scholarly journals De novo characterization of the Camellia sinensis transcriptome and comprehensive analysis of the diploid and triploid leaf morphological differences

2020 ◽  
Author(s):  
yong Qi ◽  
Xinzhuan Yao ◽  
Degang Zhao ◽  
Litang lu
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Morphological Structure ◽  
Sponge Tissue ◽  
Sequencing Analysis ◽  
Stomatal Development ◽  
Specific Expression ◽  
Hormone Synthesis ◽  
Morphological Differences ◽  
Tea Plants

Abstract Background: Polyploidization has undergone a series of significant changes in the morphology and physiology of tea plants as plants multiply, especially in terms of increased growth rate and genetic gains Result: In this study, we found that the leaves of triploid tea had obvious growth advantages compared with diploid tea leaves, which was 59.81% higher than that of diploid leaves areas. The morphological structure of the triploid leaves showed obvious changes, the xylem of the veins was more developed, the cell-to-cell gap between the palisade tissue and the sponge tissue became larger, and the stomata of the triploid leaves were enlarged. Transcriptome sequencing analysis showed that after the triploidization of tea, the changes of leaf morphology and physiological characteristics were affected by the specific expression of some key regulatory genes. We identified a large number of transcripts and genes that might play important roles in leaf development, especially those involved in cell division, photosynthesis, hormone synthesis, and stomatal development. Conclusion: This study will improve our understanding of the molecular mechanisms of tea leaf and stomatal development and provide the basis for molecular breeding of tea varieties with high quality and yield. Furthermore, it gives information to improve understanding of triploid physiology.

scholarly journals De novo characterization of the Camellia sinensis transcriptome and comprehensive analysis of the diploid and triploid leaf morphological differences

2020 ◽  
Author(s):  
yong Qi ◽  
Xinzhuan Yao ◽  
Degang Zhao ◽  
Litang Lu
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Morphological Structure ◽  
Sponge Tissue ◽  
Sequencing Analysis ◽  
Stomatal Development ◽  
Specific Expression ◽  
Hormone Synthesis ◽  
Morphological Differences ◽  
Tea Plants

Abstract Background: Polyploidization has undergone a series of significant changes in the morphology and physiology of tea plants as plants multiply, especially in terms of increased growth rate and genetic gains Result: In this study, we found that the leaves of triploid tea had obvious growth advantages compared with diploid tea leaves, which was 59.81% higher than that of diploid leaves areas. The morphological structure of the triploid leaves showed obvious changes, the xylem of the veins was more developed, the cell-to-cell gap between the palisade tissue and the sponge tissue became larger, and the stomata of the triploid leaves were enlarged. Transcriptome sequencing analysis showed that after the triploidization of tea, the changes of leaf morphology and physiological characteristics were affected by the specific expression of some key regulatory genes. we identified a large number of transcripts and genes that might play important roles in leaf development, especially those involved in cell division, photosynthesis, hormone synthesis, and stomatal development.Conclusion: This study will improve our understanding of the molecular mechanisms of tea leaf and stomatal development and provide the basis for molecular breeding of high quality and yield tea varieties. Furthermore, it gives information that may enhance understanding of triploid physiology.

scholarly journals De novo characterization of the Camellia sinensis transcriptome and comprehensive analysis of the diploid and triploid leaf morphology and physiological differences

2019 ◽  
Author(s):  
Yong QI ◽  
Xinzhuan YAO ◽  
Degang ZHAO ◽  
Litang Lu
Keyword(s):  
Leaf Morphology ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Morphological Structure ◽  
Sponge Tissue ◽  
Sequencing Analysis ◽  
Stomatal Development ◽  
Tea Leaves ◽  
Specific Expression ◽  
Hormone Synthesis

