scholarly journals Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation

2021 ◽  
Author(s):  
Carrie M. Tribble ◽  
Jesús Martínez‐Gómez ◽  
Fernando Alzate‐Guarín ◽  
Carl J. Rothfels ◽  
Chelsea D. Specht
Keyword(s):  
Molecular Mechanisms ◽  
Comparative Transcriptomics ◽  
Underground Storage ◽  
Storage Organ ◽  
Organ Formation

scholarly journals Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation

2019 ◽  
Author(s):  
Carrie M. Tribble ◽  
Jesús Martínez-Gómez ◽  
Fernando Alzate-Guarin ◽  
Carl J. Rothfels ◽  
Chelsea D. Specht
Keyword(s):  
Molecular Mechanisms ◽  
Vascular Plant ◽  
Gene Tree ◽  
Comparative Transcriptomics ◽  
Differentially Expressed ◽  
Underground Storage ◽  
Cell Wall Modification ◽  
Evolutionary Forces ◽  
Tuberous Roots ◽  
Root Tuber

AbstractMany species from across the vascular plant tree-of-life have modified standard plant tissues into tubers, bulbs, corms, and other underground storage organs (USOs), unique innovations which allow these plants to retreat underground. Our ability to understand the developmental and evolutionary forces that shape these morphologies is limited by a lack of studies on certain USOs and plant clades. Bomarea multiflora (Alstroemeriaceae) is a monocot with tuberous roots, filling a key gap in our understanding of USO development. We take a comparative transcriptomics approach to characterizing the molecular mechanisms of tuberous root formation in B. multiflora and compare these mechanisms to those identified in other USOs across diverse plant lineages. We sequenced transcriptomes from the growing tip of four tissue types (aerial shoot, rhizome, fibrous root, and root tuber) of three individuals of B. multiflora. We identify differentially expressed isoforms between tuberous and non-tuberous roots and test the expression of a priori candidate genes implicated in underground storage in other taxa. We identify 271 genes that are differentially expressed in root tubers versus non-tuberous roots, including genes implicated in cell wall modification, defense response, and starch biosynthesis. We also identify a phosphatidylethanolamine-binding protein (PEBP), which has been implicated in tuberization signalling in other taxa and, through gene-tree analysis, place this copy in a phylogenytic context. These findings suggest that some similar molecular processes underlie the formation of underground storage structures across flowering plants despite the long evolutionary distances among taxa and non-homologous morphologies (e.g., bulbs versus tubers).

scholarly journals Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes

Genetics ◽  
2019 ◽  
Vol 213 (4) ◽  
pp. 1545-1563 ◽  
Author(s):  
Ramona Lütkenhaus ◽  
Stefanie Traeger ◽  
Jan Breuer ◽  
Laia Carreté ◽  
Alan Kuo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruiting Body ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Comparative Transcriptomics ◽  
Fruiting Bodies ◽  
Body Development ◽  
Fruiting Body Development ◽  
Genes Encoding

Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora. With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes.

Control of flowering and storage organ formation in potato by FLOWERING LOCUS T

Nature ◽  
2011 ◽  
Vol 478 (7367) ◽  
pp. 119-122 ◽  
Author(s):  
Cristina Navarro ◽  
José A. Abelenda ◽  
Eduard Cruz-Oró ◽  
Carlos A. Cuéllar ◽  
Shojiro Tamaki ◽  
...  
Keyword(s):  
Storage Organ ◽  
Flowering Locus T ◽  
Organ Formation ◽  
Flowering Locus ◽  
And Storage

scholarly journals Foraging potential of underground storage organ plants in the southern Cape, South Africa

2016 ◽  
Vol 101 ◽  
pp. 79-89 ◽  
Author(s):  
Elzanne Singels ◽  
Alastair J. Potts ◽  
Richard M. Cowling ◽  
Curtis W. Marean ◽  
Jan De Vynck ◽  
...  
Keyword(s):  
South Africa ◽  
Underground Storage ◽  
Storage Organ

scholarly journals Potato StCONSTANS-like1 Suppresses Storage Organ Formation by Directly Activating the FT-like StSP5G Repressor

