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Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

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Related Experiment Video

Updated: Dec 14, 2025

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Plant pan-genomes are the new reference.

Philipp E Bayer¹, Agnieszka A Golicz², Armin Scheben³

¹School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia.

|July 22, 2020

Summary

Plant pan-genomics reveals species-wide genomic diversity beyond single reference genomes. Understanding gene presence and absence variation aids plant breeding and evolution studies.

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Area of Science:

Genomics
Plant Biology
Evolutionary Biology

Background:

Recent advances in plant genome sequencing highlight significant genomic variation within species.
Single reference genomes are insufficient to capture the full genetic diversity of a species.
The concept of the pan-genome has emerged to encompass this diversity.

Purpose of the Study:

To review the expansion of pan-genomics in plants.
To explore the origins of gene presence and absence variation.
To demonstrate the utility of pan-genomes in plant breeding and evolution.

Main Methods:

Comparative genomics analysis of multiple plant individuals.
Identification of core and variable genes within a species.
Annotation and functional enrichment analysis of variable gene sets.

Main Results:

Pan-genomes reveal core genes present in all individuals and variable genes found in subsets.
Variable gene annotations frequently show conserved functions across plant species, particularly for stress responses.
Gene presence and absence variation provides insights into adaptation and evolution.

Conclusions:

Pan-genomics is crucial for understanding the complete genomic landscape of plant species.
The study of gene presence and absence variation offers valuable information for crop improvement.
Pan-genome data can significantly advance evolutionary studies in plants.