Abstract Background Polyploidization has undergone a series of significant changes in the morphology and physiology of tea plants as plants multiply, especially in terms of increased growth rate and genetic gainsResult In this study, we found that the leaves of triploid tea had obvious growth advantages compared with diploid tea leaves, which was 59.81% higher than that of diploid leaves areas. The morphological structure of the triploid leaves showed obvious changes, the xylem of the veins was more developed, the cell-to-cell gap between the palisade tissue and the sponge tissue became larger, and the stomata of the triploid leaves were enlarged. After the polyploidy of tea, the content of secondary metabolites in tea leaves also changed significantly. Transcriptome sequencing analysis showed that after the triploidization of tea, the changes of leaf morphology and physiological characteristics were affected by the specific expression of some key regulatory genes. we identified a large number of transcripts and genes that might play important roles in leaf development, especially those involved in cell division, photosynthesis, hormone synthesis, and stomatal development.Conclusion This study will improve our understanding of the molecular mechanisms of tea leaf and stomatal development and provide the basis for molecular breeding of high quality and yield tea varieties. Furthermore, it gives information that may enhance understanding of triploid physiology.

scholarly journals Genome-wide identification, characterization, and expression analysis of tea plant autophagy-related genes (CsARGs) demonstrates that they play diverse roles during development and under abiotic stress

2020 ◽  
Author(s):  
Huan Wang ◽  
ZhaoTang Ding ◽  
Mengjie Gou ◽  
Jianhui Hu ◽  
Yu Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Expression Analysis ◽  
Molecular Mechanisms ◽  
Tea Plant ◽  
Future Research ◽  
Specific Expression ◽  
Genome Wide ◽  
Physiological Analysis ◽  
Response To Stress ◽  
Tea Plants

Abstract Background: Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay aging and longevity in eukaryotes. To date, the functions of autophagy have been heavily studied in yeast, mammals and model plants, but few studies have focused on economically important crops, especially tea plants (Camellia sinensis). The roles played by autophagy in coping with various environmental stimuli have not been fully elucidated to date. Therefore, investigating the functions of autophagy-related genes in tea plants may help to elucidate the mechanism governing autophagy in response to stresses in woody plants.Results: In this study, we identified 35 C. sinensis autophagy-related genes (CsARGs). Each CsARG is highly conserved with its homologues from other plant species, except for CsATG14. Tissue-specific expression analysis demonstrated that the abundances of CsARGs varied across different tissues, but CsATG8c/i showed a degree of tissue specificity. Under hormone and abiotic stress conditions, most CsARGs were upregulated at different time points during the treatment. In addition, the expression levels of 10 CsARGs were higher in the cold-resistant cultivar ‘Longjing43’ than in the cold-susceptible cultivar ‘Damianbai’ during the CA period; however, the expression of CsATG101 showed the opposite tendency.Conclusions: We performed a comprehensive bioinformatic and physiological analysis of CsARGs in tea plants, and these results may help to establish a foundation for further research investigating the molecular mechanisms governing autophagy in tea plant growth, development and response to stress. Meanwhile, some CsARGs could serve as putative molecular markers for the breeding of cold-resistant tea plants in future research.

scholarly journals Transcriptome profiles of sturgeon lateral line electroreceptor and mechanoreceptor during regeneration

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Jian Wang ◽  
Chengcheng Lu ◽  
Yifan Zhao ◽  
Zhijiao Tang ◽  
Jiakun Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Lateral Line ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Sensory Organs ◽  
Specific Expression ◽  
Voltage Gated ◽  
Voltage Gated Calcium Channels ◽  
Early Regeneration

Abstract Background The electrosensory ampullary organs (AOs) and mechanosensory neuromasts (NMs) found in sturgeon and some other non-neopterygian fish or amphibians are both originated from lateral line placodes. However, these two sensory organs have characteristic morphological and physiological differences. The molecular mechanisms for the specification of AOs and NMs are not clearly understood. Results We sequenced the transcriptome for neomycin treated sturgeon AOs and NMs in the early regeneration stages, and de novo assembled a sturgeon transcriptome. By comparing the gene expression differences among untreated AOs, NMs and general epithelia (EPs), we located some specific genes for these two sensory organs. In sturgeon lateral line, the voltage-gated calcium channels and voltage-gated potassium channels were predominant calcium and potassium channel subtypes, respectively. And by correlating gene expression with the regeneration process, we predicated several candidate key transcriptional regulation related genes might be involved in AOs and NMs regeneration. Conclusions Genes with specific expression in the two lateral line sensory organs suggests their important roles in mechanoreceptor and electroreceptor formation. The candidate transcriptional regulation related genes may be important for mechano- and electro- receptor specification, in a “dosage-related” manner. These results suggested the molecular basis for specification of these two sensory organs in sturgeon.

