PSDX: A Comprehensive Multi-Omics Association Database of Populus trichocarpa With a Focus on the Secondary Growth in Response to Stresses
Populus trichocarpa ( P. trichocarpa ) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in P. trichocarpa . However, no comprehensive database that provides multi-omics associations for the investig...
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| Published in | Frontiers in plant science Vol. 12; p. 655565 |
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| Main Authors | , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
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Frontiers Media S.A
20.05.2021
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| Abstract | Populus trichocarpa
(
P. trichocarpa
) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in
P. trichocarpa
. However, no comprehensive database that provides multi-omics associations for the investigation of secondary growth in response to diverse stresses has been reported. Therefore, we developed a public repository that presents comprehensive measurements of gene expression and post-transcriptional regulation by integrating 144 RNA-Seq, 33 ChIP-seq, and six single-molecule real-time (SMRT) isoform sequencing (Iso-seq) libraries prepared from tissues subjected to different stresses. All the samples from different studies were analyzed to obtain gene expression, co-expression network, and differentially expressed genes (DEG) using unified parameters, which allowed comparison of results from different studies and treatments. In addition to gene expression, we also identified and deposited pre-processed data about alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI). The post-transcriptional regulation, differential expression, and co-expression network datasets were integrated into a new
P. trichocarpa
Stem Differentiating Xylem (PSDX) database (
http://forestry.fafu.edu.cn/db/SDX
), which further highlights gene families of RNA-binding proteins and stress-related genes. The PSDX also provides tools for data query, visualization, a genome browser, and the BLAST option for sequence-based query. Much of the data is also available for bulk download. The availability of PSDX contributes to the research related to the secondary growth in response to stresses in
P. trichocarpa
, which will provide new insights that can be useful for the improvement of stress tolerance in woody plants. |
|---|---|
| AbstractList | Populus trichocarpa
(
P. trichocarpa
) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in
P. trichocarpa
. However, no comprehensive database that provides multi-omics associations for the investigation of secondary growth in response to diverse stresses has been reported. Therefore, we developed a public repository that presents comprehensive measurements of gene expression and post-transcriptional regulation by integrating 144 RNA-Seq, 33 ChIP-seq, and six single-molecule real-time (SMRT) isoform sequencing (Iso-seq) libraries prepared from tissues subjected to different stresses. All the samples from different studies were analyzed to obtain gene expression, co-expression network, and differentially expressed genes (DEG) using unified parameters, which allowed comparison of results from different studies and treatments. In addition to gene expression, we also identified and deposited pre-processed data about alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI). The post-transcriptional regulation, differential expression, and co-expression network datasets were integrated into a new
P. trichocarpa
Stem Differentiating Xylem (PSDX) database (
http://forestry.fafu.edu.cn/db/SDX
), which further highlights gene families of RNA-binding proteins and stress-related genes. The PSDX also provides tools for data query, visualization, a genome browser, and the BLAST option for sequence-based query. Much of the data is also available for bulk download. The availability of PSDX contributes to the research related to the secondary growth in response to stresses in
