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Series GSE128409 Query DataSets for GSE128409
Status Public on Mar 17, 2019
Title Deciphering the biological processes underlying tomato biomass production and composition.
Organisms Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii
Experiment type Expression profiling by high throughput sequencing
Summary After tomato fruits harvesting huge amounts of biomass residues, including plant and immature fruit, remaining in the field can be utilized to produce bioenergy. Little is known about the molecular aspects underlying tomato plant biomass production and hydrolysis. To identify genes involved in the regulation of plant biomass accumulation and composition, two Solanum pennellii introgression lines (ILs) with contrasting phenotypes for plant architecture and biomass characteristics, were analyzed. A multiple approach aimed to characterize such near-isogenic lines was carried out for studying gene expression dynamics, microscopy cell traits and qualitative and quantitative cell wall chemical compounds variation. Transcriptomic analysis showed that the enhanced biomass production observed in IL2-6 line is due to a more effective coordination of chloroplast and mitochondria energy fluxes (photosynthesis, cell division, cell wall and hormone metabolism activation). In parallel, microscopy analysis revealed a higher number of cells and chloroplasts in leaf epidermis in the high biomass line whilst chemical measurements on the two lines pointed out striking differences in the cell wall composition and organization. Taken together, our findings shed light on the mechanisms underlying the tomato biomass production and open new routes for improving the tomato lignocellulosic processability.
Overall design Transcriptome profiles of two tomato introgression lines, IL2-6 and IL3-2 (in triplicate), and the control M82 (one replicate) were generated by RNA sequencing.
Please note that the 'M82 Rep 2' (through the variant calling) was used as control to confirm that IL2-6 and IL3-2 were, at genotype level, as expected. After checked this, the IL2-6 and IL3-2 samples were used for differentially expression analysis that is the central part of the current study.
Contributor(s) D’Esposito D, Cappetta E, Andolfo G, Ferriello F, Borgonuovo C, Caruso G, De Natale A, Frusciante L, Ercolano MR
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Submission date Mar 16, 2019
Last update date Mar 18, 2019
Contact name Daniela D'Esposito
Organization name University of Naples Federico II
Department Department of Agriculture
Street address Via Università 100
City Portici
ZIP/Postal code 80055
Country Italy
Platforms (2)
GPL26312 Illumina HiSeq 1500 (Solanum lycopersicum x Solanum pennellii)
GPL26313 Illumina HiSeq 1500 (Solanum lycopersicum)
Samples (7)
GSM3673796 IL2-6 Rep1
GSM3673797 IL2-6 Rep2
GSM3673798 IL2-6 Rep3
BioProject PRJNA527463
SRA SRP188597

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE128409_RAW.tar 1.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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