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Gene Families01:57

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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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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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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
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Gene-Family Extension Measures and Correlations.

Gon Carmi1, Alexander Bolshoy2

  • 1Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel. goncarmi@gmail.com.

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|August 17, 2016
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Summary

Gene family size generally increases with genome size in prokaryotes. This study analyzed 1484 genomes, confirming the correlation and identifying atypical microbes like Mycoplasmataceae and Halobacteria for further gene duplication research.

Keywords:
HalophilesMycobacterium lepraeMycoplasmasOrientiacombinatorial optimizationcomparative genomicsgenome sizenumber of paralogs

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Gene families, sets of similar genes formed by duplication, are common.
  • Previous studies on limited genomes showed a positive correlation between gene family size and genome size.
  • Atypical microbes have been observed to deviate from this general trend.

Purpose of the Study:

  • To re-examine the correlation between gene family size and genome size using a larger dataset.
  • To investigate atypical prokaryotic genomes that deviate from the general trend.
  • To apply advanced ranking methods, including Kemeny optimal aggregation, for a more robust analysis.

Main Methods:

  • Analysis of 1484 prokaryotic genomes.
  • Application of multiple ranking approaches, including Kemeny optimal aggregation.
  • Regression and correlation analysis to quantify relationships.
  • Boxplot analysis for outlier detection.

Main Results:

  • A general positive correlation was found between paralog indices and genome size across prokaryotes.
  • Different groups of atypical prokaryotic genomes were identified based on paralog quantities.
  • Mycoplasmataceae and Halobacteria emerged as notable outliers for further study.

Conclusions:

  • The positive correlation between genome size and gene family size is robust across a large prokaryotic dataset.
  • Atypical prokaryotic genomes offer unique insights into the mechanisms of gene duplication and evolution.
  • Mycoplasmataceae and Halobacteria warrant further investigation into their evolutionary trajectories driven by gene duplication.