scholarly journals Transcriptomic analysis of Verbena bonariensis roots in response to cadmium stress

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Meng-qi Wang ◽  
Zhen-yu Bai ◽  
Ya-fang Xiao ◽  
Yan Li ◽  
Qing-lin Liu ◽  
...  
Keyword(s):  
Cell Structure ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Cadmium Stress ◽  
The Novel ◽  
Rna Seq ◽  
Cd Stress ◽  
Ros Scavenging ◽  
Molecular Alterations ◽  
Cd Tolerance

Abstract Background Cadmium (Cd) is a serious heavy metal (HM) soil pollutant. To alleviate or even eliminate HM pollution in soil, environmental-friendly methods are applied. One is that special plants are cultivated to absorb the HM in the contaminated soil. As an excellent economical plant with ornamental value and sound adaptability, V. bonariensis could be adapted to this very situation. In our study, the Cd tolerance in V. bonariensis was analyzed as well as an overall analysis of transcriptome. Results In this study, the tolerance of V. bonariensis to Cd stress was investigated in four aspects: germination, development, physiological changes, and molecular alterations. The results showed that as a non-hyperaccumulator, V. bonariensis did possess the Cd tolerance and the capability to concentration Cd. Under Cd stress, all 237, 866 transcripts and 191, 370 unigenes were constructed in the transcriptome data of V. bonariensis roots. The enrichment analysis of gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway revealed that differentially expressed genes (DEGs) under Cd stress were predominately related to cell structure, reactive oxygen species (ROS) scavenging system, chelating reaction and secondary metabolites, transpiration and photosynthesis. DEGs encoding lignin synthesis, chalcone synthase (CHS) and anthocyanidin synthase (ANS) were prominent in V. bonariensis under Cd stress. The expression patterns of 10 DEGs, validated by quantitative real-time polymerase chain reaction (qRT-PCR), were in highly accordance with the RNA-Sequence (RNA-Seq) results. The novel strategies brought by our study was not only benefit for further studies on the tolerance of Cd and functional genomics in V. bonariensis, but also for the improvement molecular breeding and phytoremediation.

scholarly journals Transcriptomic analysis of Verbena bonariensis roots in response to cadmium stress

2019 ◽  
Author(s):  
Meng-qi Wang ◽  
Zhen-yu Bai ◽  
Ya-fang Xiao ◽  
Yan Li ◽  
Qing-lin Liu ◽  
...  
Keyword(s):  
Cell Structure ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Cadmium Stress ◽  
The Novel ◽  
Rna Seq ◽  
Cd Stress ◽  
Ros Scavenging ◽  
Molecular Alterations ◽  
Cd Tolerance

Abstract Background: Cadmium (Cd) is a serious heavy metal (HM) soil pollutant. To alleviate or even eliminate HM pollution in soil, environmental-friendly methods are applied. One is that special plants are cultivated to absorb the HM in the contaminated soil. As an excellent economical plant with ornamental value and sound adaptability, V.bonariensis could be adapted to this very situation. In our study, the Cd tolerance in V.bonariensis was analyzed as well as overall analysis of transcriptome. Results: In this study, the tolerance of V.bonariensis to Cd stress was investigated in four aspects: germination, development, pysiological changes, and molecular alterations. The results showed that as a non-hyperaccumulator, V. bonariensis did possess the Cd tolerance and the capability to concentration Cd. Under Cd stress, all 237,866 transcripts and 191,370 unigenes were constructed in the transcriptome data of V.bonariensis roots . The enrichment analysis of gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway revealed that differentially expressed genes (DEGs) under Cd stress were predominately related to cell structure, reactive oxygen species (ROS) scavenging system, chelating reaction and secondary metabolites, transpiration and photosynthesis. DEGs encoding lignin synthesis, chalcone synthase (CHS) and anthocyanidin synthase (ANS) were prominent in V. bonariensis under Cd stress. The expression patterns of 10 DEGs, validated by quantitative real-time polymerase chain reaction (qRT-PCR), were in highly accordance with the RNA-Sequence (RNA-Seq) results. The novel strategies brought by our study was not only benefit for further studies on the tolerance of Cd and functional genomics in V. bonariensis , but also for the improvement molecular breeding and phytoremediation.