scholarly journals Genome-wide identification, characterization, and expression analysis of tea plant autophagy-related genes (CsARGs) demonstrates that they play diverse roles during development and under abiotic stress

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huan Wang ◽  
Zhaotang Ding ◽  
Mengjie Gou ◽  
Jianhui Hu ◽  
Yu Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Expression Analysis ◽  
Molecular Mechanisms ◽  
Tea Plant ◽  
Future Research ◽  
Specific Expression ◽  
Genome Wide ◽  
Physiological Analysis ◽  
Response To Stress ◽  
Tea Plants

Abstract Background Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay aging and longevity in eukaryotes. To date, the functions of autophagy have been heavily studied in yeast, mammals and model plants, but few studies have focused on economically important crops, especially tea plants (Camellia sinensis). The roles played by autophagy in coping with various environmental stimuli have not been fully elucidated to date. Therefore, investigating the functions of autophagy-related genes in tea plants may help to elucidate the mechanism governing autophagy in response to stresses in woody plants. Results In this study, we identified 35 C. sinensis autophagy-related genes (CsARGs). Each CsARG is highly conserved with its homologues from other plant species, except for CsATG14. Tissue-specific expression analysis demonstrated that the abundances of CsARGs varied across different tissues, but CsATG8c/i showed a degree of tissue specificity. Under hormone and abiotic stress conditions, most CsARGs were upregulated at different time points during the treatment. In addition, the expression levels of 10 CsARGs were higher in the cold-resistant cultivar ‘Longjing43’ than in the cold-susceptible cultivar ‘Damianbai’ during the CA period; however, the expression of CsATG101 showed the opposite tendency. Conclusions We performed a comprehensive bioinformatic and physiological analysis of CsARGs in tea plants, and these results may help to establish a foundation for further research investigating the molecular mechanisms governing autophagy in tea plant growth, development and response to stress. Meanwhile, some CsARGs could serve as putative molecular markers for the breeding of cold-resistant tea plants in future research.

scholarly journals Genome-wide identification, characterization, and expression analysis of tea plant autophagy-related genes (CsARGs) demonstrates that they play diverse roles during development and under abiotic stress

2021 ◽  
Author(s):  
Huan Wang ◽  
ZhaoTang Ding ◽  
Mengjie Gou ◽  
Jianhui Hu ◽  
Yu Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Expression Analysis ◽  
Molecular Mechanisms ◽  
Tea Plant ◽  
Future Research ◽  
Specific Expression ◽  
Genome Wide ◽  
Physiological Analysis ◽  
Response To Stress ◽  
Tea Plants

Abstract Background: Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay aging and longevity in eukaryotes. To date, the functions of autophagy have been heavily studied in yeast, mammals and model plants, but few studies have focused on economically important crops, especially tea plants (Camellia sinensis). The roles played by autophagy in coping with various environmental stimuli have not been fully elucidated to date. Therefore, investigating the functions of autophagy-related genes in tea plants may help to elucidate the mechanism governing autophagy in response to stresses in woody plants.Results: In this study, we identified 35 C. sinensis autophagy-related genes (CsARGs). Each CsARG is highly conserved with its homologues from other plant species, except for CsATG14. Tissue-specific expression analysis demonstrated that the abundances of CsARGs varied across different tissues, but CsATG8c/i showed a degree of tissue specificity. Under hormone and abiotic stress conditions, most CsARGs were upregulated at different time points during the treatment. In addition, the expression levels of 10 CsARGs were higher in the cold-resistant cultivar ‘Longjing43’ than in the cold-susceptible cultivar ‘Damianbai’ during the CA period; however, the expression of CsATG101 showed the opposite tendency.Conclusions: We performed a comprehensive bioinformatic and physiological analysis of CsARGs in tea plants, and these results may help to establish a foundation for further research investigating the molecular mechanisms governing autophagy in tea plant growth, development and response to stress. Meanwhile, some CsARGs could serve as putative molecular markers for the breeding of cold-resistant tea plants in future research.