2016 ◽  
Vol 26 (7) ◽  
pp. 872-881 ◽  
Author(s):  
José A. Abelenda ◽  
Eduard Cruz-Oró ◽  
José Manuel Franco-Zorrilla ◽  
Salomé Prat
Keyword(s):  
Storage Organ ◽  
Organ Formation

scholarly journals Tissue-Specific Metabolic Reprogramming during Wound-Induced Organ Formation in Tomato Hypocotyl Explants

2021 ◽  
Vol 22 (18) ◽  
pp. 10112
Author(s):  
Eduardo Larriba ◽  
Ana Belén Sánchez-García ◽  
Cristina Martínez-Andújar ◽  
Alfonso Albacete ◽  
José Manuel Pérez-Pérez
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Metabolic Reprogramming ◽  
Apical Region ◽  
Crop Species ◽  
Metabolic Switch ◽  
Tissue Specific ◽  
Hypocotyl Explants ◽  
Organ Formation ◽  
Organ Regeneration

Plants have remarkable regenerative capacity, which allows them to survive tissue damage after exposure to biotic and abiotic stresses. Some of the key transcription factors and hormone crosstalk mechanisms involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. However, little is known about the role of metabolism in wound-induced organ formation. Here, we performed detailed transcriptome analysis and used a targeted metabolomics approach to study de novo organ formation in tomato hypocotyl explants and found tissue-specific metabolic differences and divergent developmental pathways. Our results indicate that successful regeneration in the apical region of the hypocotyl depends on a specific metabolic switch involving the upregulation of photorespiratory pathway components and the differential regulation of photosynthesis-related gene expression and gluconeogenesis pathway activation. These findings provide a useful resource for further investigation of the molecular mechanisms involved in wound-induced organ formation in crop species such as tomato.

scholarly journals Transcriptome Analysis of Gene Expression during Chinese Water Chestnut Storage Organ Formation

PLoS ONE ◽  
2016 ◽  
Vol 11 (10) ◽  
pp. e0164223 ◽  
Author(s):  
Libao Cheng ◽  
Shuyan Li ◽  
Sainan Chen ◽  
Yan Wang ◽  
Meizhen Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Storage Organ ◽  
Organ Formation ◽  
Chinese Water ◽  
Water Chestnut

scholarly journals Botanical nepotism — Keeping storage organ formation in the family

2007 ◽  
Vol 73 (2) ◽  
pp. 277
Author(s):  
G.D. Ascough ◽  
J.E. Erwin ◽  
J. Van Staden
Keyword(s):  
Storage Organ ◽  
Organ Formation ◽  
The Family

scholarly journals Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation

2018 ◽  
Author(s):  
Bob G. Blasdel ◽  
Pieter-Jan Ceyssens ◽  
Anne Chevallereau ◽  
Laurent Debarbieux ◽  
Rob Lavigne
Keyword(s):  
Molecular Mechanisms ◽  
Defense Mechanism ◽  
Resistance Mechanism ◽  
Comparative Transcriptomics ◽  
Adaptive Resistance ◽  
Pseudomonas Quinolone Signal ◽  
Host Defense Mechanism ◽  
Infected Cells ◽  
Adaptive Stress Response ◽  
Restriction Modification

AbstractIntrinsic and acquired defenses against bacteriophages, including Restriction/Modification, CRISPR/Cas, and Toxin/Anti-toxin systems have been intensely studied, with profound scientific impacts. However, adaptive defenses against phage infection analogous to adaptive resistance to antimicrobials have yet to be described. To identify such mechanisms, we applied an RNAseq-based, comparative transcriptomics approach in differentPseudomonas aeruginosastrains after independent infection by a set of divergent virulent bacteriophages. A common host-mediated adaptive stress response to phages was identified that includes the Pseudomonas Quinolone Signal, through which infected cells inform their neighbors of infection, and what may be a resistance mechanism that functions by reducing infection vigor. With host transcriptional machinery left intact, we also observe phage-mediated differential expression caused by phage-specific stresses and molecular mechanisms. These responses suggest the presence of a conserved Bacterial Adaptive Phage Response mechanism as a novel type of host defense mechanism, and which may explain transient forms of phage persistence.

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