scholarly journals Transcriptomic analysis of Verbena bonariensis roots in response to cadmium stress

2019 ◽  
Author(s):  
Meng-qi Wang ◽  
Zhen-yu Bai ◽  
Ya-fang Xiao ◽  
Yan Li ◽  
Qing-lin Liu ◽  
...  
Keyword(s):  
Cell Structure ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Cadmium Stress ◽  
The Novel ◽  
Rna Seq ◽  
Cd Stress ◽  
Ros Scavenging ◽  
Molecular Alterations ◽  
Cd Tolerance

Abstract Background: Cadmium (Cd) is a serious heavy metal (HM) soil pollutant. To alleviate or even eliminate HM pollution in soil, environmental-friendly methods are applied. One is that special plants are cultivated to absorb the HM in the contaminated soil. As an excellent economical plant with ornamental value and sound adaptability, V.bonariensis could be adapted to this very situation. In our study, the Cd tolerance in V.bonariensis was analyzed as well as overall analysis of transcriptome. Results: In this study, the tolerance of V.bonariensis to Cd stress was investigated in four aspects: germination, development, pysiological changes, and molecular alterations. The results showed that as a non-hyperaccumulator, V. bonariensis did possess the Cd tolerance and the capability to concentration Cd. Under Cd stress, all 237,866 transcripts and 191,370 unigenes were constructed in the transcriptome data of V.bonariensis roots . The enrichment analysis of gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway revealed that differentially expressed genes (DEGs) under Cd stress were predominately related to cell structure, reactive oxygen species (ROS) scavenging system, chelating reaction and secondary metabolites, transpiration and photosynthesis. DEGs encoding lignin synthesis, chalcone synthase (CHS) and anthocyanidin synthase (ANS) were prominent in V. bonariensis under Cd stress. The expression patterns of 10 DEGs, validated by quantitative real-time polymerase chain reaction (qRT-PCR), were in highly accordance with the RNA-Sequence (RNA-Seq) results. The novel strategies brought by our study was not only benefit for further studies on the tolerance of Cd and functional genomics in V. bonariensis , but also for the improvement molecular breeding and phytoremediation.

scholarly journals Transcriptomic analysis of Verbena bonariensis roots in response to cadmium stress

2019 ◽  
Author(s):  
Meng-qi Wang ◽  
Zhen-yu Bai ◽  
Ya-fang Xiao ◽  
Yan Li ◽  
Qing-lin Liu ◽  
...  
Keyword(s):  
Cell Structure ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Cadmium Stress ◽  
Pathway Enrichment Analysis ◽  
Rna Seq ◽  
Cd Stress ◽  
Ros Scavenging ◽  
Garden Plant ◽  
Environmentally Friendly Approach

Abstract Background: Cadmium (Cd) has caused serious heavy metal (HM) pollution in the soil and finding suitable plants to remediate HM pollution is an environmentally friendly approach. Verbena bonariensis is a kind of garden plant with excellent ornamental, good environmental adaptability, which has great potential for future development. This study firstly reported Cd tolerance and an overall analysis of transcriptome in V. bonariensis. Results: In this study, the tolerance of V. bonariensis to Cd stress was investigated in four ways, including germination, growth response, physiological and molecular changes. The results showed that V. bonariensis is not a hyperaccumulator, but it is tolerant to Cd and has the ability to enrich Cd. In the transcriptome data of V. bonariensis roots under Cd stress, 237, 866 transcripts and 191, 370 unigenes were constructed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that differentially expressed genes (DEGs) under Cd stress are predominately involved in cell structure, ROS scavenging system, chelating reaction and secondary metabolites, transpiration and photosynthesis. DEGs encoding lignin synthesis, chalcone synthase (CHS) and anthocyanidin synthase (ANS) were prominent in V. bonariensis response to Cd stress. The expression patterns of 10 DEGs, validated by quantitative real-time PCR (qRT-PCR), were highly accordant with the RNA-seq results. This study provided novel strategies for further studies on tolerance to Cd exposure and functional genomics in V. bonariensis，which was useful information in improving molecular breeding to Cd and phytoremediation.

