LIVIVO - Search results -

Search results

Result 1 - 10 of total 50

Search options

Article ; Online: Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses.

Tan, Qiao Wen / Lim, Peng Ken / Chen, Zhong / Pasha, Asher / Provart, Nicholas / Arend, Marius / Nikoloski, Zoran / Mutwil, Marek

Nature communications

2023 Volume 14, Issue 1, Page(s) 986

Abstract: Abiotic stresses negatively impact ecosystems and the yield of crops, and climate change will increase their frequency and intensity. Despite progress in understanding how plants respond to individual stresses, our knowledge of plant acclimatization to ... ...

Abstract	Abiotic stresses negatively impact ecosystems and the yield of crops, and climate change will increase their frequency and intensity. Despite progress in understanding how plants respond to individual stresses, our knowledge of plant acclimatization to combined stresses typically occurring in nature is still lacking. Here, we used a plant with minimal regulatory network redundancy, Marchantia polymorpha, to study how seven abiotic stresses, alone and in 19 pairwise combinations, affect the phenotype, gene expression, and activity of cellular pathways. While the transcriptomic responses show a conserved differential gene expression between Arabidopsis and Marchantia, we also observe a strong functional and transcriptional divergence between the two species. The reconstructed high-confidence gene regulatory network demonstrates that the response to specific stresses dominates those of others by relying on a large ensemble of transcription factors. We also show that a regression model could accurately predict the gene expression under combined stresses, indicating that Marchantia performs arithmetic multiplication to respond to multiple stresses. Lastly, two online resources ( https://conekt.plant.tools and http://bar.utoronto.ca/efp_marchantia/cgi-bin/efpWeb.cgi ) are provided to facilitate the study of gene expression in Marchantia exposed to abiotic stresses.
MeSH term(s)	Marchantia/metabolism ; Ecosystem ; Plants/genetics ; Transcriptome ; Stress, Physiological ; Gene Expression Regulation, Plant
Language	English
Publishing date	2023-02-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-36517-w
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Article ; Online: A high-resolution gene expression map of the medial and lateral domains of the gynoecium of Arabidopsis.

Luna-García, Valentín / Bernal Gallardo, Judith Jazmin / Rethoret-Pasty, Martin / Pasha, Asher / Provart, Nicholas J / de Folter, Stefan

Plant physiology

2023 Volume 195, Issue 1, Page(s) 410–429

Abstract: Angiosperms are characterized by the formation of flowers, and in their inner floral whorl, one or various gynoecia are produced. These female reproductive structures are responsible for fruit and seed production, thus ensuring the reproductive ... ...

Abstract	Angiosperms are characterized by the formation of flowers, and in their inner floral whorl, one or various gynoecia are produced. These female reproductive structures are responsible for fruit and seed production, thus ensuring the reproductive competence of angiosperms. In Arabidopsis (Arabidopsis thaliana), the gynoecium is composed of two fused carpels with different tissues that need to develop and differentiate to form a mature gynoecium and thus the reproductive competence of Arabidopsis. For these reasons, they have become the object of study for floral and fruit development. However, due to the complexity of the gynoecium, specific spatio-temporal tissue expression patterns are still scarce. In this study, we used precise laser-assisted microdissection and high-throughput RNA sequencing to describe the transcriptional profiles of the medial and lateral domain tissues of the Arabidopsis gynoecium. We provide evidence that the method used is reliable and that, in addition to corroborating gene expression patterns of previously reported regulators of these tissues, we found genes whose expression dynamics point to being involved in cytokinin and auxin homeostasis and in cell cycle progression. Furthermore, based on differential gene expression analyses, we functionally characterized several genes and found that they are involved in gynoecium development. This resource is available via the Arabidopsis eFP browser and will serve the community in future studies on developmental and reproductive biology.
MeSH term(s)	Arabidopsis/genetics ; Arabidopsis/growth & development ; Flowers/genetics ; Flowers/growth & development ; Gene Expression Regulation, Plant ; Gene Expression Profiling/methods ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Indoleacetic Acids/metabolism ; Genes, Plant
Chemical Substances	Arabidopsis Proteins ; Indoleacetic Acids
Language	English
Publishing date	2023-12-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1093/plphys/kiad658
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Bonn / Germany

Z 1193: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Laser Capture Microdissection Transcriptome Reveals Spatiotemporal Tissue Gene Expression Patterns of Medicago truncatula Roots Responding to Rhizobia

Schnabel, Elise / Thomas, Jacklyn / El-Hawaz, Rabia / Gao, Yueyao / Poehlman, William L. / Chavan, Suchitra / Pasha, Asher / Esteban, Eddi / Provart, Nicholas / Feltus, F. Alex / Frugoli, Julia

Molecular Plant-Microbe Interactions. 2023 Dec. 23, v. 36, no. 12 p.805-820

2023

Abstract: We report a public resource for examining the spatiotemporal RNA expression of 54,893 Medicago truncatula genes during the first 72 h of response to rhizobial inoculation. Using a methodology that allows synchronous inoculation and growth of more than ... ...