P. trichocarpa
, which will provide new insights that can be useful for the improvement of stress tolerance in woody plants. Populus trichocarpa (P. trichocarpa) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in P. trichocarpa. However, no comprehensive database that provides multi-omics associations for the investigation of secondary growth in response to diverse stresses has been reported. Therefore, we developed a public repository that presents comprehensive measurements of gene expression and post-transcriptional regulation by integrating 144 RNA-Seq, 33 ChIP-seq, and six single-molecule real-time (SMRT) isoform sequencing (Iso-seq) libraries prepared from tissues subjected to different stresses. All the samples from different studies were analyzed to obtain gene expression, co-expression network, and differentially expressed genes (DEG) using unified parameters, which allowed comparison of results from different studies and treatments. In addition to gene expression, we also identified and deposited pre-processed data about alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI). The post-transcriptional regulation, differential expression, and co-expression network datasets were integrated into a new P. trichocarpa Stem Differentiating Xylem (PSDX) database (http://forestry.fafu.edu.cn/db/SDX), which further highlights gene families of RNA-binding proteins and stress-related genes. The PSDX also provides tools for data query, visualization, a genome browser, and the BLAST option for sequence-based query. Much of the data is also available for bulk download. The availability of PSDX contributes to the research related to the secondary growth in response to stresses in P. trichocarpa, which will provide new insights that can be useful for the improvement of stress tolerance in woody plants.Populus trichocarpa (P. trichocarpa) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in P. trichocarpa. However, no comprehensive database that provides multi-omics associations for the investigation of secondary growth in response to diverse stresses has been reported. Therefore, we developed a public repository that presents comprehensive measurements of gene expression and post-transcriptional regulation by integrating 144 RNA-Seq, 33 ChIP-seq, and six single-molecule real-time (SMRT) isoform sequencing (Iso-seq) libraries prepared from tissues subjected to different stresses. All the samples from different studies were analyzed to obtain gene expression, co-expression network, and differentially expressed genes (DEG) using unified parameters, which allowed comparison of results from different studies and treatments. In addition to gene expression, we also identified and deposited pre-processed data about alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI). The post-transcriptional regulation, differential expression, and co-expression network datasets were integrated into a new P. trichocarpa Stem Differentiating Xylem (PSDX) database (http://forestry.fafu.edu.cn/db/SDX), which further highlights gene families of RNA-binding proteins and stress-related genes. The PSDX also provides tools for data query, visualization, a genome browser, and the BLAST option for sequence-based query. Much of the data is also available for bulk download. The availability of PSDX contributes to the research related to the secondary growth in response to stresses in P. trichocarpa, which will provide new insights that can be useful for the improvement of stress tolerance in woody plants. Populus trichocarpa (P. trichocarpa) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in P. trichocarpa. However, no comprehensive database that provides multi-omics associations for the investigation of secondary growth in response to diverse stresses has been reported. Therefore, we developed a public repository that presents