RIFA by comparing gene expression profiles after exposing ants to low (10 °C) and high (40 °C) temperature stress and comparing them to untreated controls (30 °C). A total of 99,085 unigenes (the clustered non-redundant transcripts that are filtered from the longest assembled contigs) were obtained, of which 19,154 were annotated with gene descriptions, gene ontology terms, and metabolic pathways. 86 gene ontology (GO) functional sub-groups and 23 EggNOG terms resulted. Differentially expressed genes (DEGs) with log2FC ≥ 10 were screened and were compared at different temperatures. We found 203, 48, and 66 specific DEGs co-regulated at 10, 20, and 40 °C. Comparing transcriptome profiles for differential gene expression resulted in various DE genes, including cytochrome P450, NADH dehydrogenase subunit 1, cuticle protein and heat shock protein (HSP), which have previously been reported to be involved in cold and high temperature resistance. GO analysis revealed that antioxidant activity is up-regulated under high temperature stress. We verified the RNA-seq data by qPCR on 20 up- and down-regulated DEGs. These findings provide a basis for future understanding of the adaptation mechanisms of RIFA and the molecular mechanisms underlying the response to low and high temperatures.

Functional characterization of an Indian sandalwood (Santalum album L.) dual-localized bifunctional nerolidol/linalool synthase gene involved in stress response

2021 ◽  
Vol 183 ◽  
pp. 112610
Author(s):  
Xinhua Zhang ◽  
Jaime A. Teixeira da Silva ◽  
Meiyun Niu ◽  
Ting Zhang ◽  
Huanfang Liu ◽  
...  
Keyword(s):  
Stress Response ◽  
Functional Characterization ◽  
Santalum Album ◽  
Santalum Album L ◽  
Linalool Synthase
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