Abstract	We report a public resource for examining the spatiotemporal RNA expression of 54,893 Medicago truncatula genes during the first 72 h of response to rhizobial inoculation. Using a methodology that allows synchronous inoculation and growth of more than 100 plants in a single media container, we harvested the same segment of each root responding to rhizobia in the initial inoculation over a time course, collected individual tissues from these segments with laser capture microdissection, and created and sequenced RNA libraries generated from these tissues. We demonstrate the utility of the resource by examining the expression patterns of a set of genes induced very early in nodule signaling, as well as two gene families (CLE peptides and nodule specific PLAT-domain proteins) and show that despite similar whole-root expression patterns, there are tissue differences in expression between the genes. Using a rhizobial response dataset generated from transcriptomics on intact root segments, we also examined differential temporal expression patterns and determined that, after nodule tissue, the epidermis and cortical cells contained the most temporally patterned genes. We circumscribed gene lists for each time and tissue examined and developed an expression pattern visualization tool. Finally, we explored transcriptomic differences between the inner cortical cells that become nodules and those that do not, confirming that the expression of 1-aminocyclopropane-1-carboxylate synthases distinguishes inner cortical cells that become nodules and provide and describe potential downstream genes involved in early nodule cell division. Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Keywords	1-aminocyclopropane-1-carboxylic acid ; Medicago truncatula ; RNA ; cell division ; data collection ; gene expression ; genes ; laser capture microdissection ; peptides ; transcriptome ; transcriptomics ; M. truncatula ; nodulation ; RNA-Seq
Language	English
Dates of publication	2023-1223
Size	p. 805-820.
Publishing place	The American Phytopathological Society
Document type	Article ; Online
ZDB-ID	743331-1
ISSN	1943-7706 ; 0894-0282
ISSN (online)	1943-7706
ISSN	0894-0282
DOI	10.1094/MPMI-03-23-0029-R
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Bonn / Germany

Z 4734: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Profiling of the gene expression and alternative splicing landscapes of Eucalyptus grandis.

Fan, Chunjie / Lyu, Mingjie / Zeng, Bingshan / He, Qiang / Wang, Xiaoping / Lu, Meng-Zhu / Liu, Bobin / Liu, Jun / Esteban, Eddi / Pasha, Asher / Provart, Nicholas J / Wang, Huan / Zhang, Jin

Plant, cell & environment

2024 Volume 47, Issue 4, Page(s) 1363–1378

Abstract: Eucalyptus is a widely planted hardwood tree species due to its fast growth, superior wood properties and adaptability. However, the post-transcriptional regulatory mechanisms controlling tissue development and stress responses in Eucalyptus remain ... ...

Abstract	Eucalyptus is a widely planted hardwood tree species due to its fast growth, superior wood properties and adaptability. However, the post-transcriptional regulatory mechanisms controlling tissue development and stress responses in Eucalyptus remain poorly understood. In this study, we performed a comprehensive analysis of the gene expression profile and the alternative splicing (AS) landscape of E. grandis using strand-specific RNA-Seq, which encompassed 201 libraries including different organs, developmental stages, and environmental stresses. We identified 10 416 genes (33.49%) that underwent AS, and numerous differentially expressed and/or differential AS genes involved in critical biological processes, such as primary-to-secondary growth transition of stems, adventitious root formation, aging and responses to phosphorus- or boron-deficiency. Co-expression analysis of AS events and gene expression patterns highlighted the potential upstream regulatory role of AS events in multiple processes. Additionally, we highlighted the lignin biosynthetic pathway to showcase the potential regulatory functions of AS events in the KNAT3 and IRL3 genes within this pathway. Our high-quality expression atlas and AS landscape serve as valuable resources for unravelling the genetic control of woody plant development, long-term adaptation, and understanding transcriptional diversity in Eucalyptus. Researchers can conveniently access these resources through the interactive ePlant browser (https://bar.utoronto.ca/eplant_eucalyptus).
MeSH term(s)	Genes, Plant/genetics ; Eucalyptus/physiology ; Alternative Splicing/genetics ; Wood ; Transcriptome ; Gene Expression Profiling ; Gene Expression Regulation, Plant
Language	English
Publishing date	2024-01-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	391893-2
ISSN	1365-3040 ; 0140-7791
ISSN (online)	1365-3040
ISSN	0140-7791
DOI	10.1111/pce.14814
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Bonn / Germany

Z 80/729: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: The transcriptome landscape of developing barley seeds.

