Plant Bioinformatic Methods Specialization Course Syllabus

Overview: This specialization provides a comprehensive introduction to bioinformatics methods tailored for plant science research. Over approximately 14 weeks, learners will gain hands-on experience analyzing real plant datasets using industry-standard tools and best practices in reproducibility. Each module combines theoretical concepts with practical tutorials in Jupyter notebooks, command-line environments, and Galaxy platform workflows. Total time commitment is approximately 80–100 hours, depending on prior experience.

Module 1: Plant Genomic Data Analysis

Estimated time: 16 hours

• Next-generation sequencing (NGS) data formats and quality control
• Genome assembly strategies for plant genomes
• Evaluation of assembly quality using QUAST
• Gene prediction and functional annotation pipelines
• Hands-on: Using Galaxy and command-line tools for genome analysis

Module 2: Transcriptomics Applications

Estimated time: 16 hours

• RNA-Seq experimental design and library preparation
• Read quality assessment with FastQC and trimming tools
• Alignment to reference genomes using STAR and HISAT2
• Gene expression quantification with featureCounts
• Differential expression analysis using DESeq2 in R

Module 3: Evolutionary Analysis

Estimated time: 8 hours

• Multiple sequence alignment with MAFFT and MUSCLE
• Phylogenetic tree construction using RAxML and MrBayes
• Molecular dating and divergence time estimation
• Case study: Plastid genome evolution in angiosperms

Module 4: Applied Plant Bioinformatics

Estimated time: 16 hours

• Variant calling pipeline: from alignment to SNP identification
• Genome-wide association studies (GWAS) workflow and interpretation
• Metabolic pathway reconstruction using KEGG and PlantCyc
• Functional enrichment analysis of gene sets

Module 5: Reproducible Research Practices

Estimated time: 12 hours

• Version control with Git and GitHub for bioinformatics projects
• Jupyter notebook management and sharing
• Workflow automation using Snakemake or Nextflow
• Documenting analyses for transparency and reproducibility

Module 6: Final Project

Estimated time: 20 hours

• Assemble and annotate a draft genome from raw NGS data
• Perform differential expression analysis on a provided RNA-Seq dataset
• Construct a phylogenetic tree from curated plant gene sequences and interpret evolutionary relationships

Prerequisites

• Familiarity with basic molecular biology concepts (DNA, RNA, genes)
• Introductory knowledge of Linux command-line interface
• Basic understanding of genetics and plant biology

What You'll Be Able to Do After

• Analyze plant genomic data using command-line and web-based tools
• Perform RNA-Seq analysis and identify differentially expressed genes
• Construct and interpret phylogenetic trees from sequence data
• Conduct SNP calling and GWAS analyses for trait mapping
• Apply reproducible research principles to bioinformatics workflows