scholarly journals Growth and Antioxidant Responses in Iron-Biofortified Lentil under Cadmium Stress

Toxics ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. 182
Author(s):  
Ruchi Bansal ◽  
Swati Priya ◽  
Harsh Kumar Dikshit ◽  
Sherry Rachel Jacob ◽  
Mahesh Rao ◽  
...  
Keyword(s):  
Growth Parameters ◽  
Dry Weight ◽  
Cadmium Stress ◽  
Antioxidant Enzyme Activities ◽  
Limited Information ◽  
Cd Stress ◽  
Fresh Weight ◽  
Cd Uptake ◽  
Cd Tolerance ◽  
Controlled Conditions

Cadmium (Cd) is a hazardous heavy metal, toxic to our ecosystem even at low concentrations. Cd stress negatively affects plant growth and development by triggering oxidative stress. Limited information is available on the role of iron (Fe) in ameliorating Cd stress tolerance in legumes. This study assessed the effect of Cd stress in two lentil (Lens culinaris Medik.) varieties differing in seed Fe concentration (L4717 (Fe-biofortified) and JL3) under controlled conditions. Six biochemical traits, five growth parameters, and Cd uptake were recorded at the seedling stage (21 days after sowing) in the studied genotypes grown under controlled conditions at two levels (100 μM and 200 μM) of cadmium chloride (CdCl2). The studied traits revealed significant genotype, treatment, and genotype × treatment interactions. Cd-induced oxidative damage led to the accumulation of hydrogen peroxide (H2O2) and malondialdehyde in both genotypes. JL3 accumulated 77.1% more H2O2 and 75% more lipid peroxidation products than L4717 at the high Cd level. Antioxidant enzyme activities increased in response to Cd stress, with significant genotype, treatment, and genotype × treatment interactions (p < 0.01). L4717 had remarkably higher catalase (40.5%), peroxidase (43.9%), superoxide dismutase (31.7%), and glutathione reductase (47.3%) activities than JL3 under high Cd conditions. In addition, L4717 sustained better growth in terms of fresh weight and dry weight than JL3 under stress. JL3 exhibited high Cd uptake (14.87 mg g−1 fresh weight) compared to L4717 (7.32 mg g−1 fresh weight). The study concluded that the Fe-biofortified lentil genotype L4717 exhibited Cd tolerance by inciting an efficient antioxidative response to Cd toxicity. Further studies are required to elucidate the possibility of seed Fe content as a surrogacy trait for Cd tolerance.

scholarly journals A novel missense variant c.G644A (p.G215E) of the RPGR gene in a Chinese family causes X-linked retinitis pigmentosa

2019 ◽  
Vol 39 (10) ◽  
Author(s):  
Jiewen Fu ◽  
Jingliang Cheng ◽  
Qi Zhou ◽  
Chunli Wei ◽  
Hanchun Chen ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Expression Patterns ◽  
Missense Variant ◽  
Vital Role ◽  
Chinese Family ◽  
The Novel ◽  
Rna Seq ◽  
Targeted Next Generation Sequencing ◽  
Retinal Tissue ◽  
Eye Tissues

