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Comparative transcriptome analysis of the different tissues between the cultivated and wild tomato

https://doi.org/10.1371/journal.pone.0172411

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1 of the 32 references listed on this page is in the Retraction Watch database as retracted (export 2026-10-21): 10.1371/journal.pone.0149352 (notice 2024-05-22).

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s11103-015-0367-1openalex-snapshot

A transcriptomic approach to identify regulatory genes involved in fruit set of wild-type and parthenocarpic tomato genotypes

inferredcites →https://doi.org/10.1016/j.bbrc.2015.07.029openalex-snapshot

Effects of low temperature on mRNA and small RNA transcriptomes in Solanum lycopersicoides leaf revealed by RNA-Seq

inferredcites →https://doi.org/10.1016/j.cell.2006.12.006openalex-snapshot

The Molecular Genetics of Crop Domestication

inferredcites →https://doi.org/10.1016/j.copbio.2012.09.004openalex-snapshot

Transcriptome analysis using next-generation sequencing

inferredcites →https://doi.org/10.1016/j.foodchem.2010.08.024openalex-snapshot

Changes in the contents of carotenoids, phenolic compounds and vitamin C during technical processing and lyophilisation of red and yellow tomatoes

inferredcites →https://doi.org/10.1016/j.foodchem.2016.01.142openalex-snapshot

Alleviation of chilling injury in tomato fruit by exogenous application of oxalic acid

inferredcites →https://doi.org/10.1016/j.pbi.2009.01.004openalex-snapshot

DNA changes tell us about rice domestication

inferredcites →https://doi.org/10.1016/j.plaphy.2016.02.020openalex-snapshot

Genome-wide identification, characterization and expression analysis of calmodulin-like (CML) proteins in tomato (Solanum lycopersicum)

inferredcites →https://doi.org/10.1016/s0044-328x(78)80198-6openalex-snapshot

Salt Tolerance in the Wild Relatives of the Cultivated Tomato: Responses of Callus Tissue of Lycopersicon esculentum, L. peruvianum and Solanum pennellii to High Salinity

inferredcites →https://doi.org/10.1038/nature11119openalex-snapshot

The tomato genome sequence provides insights into fleshy fruit evolution

inferredcites →https://doi.org/10.1038/nmeth.1226openalex-snapshot

Mapping and quantifying mammalian transcriptomes by RNA-Seq

inferredcites →https://doi.org/10.1038/nprot.2012.016openalex-snapshot

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

inferredcites →https://doi.org/10.1038/nrg2484openalex-snapshot

RNA-Seq: a revolutionary tool for transcriptomics

inferredcites →https://doi.org/10.1038/srep21597openalex-snapshot

Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data

inferredcites →https://doi.org/10.1073/pnas.1309606110openalex-snapshot

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

inferredcites →https://doi.org/10.1080/07388550091144212openalex-snapshot

Lycopene in Tomatoes: Chemical and Physical Properties Affected by Food Processing

inferredcites →https://doi.org/10.1093/bioinformatics/bti430openalex-snapshot

Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary

inferredcites →https://doi.org/10.1093/bioinformatics/btp120openalex-snapshot

TopHat: discovering splice junctions with RNA-Seq

inferredcites →https://doi.org/10.1093/jxb/erm257openalex-snapshot

Genetic and molecular regulation of fruit and plant domestication traits in tomato and pepper

inferredcites →https://doi.org/10.1093/nar/gkl167openalex-snapshot

KOBAS server: a web-based platform for automated annotation and pathway identification

inferredcites →https://doi.org/10.1093/nar/gkm391openalex-snapshot

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine

inferredcites →https://doi.org/10.1093/nar/gkq1019openalex-snapshot

The Sequence Read Archive

inferredcites →https://doi.org/10.1093/nar/gkq310openalex-snapshot

agriGO: a GO analysis toolkit for the agricultural community

inferredcites →https://doi.org/10.1093/nar/gkr483openalex-snapshot

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

inferredcites →https://doi.org/10.1093/nar/gkv1070openalex-snapshot

KEGG as a reference resource for gene and protein annotation

inferredcites →https://doi.org/10.1155/2015/970724openalex-snapshot

Effect of Temperature, Time, and Material Thickness on the Dehydration Process of Tomato

inferredcites →https://doi.org/10.1177/153537020222701002openalex-snapshot

Chemistry, Distribution, and Metabolism of Tomato Carotenoids and Their Impact on Human Health

inferredcites →https://doi.org/10.1371/journal.pgen.0020052openalex-snapshot

The Abundance of Short Proteins in the Mammalian Proteome

inferredcites →https://doi.org/10.1371/journal.pone.0050785openalex-snapshot

Differential Modulation of Photosynthesis, Signaling, and Transcriptional Regulation between Tolerant and Sensitive Tomato Genotypes under Cold Stress

inferredcites →https://doi.org/10.1371/journal.pone.0076029openalex-snapshot

Induction of Senescence and Identification of Differentially Expressed Genes in Tomato in Response to Monoterpene

inferredcites →https://doi.org/10.1371/journal.pone.0149352openalex-snapshot

Identification of Differentially Expressed Genes Related to Dehydration Resistance in a Highly Drought-Tolerant Pear, Pyrus betulaefolia, as through RNA-Seq

inferredcites →https://doi.org/10.4137/cin.s14022openalex-snapshot

Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4517869openalex-extracted

Response of Different Tomato Accessions to Biotic and Abiotic Stresses

inferred← citeshttps://doi.org/10.1007/978-981-19-5367-5_5openalex-snapshot

Biotechnological Implications in Tomato for Drought Stress Tolerance

inferred← citeshttps://doi.org/10.1007/978-981-96-3890-1_16openalex-snapshot

Future Horizons: Emerging “Omics” Technologies and Challenges in Tomato

inferred← citeshttps://doi.org/10.1016/b978-0-323-85665-2.00011-xopenalex-snapshot