Kovacik, Martin / Nowicka, Anna / Zwyrtková, Jana / Strejčková, Beáta / Vardanega, Isaia / Esteban, Eddi / Pasha, Asher / Kaduchová, Kateřina / Krautsova, Maryna / Červenková, Marie / Šafář, Jan / Provart, Nicholas J / Simon, Rüdiger / Pecinka, Ales

The Plant cell

2024

Abstract: Cereal grains are an important source of food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley (Hordeum vulgare L. subsp. vulgare), we performed a transcriptomic study of ... ...

Abstract	Cereal grains are an important source of food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley (Hordeum vulgare L. subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from grains 4-32 days after pollination. Weighted gene co-expression network and motif enrichment analyses identified specific groups of genes and transcription factors (TFs) potentially regulating barley seed tissue development. We defined a set of tissue-specific marker genes and families of TFs for functional studies of the pathways controlling barley grain development. Assessing selected groups of chromatin regulators revealed that epigenetic processes are highly dynamic and likely play a major role during barley endosperm development. The repressive H3K27me3 modification is globally reduced in endosperm tissues and at specific genes related to development and storage compounds. Altogether, this atlas uncovers the complexity of developmentally regulated gene expression in developing barley grains.
Language	English
Publishing date	2024-04-18
Publishing country	England
Document type	Journal Article
ZDB-ID	623171-8
ISSN	1532-298X ; 1040-4651
ISSN (online)	1532-298X
ISSN	1040-4651
DOI	10.1093/plcell/koae095
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Bonn / Germany

Z 4952: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Nutri-cereal tissue-specific transcriptome atlas during development: Functional integration of gene expression to identify mineral uptake pathways in little millet (Panicum sumatrense).

Pahari, Shankar / Vaid, Neha / Soolanayakanahally, Raju / Kagale, Sateesh / Pasha, Asher / Esteban, Eddi / Provart, Nicholas / Stobbs, Jarvis A / Vu, Miranda / Meira, Debora / Karunakaran, Chithra / Boda, Praveen / Prasannakumar, Mothukapalli K / Nagaraja, Alur / Jain, Ashwani Kumar

The Plant journal : for cell and molecular biology

2024

Abstract: Little millet (Panicum sumatrense Roth ex Roem. & Schult.) is an essential minor millet of southeast Asia and Africa's temperate and subtropical regions. The plant is stress-tolerant, has a short life cycle, and has a mineral-rich nutritional profile ... ...

Abstract	Little millet (Panicum sumatrense Roth ex Roem. & Schult.) is an essential minor millet of southeast Asia and Africa's temperate and subtropical regions. The plant is stress-tolerant, has a short life cycle, and has a mineral-rich nutritional profile associated with unique health benefits. We report the developmental gene expression atlas of little millet (genotype JK-8) from ten tissues representing different stages of its life cycle, starting from seed germination and vegetative growth to panicle maturation. The developmental transcriptome atlas led to the identification of 342 827 transcripts. The BUSCO analysis and comparison with the transcriptomes of related species confirm that this study presents high-quality, in-depth coverage of the little millet transcriptome. In addition, the eFP browser generated here has a user-friendly interface, allowing interactive visualizations of tissue-specific gene expression. Using these data, we identified transcripts, the orthologs of which in Arabidopsis and rice are involved in nutrient acquisition, transport, and response pathways. The comparative analysis of the expression levels of these transcripts holds great potential for enhancing the mineral content in crops, particularly zinc and iron, to address the issue of "hidden hunger" and to attain nutritional security, making it a valuable asset for translational research.
Language	English
Publishing date	2024-04-04
Publishing country	England
Document type	Journal Article
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.16749
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Bonn / Germany

Z 6071: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Chromosome-level Genome Assembly of Euphorbia peplus, a Model System for Plant Latex, Reveals that Relative Lack of Ty3 Transposons Contributed to Its Small Genome Size.