scholarly journals Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Sjors Middelkamp ◽  
Judith M. Vlaar ◽  
Jacques Giltay ◽  
Jerome Korzelius ◽  
Nicolle Besselink ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Regulatory Elements ◽  
Chromatin Organization ◽  
Sequencing Analysis ◽  
Structural Variants ◽  
Driver Genes ◽  
Position Effects ◽  
Genomic Structural Variants

Abstract Background Genomic structural variants (SVs) can affect many genes and regulatory elements. Therefore, the molecular mechanisms driving the phenotypes of patients carrying de novo SVs are frequently unknown. Methods We applied a combination of systematic experimental and bioinformatic methods to improve the molecular diagnosis of 39 patients with multiple congenital abnormalities and/or intellectual disability harboring apparent de novo SVs, most with an inconclusive diagnosis after regular genetic testing. Results In 7 of these cases (18%), whole-genome sequencing analysis revealed disease-relevant complexities of the SVs missed in routine microarray-based analyses. We developed a computational tool to predict the effects on genes directly affected by SVs and on genes indirectly affected likely due to the changes in chromatin organization and impact on regulatory mechanisms. By combining these functional predictions with extensive phenotype information, candidate driver genes were identified in 16/39 (41%) patients. In 8 cases, evidence was found for the involvement of multiple candidate drivers contributing to different parts of the phenotypes. Subsequently, we applied this computational method to two cohorts containing a total of 379 patients with previously detected and classified de novo SVs and identified candidate driver genes in 189 cases (50%), including 40 cases whose SVs were previously not classified as pathogenic. Pathogenic position effects were predicted in 28% of all studied cases with balanced SVs and in 11% of the cases with copy number variants. Conclusions These results demonstrate an integrated computational and experimental approach to predict driver genes based on analyses of WGS data with phenotype association and chromatin organization datasets. These analyses nominate new pathogenic loci and have strong potential to improve the molecular diagnosis of patients with de novo SVs.

scholarly journals Characterization of Brassica rapa metallothionein and phytochelatin synthase genes potentially involved in heavy metal detoxification

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252899
Author(s):  
Jiayou Liu ◽  
Jie Zhang ◽  
Sun Ha Kim ◽  
Hyun-Sook Lee ◽  
Enrico Marinoia ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Molecular Mechanisms ◽  
Yeast Cells ◽  
Sequencing Analysis ◽  
Phytochelatin Synthase ◽  
Cadmium Resistance ◽  
Specific Expression ◽  
Heavy Metal Detoxification ◽  
Genes Encoding ◽  
High Concentrations

Brassica rapa is an important leafy vegetable that can potentially accumulate high concentrations of cadmium (Cd), posing a risk to human health. The aim of the present study was to identify cadmium detoxifying molecular mechanisms in B. rapa using a functional cloning strategy. A cDNA library constructed from roots of B. rapa plants treated with Cd was transformed into the Cd sensitive yeast mutant strain DTY167 that lacks the yeast cadmium factor (YCF1), and resistant yeast clones were selected on Cd containing media. Two hundred genes potentially conferring cadmium resistance were rescued from the surviving yeast clones and sequenced. Sequencing analysis revealed that genes encoding for metallothionein (MT)1, MT2a, MT2b and MT3, and phytochelatin synthase (PCS)1 and PCS2 accounted for 35.5%, 28.5%, 4%, 11.3%, 18.7% and 2%, respectively of the genes identified. MTs and PCSs expressing DTY167 cells showed resistance to Cd as well as to Zn. PCS1 expressing yeast cells were also more resistant to Pb compared to those expressing MTs or PCS2. RT-PCR results showed that Cd treatment strongly induced the expression levels of MTs in the root and shoot. Furthermore, the different MTs and PCSs exhibited tissue specific expression. The results indicate that MTs and PCS genes potentially play a central role in detoxifying Cd and other toxic metals in B. rapa.