comprehensive measurements of gene expression and post-transcriptional regulation by integrating 144 RNA-Seq, 33 ChIP-seq, and six single-molecule real-time (SMRT) isoform sequencing (Iso-seq) libraries prepared from tissues subjected to different stresses. All the samples from different studies were analyzed to obtain gene expression, co-expression network, and differentially expressed genes (DEG) using unified parameters, which allowed comparison of results from different studies and treatments. In addition to gene expression, we also identified and deposited pre-processed data about alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI). The post-transcriptional regulation, differential expression, and co-expression network datasets were integrated into a new P. trichocarpa Stem Differentiating Xylem (PSDX) database (http://forestry.fafu.edu.cn/db/SDX), which further highlights gene families of RNA-binding proteins and stress-related genes. The PSDX also provides tools for data query, visualization, a genome browser, and the BLAST option for sequence-based query. Much of the data is also available for bulk download. The availability of PSDX contributes to the research related to the secondary growth in response to stresses in P. trichocarpa, which will provide new insights that can be useful for the improvement of stress tolerance in woody plants. |
| Author | Jaiswal, Pankaj Liu, Sheng Yang, Yongkang Wei, Wentao Gu, Lianfeng Li, Wei Dai, Xiufang Luo, Yunjun Liu, Xuqing Xu, Xi Wang, Huihui Liu, Bo Reddy, Anireddy S. N. Wang, Huiyuan Gao, Yubang |
| AuthorAffiliation | 4 Department of Biology and Program in Cell and Molecular Biology, Colorado State University , Fort Collins, CO , United States 6 College of Forestry, Fujian Agriculture and Forestry University , Fuzhou , China 5 Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR , United States 1 Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou , China 3 State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University , Harbin , China 2 College of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , China |
| AuthorAffiliation_xml | – name: 3 State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University , Harbin , China – name: 1 Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou , China – name: 4 Department of Biology and Program in Cell and Molecular Biology, Colorado State University , Fort Collins, CO , United States – name: 5 Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR , United States – name: 6 College of Forestry, Fujian Agriculture and Forestry University , Fuzhou , China – name: 2 College of Life Sciences, Fujian Agriculture and Forestry University , Fuzhou , China |
| Author_xml | – sequence: 1 givenname: Huiyuan surname: Wang fullname: Wang, Huiyuan – sequence: 2 givenname: Sheng surname: Liu fullname: Liu, Sheng – sequence: 3 givenname: Xiufang surname: Dai fullname: Dai, Xiufang – sequence: 4 givenname: Yongkang surname: Yang fullname: Yang, Yongkang – sequence: 5 givenname: Yunjun surname: Luo fullname: Luo, Yunjun – sequence: 6 givenname: Yubang surname: Gao fullname: Gao, Yubang – sequence: 7 givenname: Xuqing surname: Liu fullname: Liu, Xuqing – sequence: 8 givenname: Wentao surname: Wei fullname: Wei, Wentao – sequence: 9 givenname: Huihui surname: Wang fullname: Wang, Huihui – sequence: 10 givenname: Xi surname: Xu fullname: Xu, Xi – sequence: 11 givenname: Anireddy S. N. surname: Reddy fullname: Reddy, Anireddy S. N. – sequence: 12 givenname: Pankaj surname: Jaiswal fullname: Jaiswal, Pankaj – sequence: 13 givenname: Wei surname: Li fullname: Li, Wei – sequence: 14 givenname: Bo surname: Liu fullname: Liu, Bo – sequence: 15 givenname: Lianfeng surname: Gu fullname: Gu, Lianfeng |
