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 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 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 LsAP2 regulates leaf morphology by inhibiting CIN-like TCP transcription factors and repressing LsKAN2 in lettuce

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Chen Luo ◽  
Shenglin Wang ◽  
Kang Ning ◽  
Zijing Chen ◽  
Yixin Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptional Activation ◽  
Leaf Development ◽  
Leaf Morphology ◽  
Molecular Mechanisms ◽  
Leaf Size ◽  
Leafy Vegetables ◽  
Sequencing Analysis ◽  
Agricultural Yield ◽  
Leaf Size And Shape

AbstractLeaf size and flatness directly affect photosynthesis and are closely related to agricultural yield. The final leaf size and shape are coordinately determined by cell proliferation, differentiation, and expansion during leaf development. Lettuce (Lactuca sativa L.) is one of the most important leafy vegetables worldwide, and lettuce leaves vary in shape and size. However, the molecular mechanisms of leaf development in lettuce are largely unknown. In this study, we showed that the lettuce APETALA2 (LsAP2) gene regulates leaf morphology. LsAP2 encodes a transcriptional repressor that contains the conserved EAR motif, which mediates interactions with the TOPLESS/TOPLESS-RELATED (TPL/TPR) corepressors. Overexpression of LsAP2 led to small and crinkly leaves, and many bulges were seen on the surface of the leaf blade. LsAP2 physically interacted with the CINCINNATA (CIN)-like TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors and inhibited their transcriptional activation activity. RNA sequencing analysis showed that LsAP2 affected the expression of auxin- and polarity-related genes. In addition, LsAP2 directly repressed the abaxial identity gene KANADI2 (LsKAN2). Together, these results indicate that LsAP2 regulates leaf morphology by inhibiting CIN-like TCP transcription factors and repressing LsKAN2, and our work provides insights into the regulatory mechanisms of leaf development in lettuce.

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 Leaf heteroblasty in Passiflora edulis as revealed by metabolic profiling and expression analyses of the microRNAs miR156 and miR172

2019 ◽  
Vol 123 (7) ◽  
pp. 1191-1203 ◽  
Author(s):  
Priscila O Silva ◽  
Diego S Batista ◽  
João Henrique F Cavalcanti ◽  
Andréa D Koehler ◽  
Lorena M Vieira ◽  
...  
Keyword(s):  
Phase Transition ◽  
Metabolic Profiling ◽  
Leaf Morphology ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Leaf Traits ◽  
Transcript Accumulation ◽  
Passiflora Edulis ◽  
Woody Perennial ◽  
Adult Phase

Abstract Background and Aims Juvenile-to-adult phase transition is marked by changes in leaf morphology, mostly due to the temporal development of the shoot apical meristem, a phenomenon known as heteroblasty. Sugars and microRNA-controlled modules are components of the heteroblastic process in Arabidopsis thaliana leaves. However, our understanding about their roles during phase-changing in other species, such as Passiflora edulis, remains limited. Unlike Arabidopsis, P. edulis (a semi-woody perennial climbing vine) undergoes remarkable changes in leaf morphology throughout juvenile-to-adult transition. Nonetheless, the underlying molecular mechanisms are unknown. Methods Here we evaluated the molecular mechanisms underlying the heteroblastic process by analysing the temporal expression of microRNAs and targets in leaves as well as the leaf metabolome during P. edulis development. Key Results Metabolic profiling revealed a unique composition of metabolites associated with leaf heteroblasty. Increasing levels of glucose and α-trehalose were observed during juvenile-to-adult phase transition. Accumulation of microRNA156 (miR156) correlated with juvenile leaf traits, whilst miR172 transcript accumulation was associated with leaf adult traits. Importantly, glucose may mediate adult leaf characteristics during de novo shoot organogenesis by modulating miR156-targeted PeSPL9 expression levels at early stages of shoot development. Conclusions Altogether, our results suggest that specific sugars may act as co-regulators, along with two microRNAs, leading to leaf morphological modifications throughout juvenile-to-adult phase transition in P. edulis.

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.

scholarly journals Whole-exome sequencing with targeted analysis and epilepsy after acute symptomatic neonatal seizures

2021 ◽  
Author(s):  
Adam L. Numis ◽  
Gilberto da Gente ◽  
Elliott H. Sherr ◽  
Hannah C. Glass
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
De Novo ◽  
List Type ◽  
Sequencing Analysis ◽  
Neonatal Seizures ◽  
Pathogenic Variants ◽  
Targeted Analysis ◽  
Whole Exome ◽  
Epilepsy Gene

Abstract Background The contribution of pathogenic gene variants with development of epilepsy after acute symptomatic neonatal seizures is not known. Methods Case–control study of 20 trios in children with a history of acute symptomatic neonatal seizures: 10 with and 10 without post-neonatal epilepsy. We performed whole-exome sequencing (WES) and identified pathogenic de novo, transmitted, and non-transmitted variants from established and candidate epilepsy association genes and correlated prevalence of these variants with epilepsy outcomes. We performed a sensitivity analysis with genes associated with coronary artery disease (CAD). We analyzed variants throughout the exome to evaluate for differential enrichment of functional properties using exploratory KEGG searches. Results Querying 200 established and candidate epilepsy genes, pathogenic variants were identified in 5 children with post-neonatal epilepsy yet in only 1 child without subsequent epilepsy. There was no difference in the number of trios with non-transmitted pathogenic variants in epilepsy or CAD genes. An exploratory KEGG analysis demonstrated a relative enrichment in cell death pathways in children without subsequent epilepsy. Conclusions In this pilot study, children with epilepsy after acute symptomatic neonatal seizures had a higher prevalence of coding variants with a targeted epilepsy gene sequencing analysis compared to those patients without subsequent epilepsy. Impact We performed whole-exome sequencing (WES) in 20 trios, including 10 children with epilepsy and 10 without epilepsy, both after acute symptomatic neonatal seizures. Children with post-neonatal epilepsy had a higher burden of pathogenic variants in epilepsy-associated genes compared to those without post-neonatal epilepsy. Future studies evaluating this association may lead to a better understanding of the risk of epilepsy after acute symptomatic neonatal seizures and elucidate molecular pathways that are dysregulated after brain injury and implicated in epileptogenesis.

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