PRJEB33874 - Phellem vs. Xylem

Summary
Resource Type
Analysis
Name
PRJEB33874 - Phellem vs. Xylem
Description

"Cork cambium (or phellogen) is a secondary meristem, responsible for the formation of phelloderm and phellem/cork, which together compose the periderm. In Quercus suber, the phellogen is active throughout the entire life of the tree, producing a continuous and renewable out-bark of cork. To identify specific candidate genes associated with cork cambium activity and phellem differentiation, we performed a comparative transcriptomic study of Q. suber secondary growth tissues (xylem and phellem), using RNA-seq. The present work provides for the first time a detailed description of all the transcripts identified in phellem tissues. A total of 6013 differentially expressed genes (DEGs) were identified, with 2875 of the transcripts being specifically enriched during the cork formation process versus secondary xylem formation. Furthermore, cork samples originating from the original phellogen (“virgin” cork) and from a traumatic phellogen (“amadia” cork) were also compared. Our results point out to a shortlist of potentially relevant candidate genes regulating phellogen activity and phellem differentiation, including novel genes involved in the suberization process, as well as genes associated to ethylene and jasmonate signalling, and to meristem function. The future functional characterization of some of the identified candidate genes will help to elucidate the molecular mechanisms underlying cork cambium activity and phellem differentiation."

FASTQ files were obtained from the NCBI database using the SRAtoolkit-2.9.4. Mapping to the reference genome of Q.suber (NCBI Sequence Read Archive SRP111728 (2017)) was performed using HISAT2-2.1.0 and gene expression in TPM (transcripts per million) was calculated using the counts obtained from featureCounts included in SubRead-v1.6.3.

Program, Pipeline, Workflow or Method Name
PRJEB33874 - Phellem vs. Xylem
Program Version
HISAT2-2.1.0, SRAtoolkit-2.9.4, SubRead-v1.6.3
Date Performed
Friday, May 15, 2020 - 14:15
Data Source
BioSamples
NameTissueTreatmentDescription
ERR3473078PhellemNot setThis biomaterial: ERR3473078, was created for the analysis: PRJEB33874 - Phellem vs. Xylem
ERR3473079PhellemNot setThis biomaterial: ERR3473079, was created for the analysis: PRJEB33874 - Phellem vs. Xylem
ERR3473080PhellemNot setThis biomaterial: ERR3473080, was created for the analysis: PRJEB33874 - Phellem vs. Xylem
ERR3473081PhellemNot setThis biomaterial: ERR3473081, was created for the analysis: PRJEB33874 - Phellem vs. Xylem
ERR3473082PhellemNot setThis biomaterial: ERR3473082, was created for the analysis: PRJEB33874 - Phellem vs. Xylem
ERR3473083PhellemNot setThis biomaterial: ERR3473083, was created for the analysis: PRJEB33874 - Phellem vs. Xylem
ERR3473084XylemNot setThis biomaterial: ERR3473084, was created for the analysis: PRJEB33874 - Phellem vs. Xylem
ERR3473085XylemNot setThis biomaterial: ERR3473085, was created for the analysis: PRJEB33874 - Phellem vs. Xylem
ERR3473086XylemNot setThis biomaterial: ERR3473086, was created for the analysis: PRJEB33874 - Phellem vs. Xylem
ERR3473078PhellemNot setThis biomaterial: ERR3473078, was created for the analysis: PRJEB33874 - Phellem vs. Xylem

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