Comparative Plant Transcriptomics of Heinz 1706 Tomato

By. Lauren Capoziello

Department of Chemical and Biomolecular Engineering

Figure 1: Pipeline for the experimental design and execution of identifying differentially expressed genes in SAM (Meristem) vs. Leaf tisssue samples in .Experimental design for the identification of differentially expressed genes in leaf vs. SAM tissues in Tomatoes (Solanum_lycopersicum) using Tom-Heinz1706 as a reference genome. Steps (1)-(4) describe the scope of background knowledge required to perform this analysis. Step (5) describes the first step of analysis where quality control was performed on the SAM and Leaf files to determine sample efficacy. Step (6) describes the first analysis step where the samples were indexed and aligned according to the reference genome. Step (7) describes the next step in the analysis which was to quantify the alignment data. Lastly, the quant files for each sample were combined into a quantification normalization data set using DESeq2 software.

Research Questions:

1) What are the changes in gene expression that exist between differentiated young leaves and undifferentiated stem cells from shoot meristems in different species?

2) What changes in tomato gene expression do we uncover when sequencing at different read depths?

3) What changes in tomato gene expression do we uncover when sequencing at different read depth and align reads to different reference genomes?

Approaches to Question:

1) As a learning community, the class analyzes leaf and meristem samples from Arabidopsis thaliana and compared them to leaf and meristem samples from Solanum lycopersicum (aligned to the Tomato M82 wildtype genome)

2) As a learning community, the class was split into three groups where each group analyzed the data for both Arabidopsis thaliana and Solanum lycopersicum at three different read depths (20X, 50X, and 70X)

3) As individuals, each researcher was assigned a different read depth and a different reference genome to create a portfolio. The data on the following pages describes the process of analyzing the sequence reads of leaf and meristem tissue samples at a 70X coverage by aligning the data to the reference genome Heinz 1706 Tomato.

Samples:

1) Tomato Heinz1706 Leaf Tissue Samples

2) Tomato Heinz1706 Meristem (SAM) Tissue Samples

References:

Pipeline image created using https://biorender.com/

Acknowledgements:

Spring 2022 BIT CPT Course Instructors:

Dr. Carly Sjogren, B.A. Biology, Ph.D. Genetics, Genomics & Bioinformatics

Dr. Emily Delorean, B.S. Crop Science, M.S. Plant Pathology, Ph.D. Genetics

Team Cherry Tomatoes:

Lillian Lower

Lauren Capoziello

Afiq Hafiy Mohammad Taufiq

Edmaritz Hernandez Pagan

Software

NC State HPC and Bioinformatics department