Identification of phloem-associated translatome alterations during leaf development in Prunus domestica L.

Collum, Tamara D.; Lutton, Elizabeth; Raines, Cameron; Dardick, Christopher; Culver, James N.

doi:10.1038/s41438-018-0092-4

Cited by 10 publications

(9 citation statements)

References 62 publications

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“…The number of trimmed reads (length = 60 bp) per library spanned from 16,280,829 to 32,776,054, enough to establish a differential expression analysis 38 . After trimming, high quality reads were aligned on the reference transcriptome of P. persica, a closely related species that has been often used as reference in other RNA-seq studies on Prunus species 39,40 ; on average, 84.23% of reads per sample successfully mapped on the reference transcripts (Table. 1).…”

Section: Resultsmentioning

confidence: 99%

Red versus green leaves: transcriptomic comparison of foliar senescence between two Prunus cerasifera genotypes

Vangelisti

Cavallini

Natali

et al. 2020

Sci Rep

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The final stage of leaf ontogenesis is represented by senescence, a highly regulated process driven by a sequential cellular breakdown involving, as the first step, chloroplast dismantling with consequent reduction of photosynthetic efficiency. Different processes, such as pigment accumulation, could protect the vulnerable photosynthetic apparatus of senescent leaves. Although several studies have produced transcriptomic data on foliar senescence, just few works have attempted to explain differences in red and green leaves throughout ontogenesis. In this work, a transcriptomic approach was used on green and red leaves of Prunus cerasifera to unveil molecular differences from leaf maturity to senescence. Our analysis revealed a higher gene regulation in red leaves compared to green ones, during leaf transition. Most of the observed DEGs were shared and involved in transcription factor activities, senescing processes and cell wall remodelling. Significant differences were detected in cellular functions: genes related to photosystem i and ii were highly down-regulated in the green genotype, whereas transcripts involved in flavonoid biosynthesis, such as UDP glucose-flavonoid-3-Oglucosyltransferase (UFGT) were exclusively up-regulated in red leaves. In addition, cellular functions involved in stress response (glutathione-S-transferase, Pathogen-Related) and sugar metabolism, such as three threalose-6-phosphate synthases, were activated in senescent red leaves. In conclusion, data suggests that P. cerasifera red genotypes can regulate a set of genes and molecular mechanisms that cope with senescence, promoting more advantages during leaf ontogenesis than compared to the green ones.

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Section: Resultsmentioning

confidence: 99%

Red versus green leaves: transcriptomic comparison of foliar senescence between two Prunus cerasifera genotypes

Vangelisti

Cavallini

Natali

et al. 2020

Sci Rep

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“…This RNA-seq set was created using the translatome profiling technique where epitope-tagged ribosomes are immunopurified to enrich for actively translating mRNAs. This technique enriches the mRNA fraction for fully spliced transcripts 29 , 30 .…”

Section: Methodsmentioning

confidence: 99%

Defining the ‘HoneySweet’ insertion event utilizing NextGen sequencing and a de novo genome assembly of plum (Prunus domestica)

et al. 2021

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Abstract‘HoneySweet’ plum (Prunus domestica) is resistant to Plum pox potyvirus, through an RNAi-triggered mechanism. Determining the precise nature of the transgene insertion event has been complicated due to the hexaploid genome of plum. DNA blots previously indicated an unintended hairpin arrangement of the Plum pox potyvirus coat protein gene as well as a multicopy insertion event. To confirm the transgene arrangement of the insertion event, ‘HoneySweet’ DNA was subjected to whole genome sequencing using Illumina short-read technology. Results indicated two different insertion events, one containing seven partial copies flanked by putative plum DNA sequence and a second with the predicted inverted repeat of the coat protein gene driven by a double 35S promoter on each side, flanked by plum DNA. To determine the locations of the two transgene insertions, a phased plum genome assembly was developed from the commercial plum ‘Improved French’. A subset of the scaffolds (2447) that were >10 kb in length and representing, >95% of the genome were annotated and used for alignment against the ‘HoneySweet’ transgene reads. Four of eight matching scaffolds spanned both insertion sites ranging from 157,704 to 654,883 bp apart, however we were unable to identify which scaffold(s) represented the actual location of the insertion sites due to potential sequence differences between the two plum cultivars. Regardless, there was no evidence of any gene(s) being interrupted as a result of the insertions. Furthermore, RNA-seq data verified that the insertions created no new transcriptional units and no dramatic expression changes of neighboring genes.

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“…EDTA-facilitated exudation is the most popular method; it enables phloem sap to be collected from many plants, including those species that do not naturally exude sap [ 5 , 32 , 33 ]. In this method, phloem sap is collected by submerging the ends of severed petioles in an EDTA-containing solution for several hours.…”

Section: Sample Collection Methods From Vascular Tissuesmentioning

confidence: 99%

Unraveling the Roles of Vascular Proteins Using Proteomics

et al. 2021

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Vascular bundles play important roles in transporting nutrients, growth signals, amino acids, and proteins between aerial and underground tissues. In order to understand these sophisticated processes, a comprehensive analysis of the roles of the components located in the vascular tissues is required. A great deal of data has been obtained from proteomic analyses of vascular tissues in plants, which mainly aim to identify the proteins moving through the vascular tissues. Here, different aspects of the phloem and xylem proteins are reviewed, including their collection methods, and their main biological roles in growth, and biotic and abiotic stress responses. The study of vascular proteomics shows great potential to contribute to our understanding of the biological mechanisms related to development and defense in plants.

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Identification of phloem-associated translatome alterations during leaf development in Prunus domestica L.

Cited by 10 publications

References 62 publications

Red versus green leaves: transcriptomic comparison of foliar senescence between two Prunus cerasifera genotypes

Red versus green leaves: transcriptomic comparison of foliar senescence between two Prunus cerasifera genotypes

Defining the ‘HoneySweet’ insertion event utilizing NextGen sequencing and a de novo genome assembly of plum (Prunus domestica)

Unraveling the Roles of Vascular Proteins Using Proteomics

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