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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Polytene Chromosomes02:04

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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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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.

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Single Nucleotide Polymorphism-sensitive FISH Detection of Locus-specific Ribosomal RNA Transcription in Drosophila melanogaster
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Simple sequence repeat variation in the Daphnia pulex genome.

Way Sung1, Abraham Tucker, R Daniel Bergeron

  • 1Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA. wsung@cisunix.unh.edu

BMC Genomics
|December 7, 2010
PubMed
Summary

Simple sequence repeats (SSRs) in the Daphnia pulex genome show motif-specific heterozygosity, influenced by repeat number and size. Motif-dependent biases and variation contribute to the unique spectrum of these important genomic features.

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Molecular Genetics

Background:

  • Simple sequence repeats (SSRs) are highly variable genomic regions crucial for evolutionary studies.
  • The Daphnia pulex genome offers an unbiased dataset for investigating SSR evolution.
  • SSR variability aids in tracing population history and understanding selection and mutation patterns.

Purpose of the Study:

  • To catalogue SSR loci in the Daphnia pulex genome.
  • To determine SSR heterozygosity and its relationship with repeat number, motif size, sequence, and distribution.
  • To investigate biases in SSR variation and their contribution to abundance patterns.

Main Methods:

  • Genome-wide cataloguing of SSR loci (1-100 nucleotide motif sizes, ≥3 perfect repeats).
  • Analysis of whole genome shotgun reads to assess SSR heterozygosity.
  • Correlation analysis using the Daphnia pulex genetic map.

Main Results:

  • SSR heterozygosity is motif-specific and positively correlated with repeat number and motif size.
  • A motif-dependent end-nucleotide polymorphism bias influences homopolymer, dimer, and trimer abundance.
  • Multiple unit variation at microsatellite loci depends on repeat number and motif size.
  • Dimer and trimer frequencies correlate positively with recombination rates.

Conclusions:

  • SSR variation in Daphnia pulex is significantly motif-dependent.
  • Unit length variation and end repeat biased base substitution shape the SSR landscape.
  • These findings provide insights into the evolutionary dynamics of SSRs.