Transcriptome of the coralline alga Calliarthron tuberculosum (Corallinales, Rhodophyta) reveals convergent evolution of a partial lignin biosynthesis pathway

Purpose of this page

This page should provide you with the tools to:

• Extract genes from Calliarthron (using annotations from KEGG analysis)
• Extract whole metabolic pathways from Calliarthron (using the pathview package (1))
• Identify Calliarthron sequences with genome support

Introduction

Calliarthron is a coralline red algae whoes transcriptome and genome have been recently sequenced. The trasncriptomic data has been annotated with KEGG. Here we provide a method for extracting genes directly.

The raw data can be found

• Transcriptome data: accession [PRJEB39919](link to ENA location)
• Genome data: accession [PRJEB39919](link to ENA location)

Files

The following three files are downloadable and are easily searchable for quick identification of genes you're interested in.

• SupFile1_Calliarthron_combined_transcriptome_w_genomeHit.txt - This file contains all the sequence IDs form the transcriptome that also have genomic support
• SupFile2_Calliarthron_KEGG_Identifiers.txt - This file contains all the sequence IDs and their gene annotation from the transcriptome. This is based on KEGG annotation.
• SupFile3_Calliarthron_Trinity_combined.txt.zip - This file contains the sequence IDs and their associated sequence.

To extract Calliarthron sequences that are annotated as present in a particular metabolic pathway download the file

• CalliarthronKEGGExtraction In order to do the next steps, you will need to have RStudio. Once you've downloaded the file, you'll open up the file on your computer:
• KEGGKOMappingCalliarthron.Rmd There you'll find detailed instructions of how to extract a pathway and get something like this.

Fig 1. By the end of this tutorial you should be able to extract the Calliarthron sequences in a pathway of interest and a list of the sequences present.

Citations

Luo, Weijun, Brouwer, Cory (2013). “Pathview: an R/Bioconductor package for pathway-based data integration and visualization.” Bioinformatics, 29(14), 1830-1831. doi: 10.1093/bioinformatics/btt285.