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| Cites_doi | 10.1093/mp/ssu030 10.1093/dnares/dsp016 10.1186/1471-2164-14-359 10.1111/j.1365-313X.2009.03938.x 10.1093/bioinformatics/btx830 10.1093/bioinformatics/btp616 10.1093/database/bav046 10.1186/1471-2164-15-s5-s3 10.1073/pnas.1212977109 10.1073/pnas.1419161111 10.1371/journal.pone.0046679 10.1111/tpj.13597 10.1186/s13059-016-0924-1 10.1016/j.jgg.2018.05.007 10.1101/gr.100677.109 10.1038/nmeth.1923 10.1038/nbt.3122 10.1105/tpc.113.113803 10.1038/nmeth.3317 10.1042/BST20190492 10.1111/tpj.12850 10.1111/tpj.14120 10.1007/s11103-008-9334-4 10.1111/j.1744-7909.2010.00925.x 10.1073/pnas.1308936110 10.1007/s11105-014-0759-4 10.1016/j.ecoenv.2019.109485 10.1073/pnas.1019732108 10.12688/f1000research.23297.2 10.1093/pcp/pcv190 10.1186/1471-2105-14-33 10.1111/j.1744-7909.2006.00303.x 10.1155/2013/949564 10.1038/nprot.2014.146 10.1101/gr.134106.111 10.1111/php.12680 10.1073/pnas.1714422114 10.1101/gr.093302.109 10.1105/tpc.113.114835 10.1104/pp.19.01558 10.2174/1574893614666190204151746 10.1104/pp.127.4.1513 10.1111/nph.13151 10.1016/j.plantsci.2013.01.009 10.1093/pcp/pcs053 10.1126/science.1128691 10.1007/978-981-10-9029-5 10.1186/gb-2008-9-9-r137 10.1023/a:1010699919325 10.1093/nar/gky448 10.1104/pp.113.231134 10.1101/gr.210757.116 10.1111/tpj.14671 10.1105/tpc.113.117523 10.1093/nar/gkr944 10.1093/bioinformatics/btp352 10.1093/nar/30.3.623 10.1105/tpc.18.00437 10.3390/ijms14035842 10.1002/wrna.59 10.1146/annurev.arplant.58.032806.103956 10.1038/nmeth.2714 10.1007/s00425-013-1882-4 10.1038/srep38436 10.3389/fgene.2019.00253 10.1007/s00425-016-2640-1 10.1007/978-981-15-0690-1 10.1093/nar/gkq1019 10.1105/tpc.113.117697 10.1104/pp.108.133371 10.4161/psb.6.1.14063 10.3389/fpls.2018.00005 10.1371/journal.pone.0065598 10.1093/molbev/msz185 |
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| Copyright | Copyright © 2021 Wang, Liu, Dai, Yang, Luo, Gao, Liu, Wei, Wang, Xu, Reddy, Jaiswal, Li, Liu and Gu. Copyright © 2021 Wang, Liu, Dai, Yang, Luo, Gao, Liu, Wei, Wang, Xu, Reddy, Jaiswal, Li, Liu and Gu. 2021 Wang, Liu, Dai, Yang, Luo, Gao, Liu, Wei, Wang, Xu, Reddy, Jaiswal, Li, Liu and Gu |
| Copyright_xml | – notice: Copyright © 2021 Wang, Liu, Dai, Yang, Luo, Gao, Liu, Wei, Wang, Xu, Reddy, Jaiswal, Li, Liu and Gu. – notice: Copyright © 2021 Wang, Liu, Dai, Yang, Luo, Gao, Liu, Wei, Wang, Xu, Reddy, Jaiswal, Li, Liu and Gu. 2021 Wang, Liu, Dai, Yang, Luo, Gao, Liu, Wei, Wang, Xu, Reddy, Jaiswal, Li, Liu and Gu |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Edited by: Ralf Alexander Wilhelm, Institute for Biosafety in Plant Biotechnology, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute, Germany Reviewed by: Jorge Maurício Mondego, Instituto Agronômico de Campinas (IAC), Brazil; Congting Ye, Xiamen University, China This article was submitted to Plant Biotechnology, a section of the journal Frontiers in Plant Science |
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| References | Baek (B5) 2008; 67 Perrella (B43) 2013; 25 Lu (B39) 2013; 110 Jansson (B20) 2007; 58 Kaneda (B21) 2010; 52 Langmead (B25) 2012; 9 Appels (B3) 2018; 361 Liu (B35) 2014; 15 Ye (B70) 2019; 183 You (B71) 2016; 6 Zhang (B73) 2019; 97 Lin (B33) 2017; 114 Lin (B32) 2013; 25 Reddy (B50) 2013; 25 Marquez (B40) 2012; 22 Hossain (B19) 2016 Vats (B64) 2018 Shen (B53) 2013; 8 Zhao (B76) 2019; 10 Silverman (B56) 2013; 205 Villar Salvador (B65) 2013 Li (B30) 2014; 9 Fu (B15) 2016; 26 Wang (B66) 2017; 91 Reddy (B49) 2020; 48 Lindemose (B34) 2013; 14 Potter (B47) 2018; 46 Tuskan (B63) 2006; 313 Mellerowicz (B41) 2001; 47 Singh (B57) 2019 Yang (B69) 2013; 14 Liu (B36); 82 Lorkovic (B38) 2002; 30 Li (B27) 2009; 25 Daras (B11) 2014; 7 Tian (B62) 2018; 45 Shen (B54) 2014; 111 Alter (B1) 2015; 2015 Pertea (B44) 2020; 9 Goodstein (B18) 2012; 40 Li (B28) 2012; 109 Plomion (B46) 2001; 127 Srivastava (B58) 2009; 149 Zhang (B75) 2008; 9 Lin (B31) 2006; 48 Pertea (B45) 2015; 33 Bailey-Serres (B6) 2020; 182 Shi (B55) 2017; 245 Au (B4) 2012; 7 Kim (B22) 2015; 12 Gao (B17) 2019; 14 Robinson (B51) 2010; 26 Kim (B23) 2012; 53 Zhang (B72) 2010; 20 Gao (B16) 2018; 34 Bao (B7) 2013; 14 Tang (B61) 2015; 33 Xing (B68) 2011; 2 Filichkin (B13) 2018; 9 Seo (B52) 2013; 237 Zhang (B74) 2017; 93 Chakrabarti (B10) 2020; 102 Staiger (B59) 2013; 25 Leinonen (B26) 2011; 39 Li (B29) 2019; 31 Steijger (B60) 2013; 10 Borkotoky (B8) 2013; 2013 Buels (B9) 2016; 17 Duque (B12) 2011; 6 Obayashi (B42) 2009; 16 Priyann (B48) 2019; 36 Wu (B67) 2011; 108 Filichkin (B14) 2010; 20 Zhao (B77) 2014; 164 Liu (B37); 205 Kwon (B24) 2009; 60 Aoki (B2) 2016; 57 |
