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Updated: May 25, 2026

Isolation and Transcriptome Analysis of Plant Cell Types
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Isolation and Transcriptome Analysis of Plant Cell Types

Published on: April 7, 2023

Strategies for transcriptome analysis in nonmodel plants.

Judson A Ward1, Lalit Ponnala, Courtney A Weber

  • 1Department of Horticulture, Cornell University, New York State Agricultural Experiment Station, Geneva, New York 14456, USA.

American Journal of Botany
|February 4, 2012
PubMed
Summary
This summary is machine-generated.

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Analyzing plant transcriptomes without a reference genome is challenging. This study shows that aligning sequencing data to a close relative

Area of Science:

  • Plant genomics
  • Bioinformatics
  • Transcriptome analysis

Background:

  • Most plants lack genomic resources for transcriptome analysis.
  • Short-read transcriptome data analysis is routine in model species but challenging in nonmodel species.
  • Using a close relative's genome as a reference is a viable approach for nonmodel species.

Purpose of the Study:

  • To compare two approaches for transcriptome analysis in nonmodel plants.
  • To evaluate the effectiveness of using a close relative's genome as a reference.
  • To assess de novo assembly for transcriptome analysis in nonmodel species.

Main Methods:

  • Illumina sequencing reads from Rubus idaeus (red raspberry) were aligned to the Fragaria vesca genome.
  • Publicly available bioinformatics tools (Bowtie/TopHat, Cufflinks, Trinity) were utilized.

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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

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Last Updated: May 25, 2026

Isolation and Transcriptome Analysis of Plant Cell Types
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Published on: April 7, 2023

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08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

  • BLAST searches were performed to identify sequence matches.

    • Main Results:

    • Alignment to F. vesca identified 16,956 putatively expressed genes.
    • De novo assembly with Trinity identified over 36,000 plant transcripts and over 500 Phytophthora transcripts.
    • Gene expression estimates showed a strong correlation (Pearson's r = 0.730) between the two methods.

    Conclusions:

    • Alignment to a close relative's genome and de novo assembly are powerful methods for nonmodel plant transcriptome analysis.
    • Alignment provides a framework for differential expression testing.
    • De novo assembly robustly identifies unique and foreign sequences.