Abstract The mutations in patients with X-linked retinitis pigmentosa (xlRP) have not been well described in the Chinese population. In the present study, a five-generation Chinese retinitis pigmentosa (RP) family was recruited; targeted next-generation sequencing (TGS) was used to identify causative genes and Sanger sequencing for co-segregation. RNA-seq data analysis and revere transcriptional-polymerase chain reaction (RT-PCR) were applied to investigate gene expression patterns of RP GTPase regulator (RPGR) in human and Rpgr in mouse. A novel, hemizygous, deleterious and missense variant: c.G644A (p.G215E) in the RPGR gene (NM_000328.2) exon 7 of X-chromosome was identified in the proband, which was co-segregated with the clinical phenotypes in this family. RNA-seq data showed that RPGR is ubiquitously expressed in 27 human tissues with testis in highest, but no eye tissues data. Then the expressions for Rpgr mRNA in mice including eye tissues were conducted and showed that Rpgr transcript is ubiquitously expressed very highly in retina and testis, and highly in other eye tissues including lens, sclera, and cornea; and expressed highly in the six different developmental times of retinal tissue. Ubiquitous expression in different tissues from eye and very high expression in the retina indicated that RPGR plays a vital role in eye functions, particularly in retina. In conclusion, our study is the first to indicate that the novel missense variant c.G644A (p.G215E) in the RPGR gene might be the disease-causing mutation in this xlRP family, expanding mutation spectrum. These findings facilitate better understanding of the molecular pathogenesis of this disease; provide new insights for genetic counseling and healthcare.

scholarly journals Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain

2019 ◽  
Author(s):  
Ailing Liu ◽  
Zhibo Zhou ◽  
Yake Yi ◽  
Guanghui Chen
Keyword(s):  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Critical Role ◽  
Differentially Expressed ◽  
Rice Grain ◽  
Rna Seq ◽  
Cd Stress ◽  
Cd Accumulation ◽  
Cadmium Transport ◽  
Central Organ

Abstract Background: Node is the central organ of xylem to phloem transfer of nutrients and ions in plants. Cadmium (Cd)-induced crop pollution threatens food safety. Breeding cultivar with low Cd accumulation is a chance to resolve this universal problem. This study was performed to identify tissue specific genes involved in Cd accumulation in different rice stem nodes. Panicle node and the first node under panicle (node I) were sampled in two rice cultivars: Xiangwanxian No. 12 with low Cd accumulation and Yuzhenxiang with high Cd accumulation in the grains. RNA-seq analysis was performed to identify differentially expressed genes (DEGs) and microRNAs. Results: Xiangwanxian No. 12 had lower Cd concentration in panicle node, node I and grain compared with Yuzhenxiang , and node Ⅰ had the highest Cd concentration in the two cultivars. RNA seq analysis identified 4,535 differentially expressed genes and 70 miRNAs between the two cultivars. Most genes ( OsIRT1 , OsNramp5, OsVIT2 , OsNRT1.5A, and OsABCC1 ) related to the “transporter activity” blocked the transport of Cd up to panicle and accumulation in grains of low Cd-accumulative cultivar. Among the genes related to “response to stimulus”, we identified OsHSP70 and OsHSFA2d/B2c in “X”, but not in “y”, were all down-regulated by Cd stimulus. The up-regulation of miRNAs ( osa-miR528 and osa-miR408 ) played a potent role in lowering Cd accumulation via down regulation of genes, such as bZIP , ERF , MYB , SnRK1 and HSPs in Xiangwanxian No. 12 cultivar. Conclusions: Both panicle node and node I of Xiangwanxian No. 12 played a key role in blocking the upward transportation of Cd, while node I played a critical role in Yuzhenxiang . Distinct expression patterns of various transporter genes such as OsNRT1.5A, OsNramp5, OsIRT1, OsVIT2 and OsABCC1 resulted in differential Cd accumulation in different nodes. Likewise, distinct expression patterns of these transporter genes are likely responsible for the low Cd accumulation in Xiangwanxian No. 12 cultivar . MiRNAs drove multiple transcription factors, such as OsbZIPs, OsERFs, OsMYBs , to play a role in stress response, which contribute to the response to Cd stress in rice.

