Number of species sequenced by years

Arrival  of  Next-­‐Genera1on  Sequencing  

Sequence genomes of million species

•  Over 3,000 species have sequenced last 15 years

•  Earth Biogenome Project (https://www.earthbiogenome.org) plans to sequence 1.5 million species next 10 years and with projected cost $4.7 billion.

In-depth genomics research in model species

•  ~100 species with referenced quality ready for in-depth genomics research

•  Functional genomics

–  To describe genes’ functions

–  To understand the relationship between genotype and phenotype

–  Functional genomics make use of the vast data of DNA, RNA, metabolites, and proteins

Outline

•  Resources, approaches, technologies, and tools used in functional genomics studies

–  Induced mutation

– Gene silencing

– Site-specific mutation

– QTL/association mapping and gene clone

– Gene expression profiling

– Metabolite profiling

What are gene and allele?

•  Gene is a section of DNA that codes protein; Gene is the basic physical and functional unit of heredity

•  “Every person has two copies of each gene, one inherited from each parent. Most genes are the same in all people, but a small number of genes (less than 1 percent of the total) are slightly different between people. Alleles are forms of the same gene with small differences in their sequence of DNA bases. These small differences contribute to each person’s unique physical features.”

Gene: from DNA to protein

•  Transcription -  https://dnalc.cshl.edu/

resources/3d/13-transcription-advanced.html

•  RNA splicing -  https://dnalc.cshl.edu/

resources/3d/rna-splicing.html

•  Translation -  https://dnalc.cshl.edu/

resources/3d/15-translation-basic.html

Enzymes catalyze reactions

•  Proteins encoded by genes could be structure proteins and could be enzymes

•  How enzymes work in a cell -  https://pdb101.rcsb.org/learn/videos/how-enzymes-

work

Biological pathway

•  Cell contain thousands of molecules, mostly proteins and small chemical compounds. Groups of molecules work together to perform tasks, e.g., provide energy, respond to the environment, etc.

•  A biological pathway is an ordered series of molecular events that leads to creation of a new molecule product or change in a cell

Photosynthesis pathway

•  Biological pathway database –  https://reactome.org –  https://plantreactome.gramene.org/index.php?lang=en

Restriction enzymes

•  Restriction enzymes or restriction nuclease is a protein that can cleave DNA or RNA into fragments

Restriction enzymes recognize specific sequence

•  Restriction enzymes recognize a specific sequence and cut the DNA within, near or remote from the specific site

•  For example, EcoR1 recognizes a specific sequence of 6 bp

G  A  A  T  T  C  C  T  T  A  A  G  

Restriction enzymes discovery and applications

•  1978, Noble prize for Physiology or Medicine was awarded to Werner Arber, Daniel Nathans, and Hamilton Smith for their work in the discovery and characterization of restriction enzymes

•  Hundreds of restriction enzymes have been found and allow DNA to be manipulated, leading to the development of recombinant DNA technology that has many applications

–  https://dnalc.cshl.edu/resources/3d/20-mechanism-of-recombination.html

–  https://dnalc.cshl.edu/resources/dnalc-live/watch/20200511-dnalc-short-restriction-enzymes-17187