De novo Transcriptome Sequencing and Development of Abscission Zone-Specific Microarray as a New Molecular Tool for Analysis of Tomato Organ Abscission

Frontiers in Plant Science
Srivignesh SundaresanShimon Meir

Abstract

Abscission of flower pedicels and leaf petioles of tomato (Solanum lycopersicum) can be induced by flower removal or leaf deblading, respectively, which leads to auxin depletion, resulting in increased sensitivity of the abscission zone (AZ) to ethylene. However, the molecular mechanisms that drive the acquisition of abscission competence and its modulation by auxin gradients are not yet known. We used RNA-Sequencing (RNA-Seq) to obtain a comprehensive transcriptome of tomato flower AZ (FAZ) and leaf AZ (LAZ) during abscission. RNA-Seq was performed on a pool of total RNA extracted from tomato FAZ and LAZ, at different abscission stages, followed by de novo assembly. The assembled clusters contained transcripts that are already known in the Solanaceae (SOL) genomics and NCBI databases, and over 8823 identified novel tomato transcripts of varying sizes. An AZ-specific microarray, encompassing the novel transcripts identified in this study and all known transcripts from the SOL genomics and NCBI databases, was constructed to study the abscission process. Multiple probes for longer genes and key AZ-specific genes, including antisense probes for all transcripts, make this array a unique tool for studying abscission with a comprehen...Continue Reading

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Citations

Nov 8, 2016·Frontiers in Plant Science·William D GronerSarah J Liljegren
Feb 15, 2020·International Journal of Molecular Sciences·Zhi-Lang QiuXiao-Peng Wen
Apr 16, 2019·Frontiers in Plant Science·Andreas PerrakisPanagiotis Kalaitzis
Mar 29, 2020·Science·S ReichardtA Schaller

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Datasets Mentioned

BETA
AF000999
AF001002
GSE45356
GSE64221
PRJNA192557
GSE45355

Methods Mentioned

BETA
RNA-Seq
Illumina sequencing
chip
transgenic
PCR
reverse transcription-PCR

Software Mentioned

SeqQC
Fastq
Velvet
Oases assembler
Basic Local Alignment Search Tool ( BLAST )
BLASTN
BLAST
Illumina
Bowtie
Mx3005P system

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