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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.

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

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...

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Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

Accessing complex crop genomes with next-generation sequencing.

David Edwards¹, Jacqueline Batley, Rod J Snowdon

¹Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia.

TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

|September 6, 2012

Summary

This summary is machine-generated.

Advanced sequencing and bioinformatics tools are revolutionizing the analysis of complex polyploid crop genomes. This enables breeders to discover genes for improved crop traits and understand genetic diversity.

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Area of Science:

Plant Genomics
Crop Science
Molecular Genetics

Background:

Polyploidization events in crop species create complex genomes with multiple gene copies and rearrangements.
Conventional genetics approaches face challenges in analyzing these large, recalcitrant genomes for gene discovery.
Technological advancements in molecular genetics and genomics offer new opportunities to study complex crop genomes.

Purpose of the Study:

To review next-generation sequencing (NGS) and data analysis techniques for dissecting polyploid crop genomes.
To highlight progress in understanding gene function and allelic variation in crops like wheat and oilseed rape.
To discuss the potential of genomic data for crop improvement and breeding.

Main Methods:

Review of next-generation sequencing technologies and associated data analysis pipelines.
Focus on applications in polyploid crops, specifically wheat and oilseed rape.
Discussion of bioinformatics tools for handling large genomic datasets.

Main Results:

NGS technologies have significantly advanced the ability to analyze complex polyploid genomes.
Progress has been made in unravelling the genomes of wheat and oilseed rape using different sequencing approaches.
Understanding of genetic diversity and its relation to crop traits is rapidly improving.

Conclusions:

Genomic and transcriptomic sequencing will provide deep insights into polyploid crop origins, domestication, and trait variation.
High-throughput screening of genetic variants (SNPs, PAVs, structural variants) will be crucial.
These advancements will facilitate novel genomics-assisted breeding strategies for polyploid crops.