Genome Sequencing

• The banyan (Ficus benghalensis) and peepal (Ficus religiosa) whole genomes were recently sequenced by scientists at the Indian Institute of Science Education and Research (IISER) Bhopal using leaf tissue samples.
• The research assisted in the identification of 17 genes for the banyan and 19 genes for the peepal with multiple signals of adaptive evolution (MSA), which are essential for the long-term survival of these two Ficus species.

What is Whole genome sequencing?

• The nucleotide bases adenine (A), thymine (T), cytosine (C), and guanine (G) make up the genetic code, or genome, that is unique to each and every living thing (G).
• Knowing the order of the bases in an organism allows one to identify the distinctive Deoxyribonucleic Acid (DNA) fingerprint or pattern.
• Sequencing is the process of establishing the order of bases.
• An organism's genome's base order can be determined in one step via a laboratory approach called whole genome sequencing.

Methodology:

• The first step in DNA shearing is to cut the DNA, which is made up of millions of bases (As, Cs, Ts, and Gs), into manageable bits that can be read by a sequencing machine.
• DNA bar coding: To identify which fragment of sheared DNA belongs to particular bacteria, researchers add tiny pieces of DNA tags, or bar codes.
• This is comparable to how a grocery store's bar code identifies a product.
• DNA sequencing: A DNA sequencer is used to read the bar-coded DNA from several different microorganisms.
• Each bacterial sequence's A, C, T, and G bases, or building blocks, are identified by the sequencer.
• To keep track of which bases belong to which bacteria, the sequencer uses the bar code.
• Data analysis: To compare sequences from various bacteria and spot discrepancies, scientists employ computer analysis techniques.
• How similar the bacteria are to one another and how likely it is that they are associated with the same outbreak can be determined by the amount of differences.

Advantages:

• Gives a base-by-base, high-resolution image of the genome
• Captures both large and small variations that targeted techniques could overlook
• Identifies probable causal variations for additional research on the processes governing gene expression and regulation.
• Delivers substantial amounts of data quickly to aid in the construction of new genomes
• Meaning: Understanding the mutations that cause cancer to progress and tracking disease outbreaks have all been made possible thanks to genomic knowledge.
• It is useful for sequencing animals, plants, or disease-related bacteria that are significant in agriculture.

Genome: What is it?

• The term "genome" refers to all of an organism's genetic material. The human genome is largely the same in every person, but a very small portion of their DNA does differ from person to person.
• Each organism's DNA, which makes up the fundamental elements of life, has its genetic code.
• James Watson and Francis Crick's 1953 discovery that DNA is organised as a "double helix" sparked an investigation into how genes control life, its characteristics, and the development of diseases.
• Every piece of knowledge required to create and sustain that organism is contained in each genome.
• More than 3 billion DNA base pairs make up a human's whole genome copy.

Genes

• Gene is a sequence of DNA or RNA that codes for a molecule that has a function.
• They are made of DNA and is a subdivision of DNA. They are packed in Chromosomes.
• Genes contain the bio-information that defines any individual.
• Physical attributes like height, skin or hair colour, more subtle features and even behavioural traits can be attributed to information encoded in the genetic material.

A genome is the DNA or sequence of genes in a cell.

• Human genome is made up of 23 chromosome pairs with a total of about 3 billion DNA base pairs.
• Most of the DNA is in the nucleus in the form of chromosomes and the rest is in Mitochondria (cell's powerhouse). Genes make amino acids and proteins.
• Sequencing a genome means deciphering the exact order of base pairs in an individual.
• Exome is a portion of the gene responsible for making Proteins.
• There are 24 distinct human chromosomes:

1. 22 autosomal chromosomes, plus the sex-determining X and Y chromosomes.
2. Chromosomes 1-22 are numbered roughly in order of decreasing size.
3. Somatic cells usually have one copy of chromosomes 1-22 from each parent, plus an X chromosome from the mother and either an X or Y chromosome from the father, for a total of 46.

• There are estimated 20,000-25,000 human protein-coding genes.

Genome sequencing

1. It determines the unique genetic traits, susceptibility (and resilience) to disease.
2. Now the youth will be told if they carry gene that makes them less responsive to certain types of medicines. Example, A certain gene make some people less responsive to Clopidogrel, a key drug to prevent strokes and heart attacks.
3. Genome sequencing is figuring out the order of DNA nucleotides, or bases, in a genome—the order of Adenine, Cytosine, Guanines, and Thymine that make up an organism's DNA.

Importance of Genome Sequencing

• Sequencing the genome is an important step towards understanding how genes works. Genes account for <25% of DNA in the genome. Studying entire genome sequence will help scientists study parts of genome outside the genes.
• It will represent a valuable shortcut, helping scientists find genes much more easily and quickly.
• A genome sequence does contain some clues about where genes are, even though scientists are just learning to interpret these clues.
• Genome sequencing of wild varieties of plants can be used to identify disease resistance and drought tolerance genes in various plants and develop new varieties of crop plants in lesser time.
• Genome sequencing of cop plants can be helpful in deciphering and understanding the host-pathogen realationship in crops.

Why Genome sequencing?

• Ever since the human genome was first sequenced in 2003, it opened a fresh perspective on the link between disease and the unique genetic make-up of each individual.
• Nearly 10,000 diseases — including cystic fibrosis, thalassemia — are known to be the result of a single gene malfunctioning.
• While genes may render some insensitive to certain drugs, genome sequencing has shown that cancer too can be understood from the viewpoint of genetics, rather than being seen as a disease of certain organs.

Human Genome Project

• The Human Genome Project was started in 1990, a 13 year long international research effort to determine the sequence of the human genome and identify the genes that it contains.
• The Project was coordinated by the National Institutes of Health and the U.S. Department of Energy.
• Not only did the completion of this project usher in a new era in medicine i.e. personalized medicine, but it also led to significant advances in the types of technology used to sequence DNA.

IndiGen initiative

• It is a programme for the Mapping of entire genome. CSIR will undertake genome sequencing of a sample of nearly 1000 Indian rural youth to determine unique genetic traits, susceptibility (and resilience) to disease. It is 1st of a kind initiative.
• It is managed by CSIR-Institute of Genomics and Integrative Biology (IGIB) and CSIR – Center for Cellular and Molecular Biology (CCMB).
• The aim is 2 fold:

1. If it is possible to rapidly and reliably scan several genomes.
2. Advice people on health risks in their gene i.e. disease detection.

Advtantages

1. It is important for Precision medicine and Personalised medicine.
2. It will sequence a gene which hides the information of susceptibility to attain a disease.
3. Cancer, Heart strokes etc.
4. Understanding gene functioning.

Disadvantages

1. Not everyone who signs up will be guaranteed a scan.
2. It can breach ethical standards fixed in the developement of Pluripotent stem cells.
3. It can also cause personalized biological attacks by anyone who has your gene sequence.
4. Breach of Right to Privacy.
5. The project is an adjunct to a much larger government-led programme Genome India Project, still in the works, to sequence at least 10,000 Indian genomes.
6. Under IndiGen, CSIR drafted 1000 youth from college through campsand educating attendees on genomics and the role of genes in disease.Those 1000 youth will get a Card and access to an app.

Department of Biotechnology under MoS&T has cleared the Genome India Project

• It is a gene-mapping project involving 20 leading institutions including IISc and IITs.
• The first stage of the project will look at samples of 10,000 persons from all over the country to form a grid that will enable the development of a reference genome.