Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants

Abstract Background: Genome-wide change of polyadenylation (polyA) sites (also known as alternative polyadenylation, APA) is emerging as an important strategy of gene regulation in response to stress in plants. But little is known in woody perennials that are persistently dealing with multiple abiotic stresses. Results: Here, we performed a genome-wide profiling of polyadenylation sites under heat and cold treatments in Populus trichocarpa. Through a comprehensive analysis of polyA tail sequences, we identified 25,919 polyA-site clusters (PACs), and revealed 3429 and 3139 genes shifted polyA sites under heat and cold stresses respectively. We found that a small proportion of genes possessed APA that affected the open reading frames; and some shifts were commonly identified. Functional analysis of genes displaying shifted polyA tails suggested that pathways related to RNA metabolism were linked to regulate the APA events under both heat and cold stresses. Interestingly, we found that the heat stress induced a significantly more antisense PACs comparing to cold and control conditions. Furthermore, we showed that a unique cis-element (AAAAAA) was predominately enriched downstream of PACs in P. trichocarpa genes; and this sequence signal was only absent in shifted PACs under the heat condition, indicating a distinct APA mechanism responsive to heat tolerance. Conclusions: This work provides a comprehensive picture of global polyadenylation patterns in response to temperatures stresses in trees. We show that the frequent change of polyA tail is a potential mechanism of gene regulation responsive to stress, which are associated with distinctive sequence signatures.

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Alternative Polyadenylation in Response to Temperature Stress Contributes to Gene Regulation in Trees

10.21203/rs.3.rs-48901/v1 ◽

2020 ◽

Author(s):

Chao Yan ◽

Yupeng Wang ◽

Tao Lyu ◽

Zhikang Hu ◽

Ning Ye ◽

...

Keyword(s):

Gene Regulation ◽

Populus Trichocarpa ◽

Alternative Polyadenylation ◽

Open Reading Frames ◽

Polya Tail ◽

Frequent Change ◽

Heat Condition ◽

Woody Perennials ◽

Genome Wide ◽

A Genome

Abstract Background Genome-wide change of polyadenylation (polyA) sites (also known as alternative polyadenylation, APA) is emerging as an important strategy of gene regulation in response to stress in plants. But little is known in woody perennials that are persistently dealing with multiple abiotic stresses.Results Here, we performed a genome-wide profiling of polyadenylation sites under heat and cold treatments in Populus trichocarpa. Through a comprehensive analysis of polyA tail sequences, we identified 25,919 polyA-site clusters (PACs), and revealed 3429 and 3139 genes shifted polyA sites under heat and cold stresses respectively. We found that a small proportion of genes possessed APA that affected the open reading frames; and some shifts were commonly identified. Functional analysis of genes displaying shifted polyA tails suggested that pathways related to RNA metabolism were linked to regulate the APA events under both heat and cold stresses. Interestingly, we found that the heat stress induced a significantly more antisense PACs comparing to cold and control conditions. Furthermore, we showed that a unique cis-element (AAAAAA) was predominately enriched downstream of PACs in P. trichocarpa genes; and this sequence signal was only absent in shifted PACs under the heat condition, indicating a distinct APA mechanism responsive to heat tolerance. Conclusions This work provides a comprehensive picture of global polyadenylation patterns in response to temperatures stresses in trees. We show that the frequent change of polyA tail is a potential mechanism of gene regulation responsive to stress, which are associated with distinctive sequence signatures.

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Genome-wide investigation and expression profiling of polyphenol oxidase (PPO) family genes uncover likely functions in organ development and stress responses in Populus trichocarpa

BMC Genomics ◽

10.1186/s12864-021-08028-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Fang He ◽

Yu-Jie Shi ◽

Qian Zhao ◽

Kuang-Ji Zhao ◽

Xing-Lei Cui ◽

...

