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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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Phylogenomics Using Transcriptome Data.

Johanna Taylor Cannon1, Kevin Michael Kocot2

  • 1Department of Zoology, Naturhistoriska Riksmuseet, 50007, SE-104 05, Stockholm, Sweden. Johanna.cannon@nrm.se.

Methods in Molecular Biology (Clifton, N.J.)
|July 28, 2016
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Summary
This summary is machine-generated.

This study outlines a generalized protocol for phylogenetic analysis using large-scale transcriptome data. It details methods from RNA extraction to phylogenomic inference, enabling robust evolutionary studies.

Keywords:
IlluminaPhylogenomicsPhylogenyRNAseqTranscriptomescDNA

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Phylogenetic analyses are crucial for understanding evolutionary relationships.
  • Large-scale molecular datasets, particularly transcriptome data, offer rich information for phylogenetics.
  • Standardized protocols are needed for reproducible and efficient phylogenetic inference.

Purpose of the Study:

  • To present a generalized, step-by-step protocol for phylogenetic analysis.
  • To detail the use of transcriptome data from Illumina sequencing for phylogenomics.
  • To provide a comprehensive workflow from molecular lab procedures to bioinformatic analyses.

Main Methods:

  • RNA extraction, cDNA synthesis, and Illumina sequencing.
  • Bioinformatic assembly of raw reads, identification of coding regions, and orthologous gene (OG) grouping.
  • Selection of specific OGs using a custom shell script and concatenation into a supermatrix.
  • Phylogenomic inference using maximum likelihood and Bayesian inference methods.

Main Results:

  • A generalized protocol for large-scale phylogenetic analysis using transcriptome data is established.
  • The protocol integrates molecular laboratory techniques with advanced bioinformatics pipelines.
  • The workflow facilitates the construction of a supermatrix for robust phylogenetic inference.

Conclusions:

  • The presented protocol provides a standardized framework for conducting phylogenetic analyses with large molecular datasets.
  • This approach enhances the efficiency and reproducibility of phylogenomic studies.
  • The generalized methods are applicable to diverse research questions in evolutionary biology.