| References_xml | – volume: 7 start-page: 989 year: 2014 ident: B11 article-title: Alternative transcription initiation and the AUG context configuration control dual-organellar targeting and functional competence of Arabidopsis Lon1 protease. publication-title: Mol. Plant doi: 10.1093/mp/ssu030 – volume: 16 start-page: 249 year: 2009 ident: B42 article-title: Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. publication-title: DNA Res. doi: 10.1093/dnares/dsp016 – volume: 14 year: 2013 ident: B7 article-title: The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations. publication-title: BMC Genomics doi: 10.1186/1471-2164-14-359 – volume: 60 start-page: 112 year: 2009 ident: B24 article-title: Histone occupancy-dependent and -independent removal of H3K27 trimethylation at cold-responsive genes in Arabidopsis. publication-title: Plant J. doi: 10.1111/j.1365-313X.2009.03938.x – volume: 34 start-page: 1580 year: 2018 ident: B16 article-title: PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btx830 – volume: 26 start-page: 139 year: 2010 ident: B51 article-title: edgeR: a bioconductor package for differential expression analysis of digital gene expression data. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp616 – volume: 2015 year: 2015 ident: B1 article-title: DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species. publication-title: Database (Oxford) doi: 10.1093/database/bav046 – volume: 15 year: 2014 ident: B35 article-title: Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees. publication-title: BMC Genomics doi: 10.1186/1471-2164-15-s5-s3 – volume: 109 start-page: 14699 year: 2012 ident: B28 article-title: Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa. publication-title: Proc. Natl. Acad. Sci. U.S.A. doi: 10.1073/pnas.1212977109 – volume: 111 start-page: E5593 year: 2014 ident: B54 article-title: rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. publication-title: Proc. Natl. Acad. Sci. U.S.A. doi: 10.1073/pnas.1419161111 – volume: 7 year: 2012 ident: B4 article-title: Improving PacBio long read accuracy by short read alignment. publication-title: PLoS One doi: 10.1371/journal.pone.0046679 – volume: 91 start-page: 684 year: 2017 ident: B66 article-title: Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis). publication-title: Plant J. doi: 10.1111/tpj.13597 – volume: 17 year: 2016 ident: B9 article-title: JBrowse: a dynamic web platform for genome visualization and analysis. publication-title: Genome Biol. doi: 10.1186/s13059-016-0924-1 – volume: 45 start-page: 351 year: 2018 ident: B62 article-title: MCENet: a database for maize conditional co-expression network and network characterization collaborated with multi-dimensional omics levels. publication-title: J. Genet. Genom. doi: 10.1016/j.jgg.2018.05.007 – volume: 20 start-page: 646 year: 2010 ident: B72 article-title: Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. publication-title: Genome Res. doi: 10.1101/gr.100677.109 – volume: 9 start-page: 357 year: 2012 ident: B25 article-title: Fast gapped-read alignment with Bowtie 2. publication-title: Nat. Methods doi: 10.1038/nmeth.1923 – volume: 33 start-page: 290 year: 2015 ident: B45 article-title: StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. publication-title: Nat. Biotechnol. doi: 10.1038/nbt.3122 – volume: 25 start-page: 3640 year: 2013 ident: B59 article-title: Alternative splicing at the intersection of biological timing, development, and stress responses. publication-title: Plant Cell doi: 