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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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Genomic Imprinting and Inheritance02:30

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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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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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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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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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Genomic DNA in Prokaryotes00:46

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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EchinoBase: Tools for Echinoderm Genome Analyses.

Gregory A Cary1, R Andrew Cameron2,3, Veronica F Hinman2

  • 1Department of Biological Sciences, Mellon Institute, Carnegie Mellon University, Pittsburgh, PA, USA. gregcary@andrew.cmu.edu.

Methods in Molecular Biology (Clifton, N.J.)
|May 16, 2018
PubMed
Summary
This summary is machine-generated.

EchinoBase provides a comprehensive platform for exploring echinoderm genomic data, including genomes, expression, and functional genomics. This resource aids in understanding echinoderm genome regulation and enables comparative genomics research.

Keywords:
Brittle starEchinodermExpressionGene regulatory network (GRN)GenomeSea cucumberSea starSea urchin

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Area of Science:

  • Marine Biology
  • Genomics
  • Bioinformatics

Background:

  • Echinoderms are vital invertebrate research models across various biological disciplines.
  • Access to integrated genomic data is crucial for advancing echinoderm research.

Purpose of the Study:

  • To outline the datasets and bioinformatic tools available on EchinoBase.
  • To facilitate efficient interrogation and exploration of echinoderm genomic data.
  • To provide a foundation for understanding echinoderm genome regulation and comparative genomics.

Main Methods:

  • Compilation of assembled genomes and genome annotations.
  • Inclusion of spatial and quantitative expression data.
  • Integration of functional genomics datasets.
  • Development of bioinformatic tools such as genome browsers and BLAST databases.

Main Results:

  • EchinoBase offers a rich repository of diverse echinoderm genomic datasets.
  • Bioinformatic tools are available to support data exploration and analysis.
  • Optimized strategies for data inquiry are suggested.

Conclusions:

  • EchinoBase serves as a central hub for echinoderm genomic research.
  • The platform supports the prediction of noncoding regulatory regions.
  • It facilitates comparative genomic studies within the echinoderm phylum, particularly for early development.