Structural Genomics

Functional Genomics
Comparative Genomics

Group 2:
Francis Kyomuhendo 2024/HD17/2403U
Gilbert Gumisiriza 2019/HD17/23142U
 Synopsis
Introduction
The Central Dogma
Structural Genomics
Functional Genomics
Comparative Genomics
Applications and Case Studies
Review of Trends and Future
Directions
5/6/2025 Summary and Conclusions
Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 2
Genomics studies whole genomes
Introduction
Structural Genomics:  determine 3D structure of proteins encoded by
genomes
Functional Genomics:  assign function to genes using high-throughput
assays
Comparative Genomics:  compare genomes across species to infer evolution,

Genomics: bedrock imperatives

Understand the structure of Genomes
Understand the Biology of Genomes
Understand the Biology of Variation (Genotype  Phenotype)

Source: Heba T Ebeed, S.Antony Ceasar, (2024) .

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 3

 The Central Dogma

Information flow cell: DNADNA  RNA  Protein (solid lines)

Information is stored in DNA and copied during replication genomics & epigenomics

Certain DNA sequences are transcribed into RNA species transcriptomics

Some RNA sequences are translated into proteins proteomics

Some
5/6/2025 proteins mediate in biochemical functions
Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 metabolomics 4
 Structural Genomics & Physical Mapping of
Genomes
Structural genomics Physical mapping

• Classical ways of genome • Genome sequencing,

analysis,

• Sequence assembly,
• Large fragment,

• Annotation
• Genomic libraries

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 5

 Introduction
Genome: Organism's complete set of DNA

Genomics: Study of the genome, including interactions of those genes with each other
and with the organism’s environment

Genomic library: Collection of DNA fragments that represents entire genome of an organism

Structural genomics aims to determine 3-D structure of proteins, and then investigate their function

Physical mapping of genomes determines physical location & distance between DNA sequences on a
chromosome, expressed in base pairs

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 6

 Introduction
Genome sequencing provides the order of A, T, C, and G that make up DNA

Genome assembly combines short DNA sequence fragments (reads) to reconstruct original
sequence

Genome annotation finds and designates locations of genes, biological features on nucleotide seqs

Source: microbenotes.com
5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 7
 Genome mapping
Genome mapping: Identification of the locations of genes, mutations, or traits on a chromosome

Genome maps: Genetic linkage maps, physical maps, cytologic maps

Linkage maps: Low-resolution, determine relative positions of genetic markers on chromosome

Physical maps: High-res., identify locations of recognizable landmarks on genomic DNA

Cytologic maps: Describe visible banding patterns on stained x-somes that serve as markers

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 8

 Sequencing
Detailed genome map is obtained through genome
sequencing = complete DNA sequence

Prepared DNA library loaded onto a sequencing platform

Depending on desired sequencing technologies such as;

Short read sequencing (illumina)

Long-read sequencing (PacBio, ONT, Sanger)

Source: microbenotes.com

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 9

 Sequencing
Long Read sequencing (PacBio, Nanopore)

RNA-Seq

Source: https://www.veteringroup.us/articles/figures/IJVSR-8-208-g002.gif

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 10

 Sanger sequencing
A widely used DNA sequencing method

Uses fluorescently labeled di-deoxy nucleotides to terminate DNA chains of varying lengths

Resulting fragments separated by electrophoresis & seq. determined by reading gel banding pattern

Base calling is used to assign bases for each peak in a chromatogram

Source: https://www.veteringroup.us

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 11

 Sanger sequencing
Whole Genome Sequencing (WGS): Shotgun sequencing and hierarchical sequencing

Shotgun sequencing: DNA clones are randomly sequenced from both ends;
Generates large number of DNA fragments, which
are assembled by computer program to create a
complete genome sequence

Hierarchical sequencing: Mapping x-somes using physical mapping

techniques; Longer fragments of genomic DNA are cloned
into a bacterial vector with high capacity; Physical
mapping helps determine locations & order of
cloned fragments on chromosome