Johnson, Arielle R / Yue, Yuanzheng / Carey, Sarah B / Park, Se Jin / Kruse, Lars H / Bao, Ashley / Pasha, Asher / Harkess, Alex / Provart, Nicholas J / Moghe, Gaurav D / Frank, Margaret H

Genome biology and evolution

2023 Volume 15, Issue 3

Abstract: Euphorbia peplus (petty spurge) is a small, fast-growing plant that is native to Eurasia and has become a naturalized weed in North America and Australia. Euphorbia peplus is not only medicinally valuable, serving as a source for the skin cancer drug ... ...

Abstract	Euphorbia peplus (petty spurge) is a small, fast-growing plant that is native to Eurasia and has become a naturalized weed in North America and Australia. Euphorbia peplus is not only medicinally valuable, serving as a source for the skin cancer drug ingenol mebutate, but also has great potential as a model for latex production owing to its small size, ease of manipulation in the laboratory, and rapid reproductive cycle. To help establish E. peplus as a new model, we generated a 267.2-Mb Hi-C-anchored PacBio HiFi nuclear genome assembly with a BUSCO score of 98.5%, a genome annotation based on RNA-seq data from six organs, and publicly accessible tools including a genome browser and an interactive organ-specific expression atlas. Chromosome number is highly variable across Euphorbia species. Using a comparative analysis of our newly sequenced E. peplus genome with other Euphorbiaceae genomes, we show that variation in Euphorbia chromosome number between E. peplus and Euphorbia lathyris is likely due to fragmentation and rearrangement rather than chromosomal duplication followed by diploidization of the duplicated sequence. Moreover, we found that the E. peplus genome is relatively compact compared with related members of the genus in part due to restricted expansion of the Ty3 transposon family. Finally, we identify a large gene cluster that contains many previously identified enzymes in the putative ingenol mebutate biosynthesis pathway, along with additional gene candidates for this biosynthetic pathway. The genomic resources we have created for E. peplus will help advance research on latex production and ingenol mebutate biosynthesis in the commercially important Euphorbiaceae family.
MeSH term(s)	Latex ; Genome Size ; Euphorbiaceae ; Chromosomes
Chemical Substances	3-ingenyl angelate ; Latex
Language	English
Publishing date	2023-02-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evad018
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Laser Capture Microdissection Transcriptome Reveals Spatiotemporal Tissue Gene Expression Patterns of

Schnabel, Elise / Thomas, Jacklyn / El-Hawaz, Rabia / Gao, Yueyao / Poehlman, William L / Chavan, Suchitra / Pasha, Asher / Esteban, Eddi / Provart, Nicholas / Feltus, F Alex / Frugoli, Julia

Molecular plant-microbe interactions : MPMI

2023 Volume 36, Issue 12, Page(s) 805–820

Abstract: We report a public resource for examining the spatiotemporal RNA expression of 54, ... ...

Abstract	We report a public resource for examining the spatiotemporal RNA expression of 54,893
MeSH term(s)	Root Nodules, Plant/metabolism ; Transcriptome/genetics ; Plant Roots ; Medicago truncatula/metabolism ; Laser Capture Microdissection ; Rhizobium/genetics ; RNA/metabolism ; Symbiosis/genetics ; Gene Expression Regulation, Plant ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plant Root Nodulation/genetics
Chemical Substances	RNA (63231-63-0) ; Plant Proteins
Language	English
Publishing date	2023-12-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	743331-1
ISSN	1943-7706 ; 0894-0282
ISSN (online)	1943-7706
ISSN	0894-0282
DOI	10.1094/MPMI-03-23-0029-R
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 3530: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Multi-omics atlas of combinatorial abiotic stress responses in wheat.

Da Ros, Letitia / Bollina, Venkatesh / Soolanayakanahally, Raju / Pahari, Shankar / Elferjani, Raed / Kulkarni, Manoj / Vaid, Neha / Risseuw, Eddy / Cram, Dustin / Pasha, Asher / Esteban, Eddi / Konkin, David / Provart, Nicholas / Nambara, Eiji / Kagale, Sateesh

The Plant journal : for cell and molecular biology

2023 Volume 116, Issue 4, Page(s) 1118–1135

Abstract: Field-grown crops rarely experience growth conditions in which yield can be maximized. Environmental stresses occur in combination, with advancements in crop tolerance further complicated by its polygenic nature. Strategic targeting of causal genes is ... ...

