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Related Concept Videos

Synteny and Evolution02:31

Synteny and Evolution

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John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
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Genomics02:02

Genomics

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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...
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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Genome Size and the Evolution of New Genes03:21

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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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Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

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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...
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Ultra-long Read Sequencing for Whole Genomic DNA Analysis
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Sequence-Based Synteny Analysis of Multiple Large Genomes.

Daniel Doerr1, Bernard M E Moret2

  • 1School of Computer and Communication Sciences, EPFL, Lausanne, Switzerland.

Methods in Molecular Biology (Clifton, N.J.)
|December 27, 2017
PubMed
Summary
This summary is machine-generated.

This study presents a new pipeline for synteny analysis, enabling detailed sequence-level study of large genomes. The pipeline utilizes existing tools and integration scripts for efficient genomic data analysis.

Keywords:
Genome comparisonLarge genomesMarker sequencesSynteny analysis

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Current synteny analysis methods struggle with large-scale genomic datasets at the sequence level.
  • Analyzing large genomes requires advanced computational tools and pipelines.

Purpose of the Study:

  • To describe a novel pipeline for synteny analysis of large genomic datasets.
  • To provide a practical guide for applying this pipeline using avian genomes.

Main Methods:

  • Development of a bioinformatics pipeline integrating existing tools.
  • Application of the pipeline to four avian genomes for demonstration.
  • Creation of integration scripts for data conversion and tool setup.

Main Results:

  • The pipeline enables effective synteny analysis for large genomic datasets.
  • Hands-on examples with avian genomes illustrate the pipeline's functionality.
  • Integration scripts simplify data management between tools.

Conclusions:

  • The described pipeline enhances the capacity for sequence-level synteny analysis in large genomes.
  • This approach offers a practical solution for researchers working with complex genomic data.