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 12

 Data Processing
Sequencing reads must be cleaned &
assessed for quality using QC tools
like;
FastQC,
MultiQC

Trimming and filtering tools such as;

Trimmomatic,
BBTools,
FASTP

Read error correction such as;

SPAdes error correction for Illumina

Source: gigabyte31-cover.jpg

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 13

 Genome Sequence Assembly
Genome assembly: Reconstructing complete genome sequence from a large number of short
DNA fragments called reads

Short fragments need to be joined together while removing any overlapping regions

Firstly, base calling which derives base calls and assigns quality scores to these base calls to
determine the sequence of nucleotides at every position

Quality scores assigned to each base call, which represents confidence or accuracy of base call

Then the individual sequence reads are assembled into contiguous sequences, known as contigs

Involves identifying overlaps between different fragments, determining relative order, & then
deriving a consensus sequence for each contig

Using programs for processing raw sequencing data & assembling contigs, including Phred, Phrap,
TIGR Assembler, and ARACHNE.
5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 14
 Genome Assembly
Involves reconstruction of genome sequence from short or
long sequencing reads

De novo assembly

Used in absence of any available reference genome

Overlapping reads are merged into contigs which are further

linked into scaffolds using tools like;
SPAdes for short reads,

Canu, Flye for long reads and,

MEGAHIT, MetaSPAdes for metagenomic assembly

Source: BFnmeth1935_Figb_HTML.jpg

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 15

 Source:Reference-genome-assembly-strategies-a-Generating-a-haploid-representation-reference.png
Reference Based Assembly
Reads are aligned to an already
existing reference genome

Best for variants detection &

species with known genomes

It involves tools like:

BWA for Illumina short

reads,

Mini-maps for long reads

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 16

 Post Assembly Processing
Improves assembled genome by correcting errors, ordering sequences and assessing quality before
functional analysis and interpretation through;

Quality assessment to ensure genome assembly is accurate and complete using tools like:
QUAST(checks scaffold statistics),
BUSCO(assess genome completeness)

Gap filling and error correction that closes missing regions & fixes sequencing errors
using tools like:
Pilon(Illumina),
Medaka(Nanopore)

Validation of the key findings using:

PCR,
qPCR,
Sanger sequencing
5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 17
 Genome Annotation
Identifies genes, proteins, regulatory elements in the genome by using bioinformatics tools to
compare assembled genome sequence against existing databases. It involves;

Structural annotations for finding coding genes, non coding RNAs, promoter etc. using;
Prokka,
GeneMark,
AUGUSTUS

Functional annotations for assigning functions to identified genes based on known databases like;
InterProScan(protein domains),
KEGG (metabolic pathways)

Resulting annotations are deposited into public databases like;

GenBank

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 18

 Genome Annotation

Source: whole-genome-assembly.jpg

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 19

 Data Analysis And Interpretation
Involves studying gene functions, identifying mutations, comparing genomes and linking genetic data
to biological processes. It involves;
Comparative genomics to identify conserved genes, unique genes responsible for plant adaptation,
herbicide resistance and genetic variations using tools like;
GATK,
FreeBayes,
PAML

Analyzing gene expression can also be possible if RNA-Seq data is available.

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 20

 Functional Genomics: Overview
Goal: Assign gene function by analysis of transcripts, proteins, metabolites, and phenotypes

Approaches: High-throughput assays (transcriptome, proteome, metabolome profiling)

Genetic perturbations (mutants, RNAi/RNAi screens, CRISPRa, CRISPRi)
Interaction mapping (protein–protein, gene networks)

Transcriptomics: DNA microarrays and RNA-Seq. to quantify differential genome-wide gene

expression

Reverse Genetics: Systematic gene knock-downs and/or knock-outs to phenotype gene functions

Functional assays: Reporter constructs, epigenomic profiling, and comparative expression analyses

Source: EMBL-EBI
5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 21
 Computational Assignment of Gene
Function
Genome sequencing can identify genes but does not reveal their functions

Computationally generated, tentative identification is based on homology with genes of known function.

