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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.

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...

Genomic DNA in Eukaryotes

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.

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.

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.

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Related Experiment Video

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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

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GOBASE: an organelle genome database.

Emmet A O'Brien¹, Yue Zhang, Eric Wang

¹Robert-Cedergren Center for Bioinformatics and Genomics, Département de Biochimie, Pavillon Roger-Gaudry, Université de Montréal, 2900 Edouard-Montpetit, Montreal QC, Canada H3T 1J4. eobrien@bch.umontreal.ca

Nucleic Acids Research

|October 28, 2008

Summary

The GOBASE organelle genome database now includes over 1.1 million mitochondrion and chloroplast sequences. Enhancements offer RNA editing data, human genetic disease information, and improved search functions.

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Published on: May 22, 2018

Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

Organelle genomes (mitochondrial and chloroplast) are crucial for eukaryotic cell function.
Comprehensive databases are essential for managing and analyzing the vast amount of sequence data.

Purpose of the Study:

To present the 21st release of the GOBASE organelle genome database.
To highlight recent functional enhancements and future directions for GOBASE.

Main Methods:

Compilation of published mitochondrion- and chloroplast-encoded sequences.
Integration of gene, exon, intron, and protein information.
Development of new interfaces for RNA editing, human genetic data, and sequence retrieval.

Main Results:

GOBASE release 21 contains approximately 913,000 mitochondrion-encoded and 250,000 chloroplast-encoded sequences.
New features include RNA editing data visualization, medically relevant human mitochondrial data (haplotypes, SNPs, disease states), and reannotated reference genomes.
Enhanced search functionality and sequence download options are now available.

Conclusions:

GOBASE provides a comprehensive resource for organelle genomics research.
Recent updates improve data accessibility and utility for diverse research applications, including medical genetics.
Future integration with NCBI/GenBank ensures long-term data preservation and accessibility.