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Related Concept Videos

Polytene Chromosomes02:04

Polytene Chromosomes

Polytene chromosomes are giant interphase chromosomes with several DNA strands placed side by side. They were discovered in the year 1881 by Balbiani in salivary glands, intestine, muscles, malpighian tubules, and hypoderm of larvae Chironomus plumosus. Hence, these are also called "Salivary gland chromosomes." These are found in insects of the order Diptera and Collembola; in certain organs of mammals; and synergids, antipodes of flowering plants. Polytene chromosomes are also regularly...
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The homogenate obtained after cell lysis contains various membrane-bound organelles that can be further separated into pure fractions by subcellular fractionation. These isolates are used to study specific cellular components, analyze localized protein activity, and are even employed in diagnostics. Fractionation is typically achieved using centrifugation methods, the most common being density-gradient and differential centrifugation.
Differential Centrifugation
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Formation of Species

Speciation describes the formation of one or more new species from one or sometimes multiple original species. The resulting species are discrete from the parent species, and barriers to reproduction will typically exist. There are two primary mechanisms, speciation with and without geographic isolation—allopatric and sympatric speciation, respectively.
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Manipulation of Ploidy in Caenorhabditis elegans
07:54

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Published on: March 15, 2018

A consolidation algorithm for genomes fractionated after higher order polyploidization.

Katharina Jahn1, Chunfang Zheng, Jakub Kováč

  • 1Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada K1N 6N5. sankoff@uottawa.ca

BMC Bioinformatics
|January 4, 2013
PubMed
Summary
This summary is machine-generated.

Fractionation, the loss of gene copies after genome duplication, disrupts gene order and overestimates evolutionary distances. A new consolidation algorithm improves accuracy and efficiency for polyploid genomes.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Fractionation, the random loss of gene copies post-whole genome duplication, is a primary driver of gene order disruption.
  • This process leads to significant overestimation of evolutionary distances when using classic chromosomal rearrangement metrics.
  • Consolidation, a preprocessing step, mitigates this bias by identifying and accounting for fractionation regions.

Purpose of the Study:

  • Introduce a novel consolidation algorithm that enhances previous methods.
  • Extend the definition of fractionation regions to include areas of ongoing fractionation.
  • Enable processing of higher-order polyploid genomes beyond tetraploids.

Main Methods:

  • Developed a new consolidation algorithm incorporating ongoing fractionation regions.
  • Extended algorithm applicability to hexaploid and higher-order polyploid genomes.
  • Optimized algorithm for linear time complexity concerning genome size.

Main Results:

  • The new algorithm effectively processes polyploid genomes, including ancient hexaploids.
  • Demonstrated reduced asymptotic time complexity from quadratic to linear.
  • Applied the algorithm to plant genomes and simulated data to analyze fractionation effects.

Conclusions:

  • The enhanced consolidation algorithm provides more accurate evolutionary distance estimations in polyploid genomes.
  • The algorithm's improved efficiency and broader applicability advance genomic analysis.
  • This work offers a robust method for studying the impact of fractionation in evolutionary genomics.