The best way to identify gene function is to look at their proteins (i.e. BLASTp search)

Sometimes only part of a protein is a homologous match

There are many “genes” that are classified as orphans, but in reality, they do not exist

Experimental Assignment of Gene Function

Determine gene function by deleting gene & observing phenotype when function is knocked out
RNA interference (RNAi, also called RNA silencing) uses small regulatory RNAs to silence gene expression

It does not create a permanent chromosomal change

PCR can be used to produce a gene knockout that results in a permament DNA change

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 22

DNA Microarrays (DNA Chips) –
Technology
Concept: Glass slides (“chips”) spotted with thousands of gene-specific DNA probes
Each spot corresponds to one gene (cDNA or oligo array)

Hybridisation: Labelled cDNA (from RNA) from test vs. reference samples co-hybridise
fluorescent readouts quantify relative transcript abundance

1-Colour Arrays: Use separate slides with a reference

2-Colour Arrays: Often use two dyes (e.g. Cy3/Cy5) to compare conditions on one
array

Source: EMBL-EBI

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 23

DNA Microarrays – Applications & Data
Analysis
Transcriptome Profiling: Enables simultaneous measurement of expression for 1000s of
genes
Pioneered functional profiling of developmental & stress responses in plants

Plant Microarrays: Arabidopsis whole-genome arrays (e.g. Agilent 44K) and custom slides are
widely used to study growth stages, pathogen response, etc.

Data Analysis: Diff, expression (fold-change, t-tests), clustering (co-expression modules),

and network inference. Gene set enrichment identifies pathways.

Limitations: Requires prior sequence knowledge; dynamic range and detection limits
Complemented by RNA-Seq (NGS) for transcript discovery and splicing
Valuable for large-scale screens

Sources: EMBL-EBI; Affymetrix, Life Science.

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 24

 Functional Genomics: Mutants and Genetic
Screens
Forward Genetics: Create Mutant libraries by:

 Random mutagenesis (EMS, radiation)

 Insertional mutagenesis (T-DNA, transposons)

Screen for phenotypes of interest (e.g. development, stress tolerance) by:

 Sequencing,

 Mapping causal mutations

Reverse Genetics: Systematic knockout lines (e.g. Arabidopsis T-DNA insertion collection covering genome)
 Enables analysis of gene function by disrupting known loci

CRISPR-Cas9

 Allows targeted gene knockouts/edits genome-wide

Example: Arabidopsis SALK T-DNA lines provide mutants for >80% of annotated genes;
phenotypic databases (TAIR) catalog mutant effects.

Mutants elucidate essential pathways in metabolism, development, immunity.

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 25
 Functional Genomics:
RNA Interference (RNAi): RNAi
Introduction dsRNA triggers and VIGS
sequence-specific degradation of matching
mRNA.
Plants use RNAi to regulate development and defend against viruses

Gene Silencing: Artificial hairpin constructs or transgenes produce dsRNA for target
genes.
Endogenous Dicer/RISC machinery degrades the target transcript,
effectively “knocking down” gene expression.

Virus-Induced Gene Silencing: VIGS utilises engineered plant viruses carrying a fragment of host gene.
Infection spreads fragment, triggering RNAi against host gene.
Widely used in N. benthamiana for rapid gene
function testing.

Applications: Functional screens for gene families (e.g. transcription factors),

Reverse genetics, where stable knockout is difficult.
5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 26
VIGS is high-throughput and transient, enabling analysis in weeks.
 Proteomics and Other “Omics”
Proteomics: Mass spectrometry to quantify proteins, post-translational modifications, and interactions
(e.g. LC-MS/MS, 2D gels).
Complements transcriptomics by revealing translational/post-translational
regulation.

Epigenomics: Genome-wide profiling of chromatin state (ChIP-seq for histone marks, DNA methylation
maps) to link epigenetic regulation with gene expression patterns.

Metabolomics: Global profiling of small-molecule metabolites (GC-MS, LC-MS, NMR).

