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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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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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Replication in Eukaryotes02:31

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Replication in Eukaryotes01:29

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In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity before cell division, so there are many proteins that fulfill specialized roles in the replication process. Replication occurs in three phases: initiation, elongation, and termination, and ends with two complete sets of chromosomes in the nucleus.
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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
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The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
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Related Experiment Video

Updated: Feb 1, 2026

Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics
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Published on: February 18, 2009

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Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes.

Lisa K Johnson1,2, Harriet Alexander1,3, C Titus Brown1,2,4

  • 1Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA.

Gigascience
|December 14, 2018
PubMed
Summary

Automated pipelines improve de novo transcriptome assembly, revealing novel gene content and enabling better identification of species-specific trends in marine microbial eukaryotes. Re-processing existing data with new tools enhances accuracy and community resources.

Keywords:
automated pipelinemarine microbial eukaryotere-analysistranscriptome assembly

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Area of Science:

  • Bioinformatics
  • Genomics
  • Marine Biology

Background:

  • De novo transcriptome assembly is crucial for RNA sequencing analysis in species lacking reference genomes.
  • The impact of different bioinformatics pipelines on transcriptome assembly quality is not well understood.
  • This study addresses the need for standardized and reproducible transcriptome assembly methods.

Purpose of the Study:

  • To automate a bioinformatics pipeline for de novo transcriptome assembly and annotation.
  • To evaluate and compare transcriptome assemblies generated by different pipelines.
  • To assess the impact of pipeline choice on the identification of novel gene content and taxonomic trends.

Main Methods:

  • Programmatic automation of a de novo transcriptome assembly pipeline.
  • Assembly and annotation of raw transcriptomic short-read data from the Marine Microbial Eukaryotic Transcriptome Sequencing Project.
  • Comparative analysis of new assemblies against those generated by a previously established pipeline.

Main Results:

  • New transcriptome assemblies incorporated most previous contigs and introduced novel gene content (average 7.8% novel annotated contigs).
  • Distinct taxonomic trends were observed: Dinoflagellata assemblies had higher contig and k-mer counts, while Ciliophora assemblies showed a lower percentage of open reading frames.
  • Assemblies generated by the automated pipeline contained significant new genetic information.

Conclusions:

  • No single "best" reference transcriptome exists; it is a dynamic target influenced by evolving tools.
  • Automated and programmable pipelines are essential for managing computationally intensive assembly tasks and ensuring consistent evaluation.
  • Re-assembling existing data with updated pipelines can yield more accurate taxon-specific trend identification and valuable community resources.