Comparative study of four rice cultivars with different levels of cadmium tolerance

Biologia ◽  
2013 ◽  
Vol 68 (1) ◽  
Author(s):  
Xiao Wang ◽  
Zhong-Wei Zhang ◽  
Shi-Hua Tu ◽  
Wen-Qiang Feng ◽  
Fei Xu ◽  
...  
Keyword(s):  
Contaminated Soils ◽  
Rice Cultivars ◽  
Cd Stress ◽  
Ros Scavenging ◽  
High Solubility ◽  
Cd Uptake ◽  
Solubility In Water ◽  
Cd Tolerance ◽  
Different Levels ◽  
Cyanide Resistant Respiration

AbstractCadmium (Cd) has been identified as a significant pollutant due to its high solubility in water and soil and high toxicity to plants and animals. Rice, as one of the most important food crops, is grown in soils with variable levels of Cd and therefore, is important to discriminate the Cd tolerance of different rice cultivars to determine their suitability for cultivation in Cd-contaminated soils. This study investigates the primary mechanisms employed by four rice cultivars in attaining Cd tolerance. HA63 cultivar reduces Cd uptake by increasing Fe absorption through activation of phytosiderophores. T3028 cultivar accumulates the highest level of Cd in leaves while also activating its reactive oxygen species (ROS) scavenging system, including antioxidant enzymes and phytochelatins. In some rice cultivars (such as HA63), a cyanide-resistant respiration mechanism, important in Cd detoxification, was also promoted under the Cd stress. In conclusion, different rice cultivars may adopt different biochemical strategies and respond with different efficiency to Cd stress.

scholarly journals Transcriptome sequencing and analysis reveals the molecular response to selenium stimuli in Pueraria lobata (willd.) Ohwi

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8768 ◽  
Author(s):  
Kunyuan Guo ◽  
Yiwei Yao ◽  
Meng Yang ◽  
Yanni Li ◽  
Bin Wu ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Pearson Correlation ◽  
Expression Patterns ◽  
Phosphate Transporter ◽  
Molecular Response ◽  
Pueraria Lobata ◽  
Rna Seq ◽  
Structural Genes ◽  
Ros Scavenging ◽  
Isoflavone Biosynthesis

Pueraria lobata (willd.) Ohwi is a consumable selenium-enriched plant used for medicinal purposes. The molecular response to selenium (Se) stimuli in P. lobata is currently unknown. We used RNA-Seq to identify potential genes involved in selenite metabolism and analyzed their expression profiles. We obtained a total of 150,567 unigenes, of which 90,961 were annotated, including 16 structural genes, 14 sulfate transporters, and 13 phosphate transporters that may be involved in Se metabolism, and 33 candidate structural genes involved in isoflavone biosynthesis. The genes with a —foldchange— >2 and q value <0.05 after sodium selenite treatment were identified as differentially expressed genes (DEGs). We obtained a total of 4,246 DEGs, which were enriched in GO terms that included “response to stimulus”, “response to stress”, “signal transduction”, “response to abiotic stimulus”, and “response to chemical”. Of the 4,246 DEGs, one sulfate transporter and five phosphate transporter genes involved Se metabolism, and nine structural genes involved in isoflavone biosynthesis were up-regulated. The expression patterns of 10 DEGs were selected randomly and validated using qRT-PCR. The Pearson Correlation Coefficient (r) was 0.86, indicating the reliability of RNA-Seq results. 22 Reactive Oxygen Species (ROS) scavenging DEGs were found, 11 of which were up-regulated. 436, 624 transcription factors (TFs) correlated with structural genes were identified that may be involved in Se and isoflavone biosynthesis, respectively, using r (r > 0.7 or r <  − 0.7). 556 TFs were related to at least one sulfate and phosphate transporter. Our results provided a comprehensive description of gene expression and regulation in response to Se stimuli in P. lobata.