Captures output of cellular biochemistry and pathway activity.

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 27

 Metabolomics in Functional Genomics
Role: Plants synthesize 1000s of unique metabolites. Metabolomics connects genotype to biochemical
phenotype, uncovering pathway changes due to gene perturbation

Correlation with Transcripts:

Integrated metabolite/transcript networks (“co-expression” or “cooccurrence” analysis)
identify candidate genes in biosynthetic pathways.

Example: Correlation of unknown enzymes with known metabolites to reveal pathway enzymes

Tools: Untargeted metabolomics surveys vs. targeted assays of specific pathways.

Statistical methods (PCA, PLS-DA) identify discriminating metabolites btn genotypes or
treatments.

Systems Biology:
Combining metabolite QTLs & transcriptomics aids in quantitative trait gene mapping
(mQTL) 5/6/2025
and Kyomuhendo Francisengineering.
metabolic & Gumisiriza Gilbert, MBS7228 28
 Omics Integration & Pathway
Elucidation
Integrated Analysis: Simultaneous profiling (transcriptome + proteome + metabolome) enables reconstruction
of regulatory and metabolic networks.

Example (Arabidopsis): Transcriptomics + metabolomics identified flavonoid biosynthesis genes by co-expressed

transcripts and accumulated metabolites.
Joint omics elucidated nitrogen-assimilation pathways under stress.

Network Modelling: Graph-based and ML methods predict gene function by linking multi-omics data.
GWAS can incorporate metabolite levels to pinpoint genes affecting metabolism.

Sources: EMBL-EBI; Pytozome.org; NEXTGen Cassava

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 29

 Comparative Genomics: Overview
Goal: Identify shared and divergent features among genomes of different species

Concepts: Orthologous and paralogous genes, synteny, and genomic collinearity

Applications: Transfer annotation from model to crop genomes

Infer evolutionary events (duplications, rearrangements)
Define pangenomes and genetic diversity (

Key Methods: Whole-genome alignments,

Phylogenetic tree construction,
Synteny block detection (conserved gene order)
comparative mapping across plant genomes (e.g. Arabidopsis vs. crops)

Source: EMBL-EBI

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 30

Functionally associated proteins leave evolutionary traces of their relation in
genomes
Genomics

Functional associations
Metabolic pathways
Transcription regulation
Signaling pathways
Protein complexes
Cellular processes

Comparative genomics
Comparing genomes
Gene Fusions
Gene Neighborhood conservation
Gene Presence/Absence
Comparing genomics data
Horizontal comparative genomics
Vertical comparative genomics

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 31

 Applications: Gene Function Discovery in
Plants
Regulatory Networks: Identify transcription factors and signalling components controlling development
(e.g. flowering time, root formation) using global expression data.

Stress Responses: Genome-wide profiling of drought, cold, & pathogens reveals defense genes.
RNAi or CRISPR knockout confirms function (e.g. Arabidopsis R gene
networks).

Pathway Engineering: Functional genomics pinpoints enzymes for metabolic engineering (e.g. vit. C
biosynthesis). Overexpression or silencing validated by metabolomics.

Reference: Saito et al. – transcript/metabolite cooccurrence as tool for gene discovery in A. thaliana.

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 32

 Applications: Crop Improvement &

Marker-Assisted Breeding:
Biotechnology
Comparative genomics identifies conserved trait loci (yield, disease resistance)
SNP markers from model studies accelerate breeding in related crops.

Transgenic Crops: Gene from models (pest resistance, stress tolerance) engineered into crops.
Structural genomics aids enzyme optimization (herbicide target
modification)

Phenome Databases: High-throughput phenotyping & with genomics (genomics-enabled breeding)

Integration of omics data guides selection of germplasm for desirable
traits.

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 33

 Applications: Systems Biology of
Plants
Gene Regulatory Networks: Inference of genome-scale networks (Bayesian, coexpression, motif analysis)
models how genes coordinate (circadian clock, hormonal signaling).

