The concept of genomics was first proposed in 1986 by American geneticist Thomas H. Roderick. Genomics is an interdisciplinary biological discipline for collective characterization, quantitative research and comparative study of different genomes for all genes of an organism. Genomics mainly studies the structure, function, evolution, positioning and editing of genomes, and their impact on organisms.
The purpose of genomics is to collectively characterize and quantify all the genes of an organism and study their interrelationships and effects on the organism. Genomics also includes genome sequencing and analysis through the use of high-throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Genomics also studies phenomena within the genome such as epistasis (the effect of one gene on another), pleiotropy (one gene affects multiple traits), heterosis (hybrid vigor), and loci and alleles within the genome Interactions between genes, etc.
Advances in genomics have sparked a revolution in discovery-based research and systems biology, advancing the understanding of the most complex biological systems, such as the brain. Genomics, together with transcriptomics, proteomics, and metabolomics, form the omics foundation of systems biology.
The main tools and methods of genomics include: bioinformatics, genetic analysis, gene expression measurement and gene function identification.
Genomics emerged in the 1980s and took off in the 1990s with the initiation of several species genome projects.
In 1977, the phage Φ-X174 single-stranded (5,386 bp) was completely sequenced, becoming the first genome to be determined;
In 1981, the first complete eukaryotic organelle human mitochondria (16568 bp, about 16.6 kb [kb]) genome sequence sequencing was completed;
In 1992, the first eukaryotic cell Saccharomyces cerevisiae III chromosome (315 kb) was sequenced;
In 1995, the genome sequencing of the first living species Haemophilus influenzae (1.8Mb) was completed;
In 1996, the complete genome sequence (12.1 Mb) of the first eukaryotic Saccharomyces cerevisiae was sequenced;
In 2001, the Human Genome Project published the draft human genome, opening a new page for genomics research. By October 2012, the study had sequenced the genomes of 1,092 individuals.
Functional genomics
Functional genomics is a field of molecular biology that attempts to describe the functions and interactions of genes (and proteins) using the vast amounts of data generated by genomic projects such as genome sequencing projects. Functional genomics focuses on dynamic changes in gene transcription, translation, and protein-protein interactions, as opposed to static information such as DNA sequence or structure provided by the genome. Functional genomics attempts to answer questions about DNA function at the gene, RNA transcript, and protein product levels. A key feature of functional genomics studies is their genome-wide approach to these questions, often involving high-throughput approaches rather than traditional “case-by-gene” approaches.
A major branch of genomics still focuses on sequencing the genomes of various organisms, but genome-wide knowledge opens up the possibility for functional genomics to focus on patterns of gene expression under various conditions. The most important tools involved are microarray technology and bioinformatics.
Structural Genomics
Structural genomics attempts to describe the three-dimensional structure of each protein encoded by a given genome. This genome-based approach allows high-throughput protein structure identification through a combination of experimental and modeling approaches. The main difference between structural genomics and traditional structure prediction is that structural genomics attempts to determine the structure of each protein encoded by the genome, rather than focusing on one specific protein. With the publication of whole genome sequences, protein structure predictions can be accomplished more quickly through a combination of experimentation and modeling, especially since the large number of sequenced genomes and the publication of previously resolved protein structures have allowed scientists to make predictions based on the structures of existing homologues Model protein structures.
Structural genomics involves a number of structural identification methods, including experimental methods using genomic sequences, modeling methods based on the sequence or structural homology of known homologous proteins, or based on proteins without any known structural homology. Modeling methods of chemical and physical properties. In contrast to traditional structural biology, structural genomics determines protein structure often (but not always) prior to understanding its function. This presents new challenges for structural bioinformatics, such as determining the function of a protein from its three-dimensional structure.
Epigenomics
Epigenomics is the study of the epigenome, the genetic material of all epigenetic modifications in an organism. Epigenetic modifications are reversible modifications to cellular DNA or histones that affect gene expression without altering the DNA sequence. The two most characterized epigenetic modifications are DNA methylation and histone modifications. Epigenetic modifications play important roles in gene expression and regulation and are involved in many cellular processes such as differentiation/development and tumorigenesis. Until recently, it has not been possible to study epigenetics on a genome-wide scale through high-throughput analysis of the genome.
Metagenomics
Metagenomics is the study of the metagenome of genetic material extracted directly from environmental samples. Metagenomics is also known as environmental genomics, ecological genomics or community genomics. Whereas traditional microbiology and microbial genome sequencing relied on cultivated clone cultures, earlier environmental gene sequencing cloned specific genes (usually 16S rRNA genes) to obtain diversity in natural populations. These works show that the vast majority of microbial diversity is missed by colony culture-based methods. Metagenomics uses “shotgun” sequencing or massively parallel pyrosequencing to obtain genetic information on all microbial members in a sample population without bias. Because metagenomics can reveal previously hidden microbial diversity, it provides a powerful tool for observing the microbial world, the results of which have the potential to revolutionize the entire world of life.
Applications of Genomics
Genomics has applications in many fields including medicine, biotechnology, anthropology and other social sciences.
Genomic medicine
Next-generation genomic technologies enable clinicians and biomedical researchers to dramatically increase the amount of genomic data collected from large research populations. When combined with new informatics methods to integrate diverse data with genomic data, researchers can better understand the genetic basis of drug response and disease. For example, the All of Us research program aims to collect genome sequence data from 1 million participants and become an important part of a precision medicine research platform.
Synthetic Biology and Bioengineering
The growth of genomic knowledge has made the application of synthetic biology increasingly complex. In 2010, researchers at the Craig Venter Institute announced the successful partial synthesis of a bacterium – a synthetic mycoplasma derived from the genome of Mycoplasma genitalium.
Natural resource conservation
Conservationists can use the information gleaned from genome sequencing to better assess key genetic factors for species conservation, such as the genetic diversity of a population, or whether an individual is a carrier of a recessive genetic disorder. By using genomic data to assess the impact of evolutionary processes and detect patterns of variation in specific populations, conservationists can develop plans to help specific species without leaving many unknown variables like standard genetics methods.