scholarly journals Genome-wide phylogenetic analysis, expression pattern, and transcriptional regulatory network of the pig C/EBP gene family

2020 ◽  
Author(s):  
Chaoxin Zhang ◽  
Tao Wang ◽  
Shengwei Liu ◽  
Bing Zhang ◽  
Xue Li ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Regulatory Network ◽  
Target Genes ◽  
Transcriptional Regulatory Network ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Rna Seq ◽  
Group I

Abstract Background: The vertebrate C/EBP transcription factors regulate many important biological processes, such as cell proliferation, differentiation, signal transduction, inflammation, and energy metabolism. The first C/EBP protein was identified in rat liver nuclei. Development of sequencing technology resulted in identification of the C/EBP genes in various species. In this study, a bioinformatics approach was used to determine the distribution of the members of the C/EBP family in vertebrates. A phylogenetic tree was constructed to analyze the C/EBP genes in vertebrates. Based on RNA-seq data, the expression patterns of pig C/EBP members in various tissues were analyzed. In addition, a gene transcription regulatory network was constructed with pig C/EBP members as the core.Results: We identified a total of 92 C/EBP genes in 17 vertebrate genomes. Phylogenetic analysis showed that all C/EBP TFs were classified into two groups; group I contained C/EBPβ TFs, and group II contained the remaining C/EBP TFs. The C/EBPα, C/EBPβ, C/EBPδ, C/EBPγ, and C/EBPζ genes were expressed ubiquitously with inconsistent expression patterns in various tissues. Moreover, a pig C/EBP regulatory network was constructed, including C/EBP genes, TFs, and miRNAs. A total of 39 FFL motifs were detected in the pig C/EBP regulatory network. Based on the RNA-seq data, gene expression patterns related to this FFL sub-network were analyzed in 27 adult Duroc tissues. Certain FFL motifs may be tissue specific. Functional enrichment analysis indicated that C/EBP and its target genes are involved in many important biological pathways. Conclusions: These results provide valuable information that clarifies the evolutionary relationships of the C/EBP family and contributes to the understanding of the biological function of C/EBP genes.

scholarly journals Comparative root transcriptome analysis of two soybean cultivars with different cadmium sensitivities reveals the underlying tolerant mechanisms

Genome ◽  
2021 ◽  
Author(s):  
Yuan Ma ◽  
Kuichen Liu ◽  
Chunyu Zhang ◽  
Feng Lin ◽  
Wenbo Hu ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Kegg Pathway ◽  
Economic Value ◽  
Rna Seq ◽  
Cd Stress ◽  
Toxic Heavy Metal ◽  
Soybean Cultivars ◽  
Cd Tolerance ◽  
Transgenic Hairy Roots ◽  
Soybean Roots

The soybean can provide rich protein and fat and has great economic value worldwide. Cadmium (Cd) is a toxic heavy metal to organisms. It can accumulate in plants and be transmitted to the human body via food chain. Cd is a serious threat to soybean development, especially to root growth. Some soybean cultivars present tolerant symptoms under Cd stress; however, the potential mechanisms are not fully understood. Here, we optimized RNA-seq to identify the differentially expressed genes (DEGs) in Cd-sensitive (KUAI) and Cd-tolerant (KAIYU) soybean roots and compared the DEGs between KAIYU and KUAI. A total of 1,506 and 1,870 DEGs were identified in the roots of KUAI and KAIYU, respectively. Through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and gene function analyses, we found that genes related to antioxidants and sequestration were responsible for Cd tolerance in KAIYU. In addition, overexpression of Glyma11g02661, which encodes a heavy metal transporting ATPase, significantly improved Cd tolerance in transgenic hairy roots. These results provide a preliminary understanding of the tolerance mechanisms in response to Cd stress in soybean root development and are of great importance in developing Cd-resistant soybean cultivars by using the identified DEGs through genetic modification.

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