Synthetic Biology: Design of synthetic regulatory circuits in plants (synthetic promoters controlled
by transcription factors identified via functional genomics).

Comparative Models: Use plant model (Arabidopsis, N. benthamiana) to study basic biology (e.g. virus-
host interactions) and translate to crops (e.g. brassica).

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 34

 Case Study: Arabidopsis Functional
Genomics
Genome Resource: Arabidopsis thaliana genome sequenced (2000) with ~27,000 genes; extensive mutant
libraries and microarrays enabled system-wide studies.

Co-expression Networks: Large microarray/RNA-seq atlases allowed clustering of genes by expression,

predicting functions of unknown genes. Eg. coexpression networks
identified new flavonoid enzymes.

Mutant Screens: Forward genetic screens (e.g. EMS-induced mutants) uncovered key regulators
(e.g. phytochrome signaling) and were mapped via genome sequencing.

Metabolite Profiling: Mutant collections (e.g. 50 mutants in metabolism) were profiled metabolomically to build
a metabolic network atlas.

Such data provides a “fingerprint” linking genes to biochemical phenotypes.

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 35

 Case Study: Nicotiana benthamiana &
VIGS
Model System: N. benthamiana is amenable to Agrobacterium infiltration and VIGS.

Rapid assays (weeks vs. months for transgenics) allow functional testing of plant
genes.

VIGS Example: Silencing of NbPDS (phytoene desaturase) causes photobleaching – used as a visual
control for VIGS efficiency. Many studies use TRV-VIGS in N. benthamiana to
identify disease resistance genes or metabolic enzymes.

Transient Expression: Agroinfiltration also used for protein localization, protein–protein interactions (BiFC, co-IP)
and overexpression, complementing stable transformation.

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 36

 Case Study: Metabolomics Illuminating
Pathways

Untargeted Profiling: Example – drought vs. control in Arabidopsis; LC-MS reveals accumulation of
osmo-protectants (proline, sugars). Transcriptomics of same samples pinpoints
biosynthetic genes.

Coexpression with Metabolites: Saito et al. emphasize that correlating transcript and metabolite data
in Arabidopsis is powerful for discovering pathway genes. Flavonoid and
glucosinolate pathways were elucidated this way.

Natural Variation: Integration of metabolite QTL mapping in Arabidopsis accessions (panels)

identifies genomic regions controlling metabolite levels; candidate
genes are validated by mutants.

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 37

 Case Study: Comparative Genomics in Plants
Model-to-Crop Translation:

Arabidopsis knowledge informed tomato and brassica research (homologs for disease resistance, oil biosynthesis).
Comparative maps help clone crop genes based on colinearity.

Synteny Examples:

Despite >100 MYA divergence, Arabidopsis and tomato genomes share syntenic enabling prediction of orthologous
genes. Similarity with soybean (100 MYA) is also observed.

Pan-Genome (Arabidopsis):

Recent study of 69 A. thaliana accessions reveals 60% of ~33,000 gene families are core, while 40% are
dispensable. This genomic diversity explains adaptation and is a resource for finding novel genes in wild
accessions.

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 38

 Future Directions: Structural Genomics
AI & Deep Learning:
Structure prediction (AlphaFold, RoseTTAFold) now provides high-confidence models for most
proteins, vastly extending structural coverage beyond solved structures.
This will accelerate fold classification and function inference.

Cryo-EM Advances:
Single-particle cryo-EM yields structures of large complexes and membrane proteins at
atomic resolution.
Integrative structural methods (cryo-EM, crystallography, NMR) tackle systems previously
intractable.

Drug and Agrochemical Targets:

Structural genomics will enable rational design of inhibitors or activators for key plant
enzymes (e.g. herbicide targets, metabolic enzymes).

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 39

Future Directions: Functional Genomics
Single-Cell and Spatial Omics:
Technologies (single-cell RNA-seq, spatial transcriptomics) will map gene expression and
epigenomes at cellular resolution in plant tissues (e.g. root hair vs. cortex cells).

