Computational protocol: Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists

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Protocol publication

[…] By scanning the SRA (using NCBI’s Taxonomy Browser), we identified 30 plastid-bearing species for which there are complete mitochondrial and/or plastid genome sequences and abundant RNA-seq data. We downloaded the RNA-seq reads from the SRA (https://www.ncbi.nlm.nih.gov/sra) and the organelle DNAs from the Organelle Genome Resources section of NCBI (https://www.ncbi.nlm.nih.gov/genome/organelle/) or GenBank (https://www.ncbi.nlm.nih.gov/genbank/). See Supplemental Material, Table S1 for detailed information on the RNA-seq and organelle genome data we downloaded, including accession numbers, sequencing technologies, read counts, organelle DNA features, and the strains used for genome sequencing and RNA-seq.We mapped the RNA-seq reads to the corresponding organelle genomes using Bowtie 2 () implemented through Geneious v9.1.6 (Biomatters Ltd., Auckland, NZ), a user-friendly, commercial bioinformatics software suite, which contains a graphical user interface (). All mapping experiments were carried out using default settings, the highest sensitivity option, and a min/max insert size of 50 nt/750 nt; we also allowed each read to be mapped to two locations to account for repeated regions, which are common in organelle genomes (). The mapping histograms shown in , , and were extracted from Geneious. […]

Pipeline specifications

Software tools Bowtie, Geneious
Application RNA-seq analysis