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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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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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Evolution of Microbial Genome01:08

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Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
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Genome Annotation and Assembly03:36

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Synthetic Biology02:55

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Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Ensembl Genomes 2016: more genomes, more complexity.

Paul Julian Kersey1, James E Allen2, Irina Armean2

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Ensembl Genomes offers integrated genomic data for non-vertebrate species, now including over 23,000 bacterial and 400 fungal genomes. Recent updates enhance polyploid genome representation and data integration for broader accessibility.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • Ensembl Genomes complements Ensembl by providing genome-scale data for non-vertebrate species.
  • The resource offers consistent programmatic and interactive access to diverse genomic data types.
  • Previous publications detailed the Ensembl Genomes resource and its functionalities.

Purpose of the Study:

  • To provide an update on Ensembl Genomes, focusing on recent developments and expansions.
  • To highlight new analyses and views for representing polyploid genomes.
  • To report on the significant up-scaling of the genome database.

Main Methods:

  • Integration of genome-scale data from non-vertebrate species.
  • Development of new analytical tools and visualization methods for polyploid genomes.
  • Automation of archival data integration, including genome sequence, RNA sequence data, and variant calls.

Main Results:

  • Ensembl Genomes now includes over 23,000 bacterial, 400 fungal, 100 protist, 55 invertebrate, and 39 plant genomes.
  • New features enable the representation and analysis of polyploid genomes, exemplified by bread wheat.
  • Automated data integration pipelines have been enhanced for broader archival data incorporation.

Conclusions:

  • Ensembl Genomes has significantly expanded its data holdings and analytical capabilities.
  • The resource provides a comprehensive and accessible platform for non-vertebrate genomics research.
  • Continued development focuses on up-scaling and automating data integration for diverse species.