CRISPR Screens:
Genome-wide CRISPR libraries for knockouts and CRISPRi in plants will allow pooled genetic
screens, linking genes to phenotypes at scale.

Machine Learning:
AI will integrate multi-omics data (genomics, transcriptomics, phenomics) to predict gene
functions and genotype–phenotype relationships (phenotypic prediction models for breeding).

Synthetic Genomics:
De novo synthesis of plant chromosomes or gene circuits for metabolic engineering (custom
pathways for bio-factories).
5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 40
Future Directions: Comparative Genomics
Pangenome Sequencing:
Large-scale sequencing of crop accessions (like the 69 Arabidopsis accessions) and wild
relatives will capture structural variation and dispensable genes.
Breeding will leverage this natural diversity.

Evolutionary Insight:
Comparative epigenomics across species; study of polyploidy (e.g. Brassica species, wheat)
to understand gene retention and expression dominance.

Genome Editing:
Use knowledge from comparative analyses to engineer novel traits (e.g. introduce stress-
resistance alleles from one species to another via genome editing).

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 41

Summary & Conclusions

Structural, Functional, Comparative Genomics together provide a comprehensive

framework to understand plant biology at system-level.

Techniques like DNA microarrays, RNAi/VIGS, and metabolomics have revolutionized

how we dissect plant pathways, especially in A. thaliana and N. benthamiana.

Integration of multi-omics and comparative approaches accelerates discovery of gene

function and trait improvement.

Ongoing advances (AI, single-cell, pan-genomics) promise even deeper insights into
plant genomes and their applications in biotechnology.

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 42

 References
1. Schmid, M., Davison, T. S., Henz, S. R., Pape, U. J., Demar, M., Vingron, M., Schölkopf, B., Weigel, D., & Lohmann, J. U. (2005). A gene expression
map of Arabidopsis thaliana development. Nature genetics, 37(5), 501–506. https://doi.org/10.1038/ng1543

2. O'Malley, R. C., Barragan, C. C., & Ecker, J. R. (2015). A user's guide to the Arabidopsis T-DNA insertion mutant collections. Methods in molecular
biology (Clifton, N.J.), 1284, 323–342. https://doi.org/10.1007/978-1-4939-2444-8_16

3. Todd, A. T., Liu, E., Polvi, S. L., Pammett, R. T., & Page, J. E. (2010). A functional genomics screen identifies diverse transcription factors that regulate
alkaloid biosynthesis in Nicotiana benthamiana. The Plant journal : for cell and molecular biology, 62(4), 589–600. https://doi.org/10.1111/j.1365-
313X.2010.04186.x

4. Liu, S., Li, K., Dai, X. et al. A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid
bread wheat. Nat Genet 57, 1008–1020 (2025). https://doi.org/10.1038/s41588-025-02137-x

5. Chaudhary, D., Jeena, A. S., Rohit, Gaur, S., Raj, R., Mishra, S., Kajal, Gupta, O. P., & Meena, M. R. (2024). Advances in RNA Interference for Plant
Functional Genomics: Unveiling Traits, Mechanisms, and Future Directions. Applied biochemistry and biotechnology, 196(9), 5681–5710.
https://doi.org/10.1007/s12010-023-04850-x

6. Barreda, L., Boutet, S., De Vos, D. et al. Specialized metabolome and transcriptome atlas of developing Arabidopsis thaliana seed under warm
temperatures. Sci Data 12, 306 (2025). https://doi.org/10.1038/s41597-025-04563-2

7. Watanabe, M., & Tohge, T. (2023). Species-specific 'specialized' genomic region provides the new insights into the functional genomics
characterizing metabolic polymorphisms in plants. Current opinion in plant biology, 75, 102427. https://doi.org/10.1016/j.pbi.2023.102427

8. Eckardt N. A. (2001). Everything in its place. Conservation of gene order among distantly related plant species. The Plant cell, 13(4), 723–725.
https://doi.org/10.1105/tpc.13.4.723

5/6/2025 Kyomuhendo Francis & Gumisiriza Gilbert, MBS7228 43