scholarly journals A First Insight into the Gonad Transcriptome of Hong Kong Catfish (Clarias fuscus)

Animals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 1131
Author(s):  
Xinghua Lin ◽  
Dayan Zhou ◽  
Xiaomin Zhang ◽  
Guangli Li ◽  
Yulei Zhang ◽  
...  
Keyword(s):  
Hong Kong ◽  
Sex Determination ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Sex Differentiation ◽  
Gonadal Development ◽  
Sequencing Analysis ◽  
Kegg Pathways ◽  
Clarias Fuscus ◽  
Go Terms

Hong Kong catfish (Clarias fuscus) exhibit sexual dimorphism, particularly in body size. Due to the fast growth rate of males, the sexual size dimorphism of Hong Kong catfish has become an economically important trait. However, limited knowledge is known about the molecular mechanisms of sex determination and sex differentiation in this species. In this study, a first de novo transcriptome sequencing analysis of testes and ovaries was performed to identify sex-biased genes in Hong Kong catfish. The results showed that a total of 290,291 circular consensus sequences (CCSs) were obtained, from which 248,408 full-length non-chimeric (FLNC) reads were generated. After non-redundant analysis, a total of 37,305 unigenes were predicted, in which 34,342 unigenes were annotated with multiple public databases. Comparative transcriptomic analysis identified 5750 testis-biased differentially expressed genes (DEGs) and 6991 ovary-biased DEGs. The enrichment analysis showed that DEGs were classified into 783 Gene Ontology (GO) terms and 16 Kyoto Encyclopedia of Gene and Genome (KEGG) pathways. Many DEGs were involved with sex-related GO terms and KEGG pathways, such as oocyte maturation, androgen secretion, gonadal development and steroid biosynthesis pathways. In addition, the expression levels of 23 unigenes were confirmed to validate the transcriptomic data by quantitative real-time polymerase chain reaction (qRT-PCR). This is the first investigation into the transcriptome of Hong Kong catfish testes and ovaries. This study provides an important molecular basis for the sex determination and sex control breeding of Hong Kong catfish.

scholarly journals Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants

2019 ◽  
Author(s):  
Sjors Middelkamp ◽  
Judith M. Vlaar ◽  
Jacques Giltay ◽  
Jerome Korzelius ◽  
Nicolle Besselink ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Regulatory Elements ◽  
Chromatin Organization ◽  
Computational Method ◽  
Sequencing Analysis ◽  
Structural Variants ◽  
Driver Genes ◽  
Genomic Structural Variants

AbstractBackgroundGenomic structural variants (SVs) can affect many genes and regulatory elements. Therefore, the molecular mechanisms driving the phenotypes of patients with multiple congenital abnormalities and/or intellectual disability carrying de novo SVs are frequently unknown.ResultsWe applied a combination of systematic experimental and bioinformatic methods to improve the molecular diagnosis of 39 patients with de novo SVs and an inconclusive diagnosis after regular genetic testing. In seven of these cases (18%) whole genome sequencing analysis detected disease-relevant complexities of the SVs missed in routine microarray-based analyses. We developed a computational tool to predict effects on genes directly affected by SVs and on genes indirectly affected due to changes in chromatin organization and impact on regulatory mechanisms. By combining these functional predictions with extensive phenotype information, candidate driver genes were identified in 16/39 (41%) patients. In eight cases evidence was found for involvement of multiple candidate drivers contributing to different parts of the phenotypes. Subsequently, we applied this computational method to a collection of 382 patients with previously detected and classified de novo SVs and identified candidate driver genes in 210 cases (54%), including 32 cases whose SVs were previously not classified as pathogenic. Pathogenic positional effects were predicted in 25% of the cases with balanced SVs and in 8% of the cases with copy number variants.ConclusionsThese results show that driver gene prioritization based on integrative analysis of WGS data with phenotype association and chromatin organization datasets can improve the molecular diagnosis of patients with de novo SVs.

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