Abstract	Field-grown crops rarely experience growth conditions in which yield can be maximized. Environmental stresses occur in combination, with advancements in crop tolerance further complicated by its polygenic nature. Strategic targeting of causal genes is required to meet future crop production needs. Here, we employed a systems biology approach in wheat (Triticum aestivum L.) to investigate physio-metabolic adjustments and transcriptome reprogramming involved in acclimations to heat, drought, salinity and all combinations therein. A significant shift in magnitude and complexity of plant response was evident across stress scenarios based on the agronomic losses, increased proline concentrations and 8.7-fold increase in unique differentially expressed transcripts (DETs) observed under the triple stress condition. Transcriptome data from all stress treatments were assembled into an online, open access eFP browser for visualizing gene expression during abiotic stress. Weighted gene co-expression network analysis revealed 152 hub genes of which 32% contained the ethylene-responsive element binding factor-associated amphiphilic repression (EAR) transcriptional repression motif. Cross-referencing against the 31 DETs common to all stress treatments isolated TaWRKY33 as a leading candidate for greater plant tolerance to combinatorial stresses. Integration of our findings with available literature on gene functional characterization allowed us to further suggest flexible gene combinations for future adaptive gene stacking in wheat. Our approach demonstrates the strength of robust multi-omics-based data resources for gene discovery in complex environmental conditions. Accessibility of such datasets will promote cross-validation of candidate genes across studies and aid in accelerating causal gene validation for crop resiliency.
MeSH term(s)	Triticum/physiology ; Multiomics ; Stress, Physiological/genetics ; Transcriptome/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant/genetics ; Plant Proteins/genetics ; Plant Proteins/metabolism
Chemical Substances	Plant Proteins
Language	English
Publishing date	2023-06-28
Publishing country	England
Document type	Journal Article
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.16332
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Bonn / Germany

Z 6071: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour.

Bizouerne, Elise / Buitink, Julia / Vu, Benoît Ly / Vu, Joseph Ly / Esteban, Eddi / Pasha, Asher / Provart, Nicholas / Verdier, Jérôme / Leprince, Olivier

BMC plant biology

2021 Volume 21, Issue 1, Page(s) 124

Abstract: Background: During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. Few studies have addressed the regulatory networks controlling acquisition of these traits at the tissue level ... ...

Abstract	Background: During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. Few studies have addressed the regulatory networks controlling acquisition of these traits at the tissue level particularly in endospermic seeds such as tomato, which matures in a fully hydrated environment and does not undergo maturation drying. Using temporal RNA-seq analyses of the different seed tissues during maturation, gene network and trait-based correlations were used to explore the transcriptome signatures associated with desiccation tolerance, longevity, germination under water stress and dormancy. Results: During maturation, 15,173 differentially expressed genes were detected, forming a gene network representing 21 expression modules, with 3 being specific to seed coat and embryo and 5 to the endosperm. A gene-trait significance measure identified a common gene module between endosperm and embryo associated with desiccation tolerance and conserved with non-endospermic seeds. In addition to genes involved in protection such LEA and HSP and ABA response, the module included antioxidant and repair genes. Dormancy was released concomitantly with the increase in longevity throughout fruit ripening until 14 days after the red fruit stage. This was paralleled by an increase in SlDOG1-2 and PROCERA transcripts. The progressive increase in seed vigour was captured by three gene modules, one in common between embryo and endosperm and two tissue-specific. The common module was enriched with genes associated with mRNA processing in chloroplast and mitochondria (including penta- and tetratricopeptide repeat-containing proteins) and post-transcriptional regulation, as well several flowering genes. The embryo-specific module contained homologues of ABI4 and CHOTTO1 as hub genes associated with seed vigour, whereas the endosperm-specific module revealed a diverse set of processes that were related to genome stability, defence against pathogens and ABA/GA response genes. Conclusion: The spatio-temporal co-expression atlas of tomato seed maturation will serve as a valuable resource for the in-depth understanding of the dynamics of gene expression associated with the acquisition of seed vigour at the tissue level.
MeSH term(s)	Acclimatization/genetics ; Droughts ; Endosperm/genetics ; Endosperm/growth & development ; Gene Expression Regulation, Plant ; Gene Regulatory Networks ; Genetic Association Studies ; Solanum lycopersicum/embryology ; Solanum lycopersicum/genetics ; Solanum lycopersicum/growth & development ; Seeds/genetics ; Seeds/growth & development ; Transcriptome
Language	English
Publishing date	2021-03-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2059868-3
ISSN	1471-2229 ; 1471-2229
ISSN (online)	1471-2229
ISSN	1471-2229
DOI	10.1186/s12870-021-02889-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito