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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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.
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...

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The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference

Hooman K Moghadam1, Peter W Harrison, Gergely Zachar

  • 1Institute of Marine Biology, Biotechnology & Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece. hkm@hcmr.gr

Molecular Ecology Resources
|April 5, 2013
PubMed
Summary

Researchers created a new gene atlas for the Kentish plover, a bird species with complex mating behaviors. This transcriptome assembly provides valuable genetic resources for studying avian behavioral ecology without a reference genome.

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Area of Science:

  • * Avian genomics and transcriptomics
  • * Behavioral ecology
  • * Neurogenetics

Background:

  • * The Kentish plover (Charadrius alexandrinus) exhibits a highly variable mating system and parental behavior, making it a key species for behavioral ecology research.
  • * This species lacks genomic resources, and is evolutionarily distant from available avian genome sequences, hindering genetic studies.
  • * Short-read RNA-Seq data offers a potential avenue for genomic resource generation in understudied species.

Purpose of the Study:

  • * To perform a de novo transcriptome assembly for the Kentish plover using telencephalon and diencephalon tissues.
  • * To identify single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for genetic variation studies.
  • * To investigate sex-biased gene expression patterns and identify candidate genes associated with behavioral differences between males and females.

Main Methods:

  • * Illumina RNA-Seq data from telencephalon and diencephalon tissue samples were used for de novo transcriptome assembly.
  • * Transcript contigs were identified and compared to existing avian genome sequences for homology.
  • * SNP and SSR discovery was performed on the assembled transcriptome.
  • * Differential gene expression analysis was conducted to identify sex-biased transcripts.

Main Results:

  • * Over 21,000 transcript contigs were assembled with significant expression, showing homology to avian exonic sequences.
  • * More than 31,000 high-quality SNPs and over 2,500 SSRs were identified.
  • * Over 200 autosomal transcripts exhibited significant expression differences between males and females.
  • * Female-biased transcripts were enriched for learning, cognition, and memory functions; male-biased transcripts were enriched for neural functions like neuron projection and synapses.

Conclusions:

  • * This study presents one of the first de novo transcriptome assemblies from non-normalized, short-read next-generation sequencing data.
  • * The developed transcriptome provides crucial genomic resources for the Kentish plover, enabling future research in behavioral ecology and neurogenetics.
  • * The methodology offers an effective strategy for simultaneous sequence and expression variability analysis without a reference genome.