10.1105/tpc.113.113803 – volume: 12 start-page: 357 year: 2015 ident: B22 article-title: HISAT: a fast spliced aligner with low memory requirements. publication-title: Nat. Methods doi: 10.1038/nmeth.3317 – volume: 48 start-page: 2399 year: 2020 ident: B49 article-title: Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. publication-title: Biochem. Soc. Trans. doi: 10.1042/BST20190492 – volume: 82 start-page: 887 ident: B36 article-title: A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus. publication-title: Plant J. doi: 10.1111/tpj.12850 – year: 2016 ident: B19 publication-title: Drought Stress Tolerance in Plants – volume: 97 start-page: 296 year: 2019 ident: B73 article-title: PacBio full-length cDNA sequencing integrated with RNA-seq reads drastically improves the discovery of splicing transcripts in rice. publication-title: Plant J. doi: 10.1111/tpj.14120 – volume: 67 start-page: 499 year: 2008 ident: B5 article-title: Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice. publication-title: Plant Mol. Biol. doi: 10.1007/s11103-008-9334-4 – volume: 52 start-page: 234 year: 2010 ident: B21 article-title: Secondary cell wall deposition in developing secondary xylem of poplar. publication-title: J. Integr. Plant Biol. doi: 10.1111/j.1744-7909.2010.00925.x – volume: 110 start-page: 10848 year: 2013 ident: B39 article-title: Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa. publication-title: Proc. Natl. Acad. Sci. U.S.A doi: 10.1073/pnas.1308936110 – volume: 33 start-page: 424 year: 2015 ident: B61 article-title: Analysis of the drought stress-responsive transcriptome of black cottonwood (Populus trichocarpa) using deep RNA sequencing. publication-title: Plant Mol. Biol. Rep. doi: 10.1007/s11105-014-0759-4 – start-page: 22 year: 2013 ident: B65 publication-title: Plant Responses to Drought Stress. From Morphological to Molecular Features – volume: 183 year: 2019 ident: B70 article-title: Genome-wide alternative polyadenylation dynamics in response to biotic and abiotic stresses in rice. publication-title: Ecotoxicol. Environ. Saf. doi: 10.1016/j.ecoenv.2019.109485 – volume: 108 start-page: 12533 year: 2011 ident: B67 article-title: Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. publication-title: Proc. Natl. Acad. Sci. U.S.A. doi: 10.1073/pnas.1019732108 – volume: 9 year: 2020 ident: B44 article-title: GFF Utilities: GffRead and GffCompare. publication-title: F1000Res. doi: 10.12688/f1000research.23297.2 – volume: 57 year: 2016 ident: B2 article-title: ALCOdb: gene coexpression database for microalgae. publication-title: Plant Cell Physiol. doi: 10.1093/pcp/pcv190 – volume: 14 year: 2013 ident: B69 article-title: HTQC: a fast quality control toolkit for Illumina sequencing data. publication-title: BBioinform. doi: 10.1186/1471-2105-14-33 – volume: 48 start-page: 1001 year: 2006 ident: B31 article-title: Progress in the study of molecular genetic improvements of poplar in China. publication-title: J. Integr. Plant Biol. doi: 10.1111/j.1744-7909.2006.00303.x – volume: 2013 year: 2013 ident: B8 article-title: The Arabidopsis stress responsive gene database. publication-title: Int. J. Plant Genom. doi: 10.1155/2013/949564 – volume: 9 start-page: 2180 year: 2014 ident: B30 article-title: A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue. publication-title: Nat. Protoc. doi: 10.1038/nprot.2014.146 – volume: 22 start-page: 1184 year: 2012 ident: B40 article-title: Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. publication-title: Genome Research doi: 10.1101/gr.134106.111 – volume: 93 start-page: 159 year: 2017 ident: B74 article-title: Light regulation of alternative Pre−mRNA splicing in plants. publication-title: Photochem. Photobiol. doi: 10.1111/php.12680 – volume: 114 start-page: E9722 year: 2017 ident: B33 article-title: Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa. publication-title: Proc. Natl. Acad. Sci. U.S.A. doi: 10.1073/pnas.1714422114 – volume: 20 start-page: 