Keyword(s):

Polyphenol Oxidase ◽

Stress Responses ◽

Populus Trichocarpa ◽

Expression Patterns ◽

Mechanical Damage ◽

Whole Genome Sequence ◽

Whole Genome ◽

Element Analysis ◽

Genome Wide ◽

A Genome

Abstract Background Trees such as Populus are planted extensively for reforestation and afforestation. However, their successful establishment greatly depends upon ambient environmental conditions and their relative resistance to abiotic and biotic stresses. Polyphenol oxidase (PPO) is a ubiquitous metalloproteinase in plants, which plays crucial roles in mediating plant resistance against biotic and abiotic stresses. Although the whole genome sequence of Populus trichocarpa has long been published, little is known about the PPO genes in Populus, especially those related to drought stress, mechanical damage, and insect feeding. Additionally, there is a paucity of information regarding hormonal responses at the whole genome level. Results A genome-wide analysis of the poplar PPO family was performed in the present study, and 18 PtrPPO genes were identified. Bioinformatics and qRT-PCR were then used to analyze the gene structure, phylogeny, chromosomal localization, gene replication, cis-elements, and expression patterns of PtrPPOs. Sequence analysis revealed that two-thirds of the PtrPPO genes lacked intronic sequences. Phylogenetic analysis showed that all PPO genes were categorized into 11 groups, and woody plants harbored many PPO genes. Eighteen PtrPPO genes were disproportionally localized on 19 chromosomes, and 3 pairs of segmented replication genes and 4 tandem repeat genomes were detected in poplars. Cis-acting element analysis identified numerous growth and developmental elements, secondary metabolism processes, and stress-related elements in the promoters of different PPO members. Furthermore, PtrPPO genes were expressed preferentially in the tissues and fruits of young plants. In addition, the expression of some PtrPPOs could be significantly induced by polyethylene glycol, abscisic acid, and methyl jasmonate, thereby revealing their potential role in regulating the stress response. Currently, we identified potential upstream TFs of PtrPPOs using bioinformatics. Conclusions Comprehensive analysis is helpful for selecting candidate PPO genes for follow-up studies on biological function, and progress in understanding the molecular genetic basis of stress resistance in forest trees might lead to the development of genetic resources.

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Genome-wide investigation and expression profiling of polyphenol oxidase (PPO) family genes uncover likely functions in organ development and stress responses in populus trichocarpa

10.21203/rs.3.rs-285546/v1 ◽

2021 ◽

Author(s):

Fang He ◽

Yu-Jie Shi ◽

Qian Zhao ◽

Kuang-Ji Zhao ◽

Xing-Lei Cui ◽

...

Keyword(s):

Polyphenol Oxidase ◽

Stress Responses ◽

Populus Trichocarpa ◽

Expression Patterns ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genetic Progress ◽

Element Analysis ◽

Genome Wide ◽

A Genome

Abstract Background: Trees such as Populus are planted extensively for reforestation and afforestation. However, their successful establishment greatly depends upon ambient environmental conditions and their relative resistance to abiotic as well as biotic stress. Polyphenol oxidase (PPO) is a ubiquitous metalloproteinase in plants, which plays crucial roles in plant resistance against biotic and abiotic stresses. Although the whole genome sequence of populus trichocarpa has long been published, little is known about the PPO genes in Populus, especially those related to drought stress, mechanical damage, insect feeding and hormone response at the whole genome level. Results: In the recent research, a genome-wide analysis of the Poplar PPOs family was finished and 18 PtrPPOs gene were identified. Then, bioinformatics and qRT-PCR were applied to analyze the gene structure, phylogeny, chromosomal localization, gene replication, Cis-elements, expression patterns of PtrPPOs. Sequence analysis revealed that 2/3 of the PtrPPO genes not contained introns. Phylogenetic analysis revealed that all PPOs gene were split into 11 subfamilies, and woody plants differentiated a large number of PPO genes. 18 PtrPPOs gene were disproportionally apportioned on 19 chromosomes, and the number of three pairs of segmented replication genes and four tandem repeat genomes were detected in poplars. Cis-acting element analysis identified a large number elements of growth and development, secondary metabolism process, and stress-related elements on the promoters of different PPO members. Furthermore, PtrPPO genes were expressed preferably in young plant tissues and fruits. In addition, some PtrPPOs could be significantly induced by PEG, ABA and JA, thus revealing their potential role in regulating stress response. Conclusions: Comprehensive analysis is helpful to select candidate PPO genes for the follow-up study of the biological function, and molecular genetic progress of stress resistance in forest trees provides genetic resources.

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A New Approach to the Genetics of Varicose Veins: A Genome-wide Association Study

Journal of Vascular Surgery ◽

10.1016/j.jvs.2010.11.026 ◽

2011 ◽

Vol 53 (1) ◽

pp. 260

Author(s):

A.M. van Rij ◽

J. Krysa ◽

G.T. Jones

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Varicose Veins ◽

Genome Wide Association ◽

New Approach ◽

Genome Wide ◽

A Genome

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Genome-Wide Mutagenesis Links Multiple Metabolic Pathways with Actinorhodin Production inStreptomyces coelicolor

Applied and Environmental Microbiology ◽

10.1128/aem.03005-18 ◽

2019 ◽

Vol 85 (7) ◽

Cited By ~ 6

Author(s):

Zhong Xu ◽

Yuanyuan Li ◽

Yemin Wang ◽

Zixin Deng ◽

Meifeng Tao

Keyword(s):

Metabolic Pathways ◽

Antibiotic Production ◽

Streptomyces Coelicolor ◽

Acid Biosynthesis ◽

Content Type ◽

Cellular Processes ◽

Genome Wide ◽

A Genome ◽

Wide Perspective ◽

Actinorhodin Production

ABSTRACTStreptomycesspecies are important antibiotic-producing organisms that tightly regulate their antibiotic production. Actinorhodin is a typical antibiotic produced by the model actinomyceteStreptomyces coelicolor. To discover the regulators of actinorhodin production, we constructed a library of 50,000 independent mutants with hyperactive Tn5transposase-based transposition systems. Five hundred fifty-one genes were found to influence actinorhodin production in 988 individual mutants. Genetic complementation suggested that most of the insertions (76%) were responsible for the changes in antibiotic production. Genes involved in diverse cellular processes such as amino acid biosynthesis, carbohydrate metabolism, cell wall homeostasis, and DNA metabolism affected actinorhodin production. Genome-wide mutagenesis can identify novel genes and pathways that impact antibiotic levels, potentially aiding in engineering strains to optimize the production of antibiotics inStreptomyces.IMPORTANCEPrevious studies have shown that various genes can influence antibiotic production inStreptomycesand that intercommunication between regulators can complicate antibiotic production. Therefore, to gain a better understanding of antibiotic regulation, a genome-wide perspective on genes that influence antibiotic production was needed. We searched for genes that affected production of the antibiotic actinorhodin using a genome-wide gene disruption system. We identified 551 genes that altered actinorhodin levels, and more than half of these genes were newly identified effectors. Some of these genes may be candidates for engineeringStreptomycesstrains to improve antibiotic production levels.

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Alternative Polyadenylation in response to temperature stress contributes to gene regulation in Populus trichocarpa

BMC Genomics ◽

10.1186/s12864-020-07353-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Chao Yan ◽

Yupeng Wang ◽

Tao Lyu ◽

Zhikang Hu ◽

Ning Ye ◽

...

Keyword(s):

