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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Pyrosequencing for Microbial Identification and Characterization
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Pyrosequencing for Microbial Identification and Characterization

Published on: August 22, 2013

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing.

J Cristobal Vera1, Christopher W Wheat, Howard W Fescemyer

  • 1Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA. jcv128@psu.edu

Molecular Ecology
|February 13, 2008
PubMed
Summary
This summary is machine-generated.

This study presents a de novo transcriptome assembly for the Glanville fritillary butterfly using 454 pyrosequencing. This provides crucial genomic data for a non-model organism, enabling functional genomics research.

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Area of Science:

  • Genomics
  • Transcriptomics
  • Population Biology

Background:

  • The Glanville fritillary butterfly (Melitaea cinxia) is important in population biology but lacks genomic data.
  • De novo transcriptome assembly is essential for functional genomics in non-model species.

Purpose of the Study:

  • To perform a de novo assembly of the Glanville fritillary butterfly transcriptome.
  • To develop functional genomic tools for this prominent Lepidoptera species.

Main Methods:

  • Utilized 454 pyrosequencing on normalized complementary DNA from diverse life stages.
  • Assembled expressed sequence tags into contigs and singletons.
  • Performed BLAST comparisons and designed oligonucleotide microarray probes.

Main Results:

  • Generated 608,053 expressed sequence tags, assembling into 48,354 contigs and 59,943 singletons.
  • Identified approximately 9000 unique genes and over 6000 unannotated contigs.
  • Achieved sufficient coverage depth for single nucleotide polymorphism detection and demonstrated microarray reliability.

Conclusions:

  • 454 pyrosequencing enables fast, cost-effective de novo transcriptome assembly for non-model species.
  • This approach facilitates the development of functional genomic tools, bridging the gap with model organisms.
  • The generated data supports ecological and evolutionary studies ofMelitaea cinxia.