Wild relatives of plants as sources for the development of abiotic stress tolerance in plants

inferred← citeshttps://doi.org/10.1016/b978-0-323-89905-5.00022-7openalex-snapshot

Omics in vegetable crops under the family Solanaceae

inferred← citeshttps://doi.org/10.1016/j.plgene.2020.100255openalex-snapshot

Next generation sequencing based transcriptome analysis for nematode resistance in different species of tomato

inferred← citeshttps://doi.org/10.1016/j.plgene.2021.100322openalex-snapshot

Genome-wide identification and characterization of genes involved in the acylsugar pathway in tomato

inferred← citeshttps://doi.org/10.1038/s41438-018-0096-0openalex-snapshot

Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato-Phytophthora infestans interaction

inferred← citeshttps://doi.org/10.1038/s41598-018-34202-3openalex-snapshot

New insights into tomato microRNAs

inferred← citeshttps://doi.org/10.1080/10408398.2020.1832954openalex-snapshot

Unexplored nutritive potential of tomato to combat global malnutrition

inferred← citeshttps://doi.org/10.1093/bbb/zbac209openalex-snapshot

Genes related to cell wall metabolisms are targeted by miRNAs in immature tomato fruits under drought stress

inferred← citeshttps://doi.org/10.1101/2020.10.05.326470openalex-snapshot

Transcriptomic Analyses Throughout Chili Pepper Fruit Development Reveal Novel Insights into Domestication Process

inferred← citeshttps://doi.org/10.1111/ppa.14002openalex-snapshot

Transcriptomic and physiological analyses reveal plant resistance against Ralstonia solanacearum involves salicylic acid‐mediated defences in tomato leaves

inferred← citeshttps://doi.org/10.20546/ijcmas.2020.903.235openalex-snapshot

A Decade of Tomato Transcriptomics: Status and Perspectives

inferred← citeshttps://doi.org/10.30848/pjb2019-1(2)openalex-snapshot

ASIAN CULTIVATED RICE DOMESTICATION SUPPRESSES THE EXPRESSION OF ABIOTIC STRESS- AND REACTIVE OXYGEN SPECIES SCAVENGING-RELATED GENES IN ROOTS

inferred← citeshttps://doi.org/10.3389/fpls.2017.01981openalex-snapshot

Transcriptomic Response of Resistant (PI613981–Malus sieversii) and Susceptible (“Royal Gala”) Genotypes of Apple to Blue Mold (Penicillium expansum) Infection

inferred← citeshttps://doi.org/10.3389/fpls.2018.01997openalex-snapshot

The Occurrence of Seedlessness in Higher Plants; Insights on Roles and Mechanisms of Parthenocarpy

inferred← citeshttps://doi.org/10.3389/fpls.2019.00689openalex-snapshot

Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato

inferred← citeshttps://doi.org/10.3390/biology8040090openalex-snapshot

Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato

inferred← citeshttps://doi.org/10.3390/cimb46080535openalex-snapshot

Transcriptomic Approach for Investigation of Solanum spp. Resistance upon Early-Stage Broomrape Parasitism

inferred← citeshttps://doi.org/10.3390/ijms252011012openalex-snapshot

Comparative Transcriptomic Analysis Reveals Domestication and Improvement Patterns of Broomcorn Millet (Panicum miliaceum L.)

inferred← citeshttps://doi.org/10.3390/plants10030585openalex-snapshot

Transcriptome Analyses Throughout Chili Pepper Fruit Development Reveal Novel Insights into the Domestication Process

inferred← citeshttps://doi.org/10.3390/plants9010063openalex-snapshot

Comparative Analysis between Wild and Cultivated Cucumbers Reveals Transcriptional Changes during Domestication Process

inferred← citeshttps://doi.org/10.48130/vr-2023-0016openalex-snapshot

Genome-wide identification of the plant U-box (PUB) gene family and their global expression analysis in tomato (Solanum lycopersicum)

inferred← citeshttps://doi.org/10.7287/peerj.11681v0.1/reviews/1openalex-snapshot

Peer Review #1 of "Comparative analysis of fatty acid metabolism based on transcriptome sequencing of wild and cultivated Ophiocordyceps sinensis (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.11681v0.1/reviews/2openalex-snapshot

Peer Review #2 of "Comparative analysis of fatty acid metabolism based on transcriptome sequencing of wild and cultivated Ophiocordyceps sinensis (v0.1)"

inferred← citeshttps://doi.org/10.7717/peerj.11681openalex-snapshot

Comparative analysis of fatty acid metabolism based on transcriptome sequencing of wild and cultivated Ophiocordyceps sinensis

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