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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Automating Citrus Budwood Processing for Downstream Pathogen Detection Through Instrument Engineering

Automating Citrus Budwood Processing for Downstream Pathogen Detection Through Instrument Engineering

Published on: April 21, 2023

An RNA-Seq-based reference transcriptome for Citrus.

Javier Terol¹, Francisco Tadeo¹, Daniel Ventimilla¹

¹Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain.

Plant Biotechnology Journal

|August 12, 2015

Summary

This summary is machine-generated.

This study provides a comprehensive citrus transcriptome landscape, revealing new genes and alternative splicing events. It identifies genetic markers linked to fruit quality and productivity across 12 species.

Keywords:

RNA-seq citrus transcriptome

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Area of Science:

Plant Genomics
Transcriptomics
Citrus Research

Background:

Previous RNA-Seq studies in citrus primarily focused on fruit quality and major species.
Limited research has explored vegetative and reproductive tissues across diverse Citrus species.

Purpose of the Study:

To characterize the transcriptome of vegetative and reproductive tissues from 12 Citrus species.
To improve functional annotations and identify genetic markers for agronomic traits.
To gain a comprehensive view of the citrus transcriptome landscape.

Main Methods:

RNA-Seq analysis of 28 samples from 12 Citrus species (including root, phloem, leaf, and flower).
Transcript discovery pipeline and analysis of alternative splicing.
Differential gene expression analysis and variant discovery (SNPs, indels).

Main Results:

Identification of 3326 new genes and 73,797 total transcripts, with alternative splicing in 19,739 genes.
Gene expression patterns strongly correlate with organ-specific physiological functions.
Discovery of variants in genes related to fruit quality and productivity, with detailed analysis of key pathways.

Conclusions:

This work significantly expands the understanding of the citrus transcriptome across diverse species and tissues.
Identified genetic variations offer potential for marker-assisted breeding in citrus.
The findings provide a valuable resource for future citrus genomics and breeding programs.