45 year: 2010 ident: B14 article-title: Genome-wide mapping of alternative splicing in Arabidopsis thaliana. publication-title: Genome Res. doi: 10.1101/gr.093302.109 – volume: 25 start-page: 3491 year: 2013 ident: B43 article-title: Histone deacetylase complex1 expression level titrates plant growth and abscisic acid sensitivity in Arabidopsis. publication-title: Plant Cell doi: 10.1105/tpc.113.114835 – volume: 182 start-page: 1 year: 2020 ident: B6 article-title: The dynamic kaleidoscope of RNA biology in plants. publication-title: Plant Physiol. doi: 10.1104/pp.19.01558 – volume: 14 start-page: 566 year: 2019 ident: B17 article-title: Single-molecule Real-time (SMRT) Isoform Sequencing (Iso-Seq) in plants: the status of the bioinformatics tools to unravel the transcriptome complexity. publication-title: Curr. Bioinform. doi: 10.2174/1574893614666190204151746 – volume: 127 start-page: 1513 year: 2001 ident: B46 article-title: Wood formation in trees. publication-title: Plant Physiol. doi: 10.1104/pp.127.4.1513 – volume: 361 year: 2018 ident: B3 article-title: Shifting the limits in wheat research and breeding using a fully annotated reference genome. publication-title: Science – volume: 205 start-page: 682 ident: B37 article-title: The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function. publication-title: N. Phytol. doi: 10.1111/nph.13151 – volume: 205 start-page: 55 year: 2013 ident: B56 article-title: Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants. publication-title: Plant Sci. doi: 10.1016/j.plantsci.2013.01.009 – volume: 53 start-page: 847 year: 2012 ident: B23 article-title: Transition of chromatin status during the process of recovery from drought stress in Arabidopsis thaliana. publication-title: Plant Cell Physiol. doi: 10.1093/pcp/pcs053 – volume: 313 start-page: 1596 year: 2006 ident: B63 article-title: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). publication-title: Science doi: 10.1126/science.1128691 – year: 2018 ident: B64 publication-title: Biotic and Abiotic Stress Tolerance in Plants. doi: 10.1007/978-981-10-9029-5 – volume: 9 year: 2008 ident: B75 article-title: Model-based analysis of ChIP-Seq (MACS). publication-title: Genome Biol. doi: 10.1186/gb-2008-9-9-r137 – volume: 47 start-page: 239 year: 2001 ident: B41 article-title: Unravelling cell wall formation in the woody dicot stem. publication-title: Plant Mol. Biol. doi: 10.1023/a:1010699919325 – volume: 46 start-page: W200 year: 2018 ident: B47 article-title: HMMER web server: 2018 update. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gky448 – volume: 164 start-page: 765 year: 2014 ident: B77 article-title: Intron-mediated alternative splicing of wood-associated nac transcription factor1b regulates cell wall thickening during fiber development in Populus Species. publication-title: Plant Physiol. doi: 10.1104/pp.113.231134 – volume: 26 start-page: 1753 year: 2016 ident: B15 article-title: Genome-wide dynamics of alternative polyadenylation in rice. publication-title: Genome Res. doi: 10.1101/gr.210757.116 – volume: 102 start-page: 916 year: 2020 ident: B10 article-title: Wide−ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum. publication-title: Plant J. doi: 10.1111/tpj.14671 – volume: 25 start-page: 3657 year: 2013 ident: B50 article-title: Complexity of the alternative splicing landscape in plants. publication-title: Plant Cell doi: 10.1105/tpc.113.117523 – volume: 40 start-page: D1178 year: 2012 ident: B18 article-title: Phytozome: a comparative platform for green plant genomics. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkr944 – volume: 25 start-page: 2078 year: 2009 ident: B27 article-title: The sequence alignment/map format and SAMtools. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp352 – volume: 30 start-page: 623 year: 2002 ident: B38 article-title: Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana. publication-title: Nucleic Acids Re.s doi: 10.1093/nar/30.3.623 – volume: 31 start-page: 663 year: 2019 ident: B29 article-title: The AREB1 transcription factor influences histone acetylation to regulate drought responses and tolerance in Populus trichocarpa. publication-title: Plant Cell doi: 10.1105/tpc.18.00437 – volume: 14 start-page: 5842 year: 2013 ident: B34 article-title: Structure, function and networks of transcription factors involved in abiotic stress responses. publication-title: Int. J. Mol. Sci. doi: 10.3390/ijms14035842 – volume: 2 start-page: 445 year: 2011 ident: B68 article-title: Alternative polyadenylation and gene expression regulation in plants. publication-title: Wiley Interdisc. Rev. RNA doi: 10.1002/wrna.59 – volume: 58 start-page: 435 year: 2007 ident: B20 article-title: Populus: a model system for plant biology. publication-title: Annu. Rev. Plant Biol. doi: 10.1146/annurev.arplant.58.032806.103956 – volume: 10 start-page: 1177 year: 2013 ident: B60 article-title: Assessment of transcript reconstruction methods for RNA-seq. publication-title: Nat. Methods doi: 10.1038/nmeth.2714 – volume: 237 start-page: 1415 year: 2013 ident: B52 article-title: Alternative splicing of transcription factors in plant responses to low temperature stress: mechanisms and functions. publication-title: Planta doi: 10.1007/s00425-013-1882-4 – volume: 6 year: 2016 ident: B71 article-title: Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum. publication-title: Sci. Rep. doi: 10.1038/srep38436 – volume: 10 year: 2019 ident: B76 article-title: Analysis of transcriptome and epitranscriptome in plants using pacbio iso-seq and nanopore-based direct RNA sequencing. publication-title: Front. Genet. doi: 10.3389/fgene.2019.00253 – volume: 245 start-page: 927 year: 2017 ident: B55 article-title: Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa. publication-title: Planta doi: 10.1007/s00425-016-2640-1 – year: 2019 ident: B57 publication-title: Molecular Approaches in Plant Biology and Environmental Challenges. doi: 10.1007/978-981-15-0690-1 – volume: 39 start-page: D19 year: 2011 ident: B26 article-title: The sequence read archive. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkq1019 – volume: 25 start-page: 4324 year: 2013 ident: B32 article-title: SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa. publication-title: Plant Cell doi: 10.1105/tpc.113.117697 – volume: 149 start-page: 1848 year: 2009 ident: B58 article-title: Alternative splicing studies of the reactive oxygen species gene network in populus reveal two isoforms of high-isoelectric-point superoxide dismutase. publication-title: Plant Physiol. doi: 10.1104/pp.108.133371 – volume: 6 start-page: 49 year: 2011 ident: B12 article-title: A role for SR proteins in plant stress responses. publication-title: Plant Signal. Behav. doi: 10.4161/psb.6.1.14063 – volume: 9 year: 2018 ident: B13 article-title: Abiotic stresses modulate landscape of poplar transcriptome via alternative splicing, differential intron retention, and isoform ratio switching. publication-title: Front. Plant Sci. doi: 10.3389/fpls.2018.00005 – volume: 8 year: 2013 ident: B53 article-title: diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. publication-title: PLoS One doi: 10.1371/journal.pone.0065598 – volume: 36 start-page: 2922 year: 2019 ident: B48 article-title: Sequenceserver: a modern graphical user interface for custom blast databases. publication-title: Molecular Biol. Evol. doi: 10.1093/molbev/msz185 |
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| Snippet | Populus trichocarpa
(
P. trichocarpa
) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of... Populus trichocarpa (P. trichocarpa) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of... |
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| Title | PSDX: A Comprehensive Multi-Omics Association Database of Populus trichocarpa With a Focus on the Secondary Growth in Response to Stresses |
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