Gene Regulation ◽

Populus Trichocarpa ◽

Alternative Polyadenylation ◽

Open Reading Frames ◽

Polya Tail ◽

Frequent Change ◽

Heat Condition ◽

Woody Perennials ◽

Genome Wide ◽

A Genome

Abstract Background Genome-wide change of polyadenylation (polyA) sites (also known as alternative polyadenylation, APA) is emerging as an important strategy of gene regulation in response to stress in plants. But little is known in woody perennials that are persistently dealing with multiple abiotic stresses. Results Here, we performed a genome-wide profiling of polyadenylation sites under heat and cold treatments in Populus trichocarpa. Through a comprehensive analysis of polyA tail sequences, we identified 25,919 polyA-site clusters (PACs), and revealed 3429 and 3139 genes shifted polyA sites under heat and cold stresses respectively. We found that a small proportion of genes possessed APA that affected the open reading frames; and some shifts were commonly identified. Functional analysis of genes displaying shifted polyA tails suggested that pathways related to RNA metabolism were linked to regulate the APA events under both heat and cold stresses. Interestingly, we found that the heat stress induced a significantly more antisense PACs comparing to cold and control conditions. Furthermore, we showed that a unique cis-element (AAAAAA) was predominately enriched downstream of PACs in P. trichocarpa genes; and this sequence signal was only absent in shifted PACs under the heat condition, indicating a distinct APA mechanism responsive to heat tolerance. Conclusions This work provides a comprehensive picture of global polyadenylation patterns in response to temperatures stresses in trees. We show that the frequent change of polyA tail is a potential mechanism of gene regulation responsive to stress, which are associated with distinctive sequence signatures.

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Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant–pathogen interactions in a tree

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1804428115 ◽

2018 ◽

Vol 115 (45) ◽

pp. 11573-11578 ◽

Cited By ~ 20

Author(s):

Wellington Muchero ◽

Kelsey L. Sondreli ◽

Jin-Gui Chen ◽

Breeanna R. Urbanowicz ◽

Jin Zhang ◽

...

Keyword(s):

Association Mapping ◽

Candidate Genes ◽

Populus Trichocarpa ◽

Binding Assays ◽

Type D ◽

Genome Wide ◽

A Genome ◽

Receptor Like Kinase ◽

Membrane Bound ◽

Plant Pathogen Interactions

Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and economies around the world. The deployment of resistant genotypes for combating introduced diseases typically relies on breeding programs that can take decades to complete. To demonstrate how this process can be accelerated, we employed a genome-wide association mapping ofca. 1,000 resequencedPopulus trichocarpatrees individually challenged withSphaerulina musiva, an invasive fungal pathogen. Among significant associations, three loci associated with resistance were identified and predicted to encode one putative membrane-bound L-type receptor-like kinase and two receptor-like proteins. A susceptibility-associated locus was predicted to encode a putative G-type D-mannose–binding receptor-like kinase. Multiple lines of evidence, including allele analysis, transcriptomics, binding assays, and overexpression, support the hypothesized function of these candidate genes in theP. trichocarparesponse toS. musiva.

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Chromatin accessibility dynamics of myogenesis at single cell resolution

10.1101/155473 ◽

2017 ◽

Cited By ~ 11

Author(s):

Hannah A. Pliner ◽

Jonathan Packer ◽

José L. McFaline-Figueroa ◽

Darren A. Cusanovich ◽

Riza Daza ◽

...

Keyword(s):

Single Cell ◽

Chromatin Remodeling ◽

Target Genes ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

New Approach ◽

Genome Wide ◽

A Genome ◽

Histone Modifying Enzymes ◽

Dna Regulatory Elements

AbstractOver a million DNA regulatory elements have been cataloged in the human genome, but linking these elements to the genes that they regulate remains challenging. We introduce Cicero, a statistical method that connects regulatory elements to target genes using single cell chromatin accessibility data. We apply Cicero to investigate how thousands of dynamically accessible elements orchestrate gene regulation in differentiating myoblasts. Groups of co-accessible regulatory elements linked by Cicero meet criteria of “chromatin hubs”, in that they are physically proximal, interact with a common set of transcription factors, and undergo coordinated changes in histone marks that are predictive of gene expression. Pseudotemporal analysis revealed a subset of elements bound by MYOD in myoblasts that exhibit early opening, potentially serving as the initial sites of recruitment of chromatin remodeling and histone-modifying enzymes. The methodological framework described here constitutes a powerful new approach for elucidating the architecture, grammar and mechanisms of cis-regulation on a genome-wide basis.

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