Computational protocol: Population Genomic Analysis of a Pitviper Reveals Microevolutionary Forces Underlying Venom Chemistry

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Protocol publication

[…] Venom gland RNA seq libraries were prepared as described previously (), except that ERCC92 synthetic spike-ins were added to the RNA extracts as described by for quality control. In addition, pooled libraries were normalized using the Evrogen Trimmer-2 cDNA normalization kit and sequenced to improve genome annotation for nonvenom transcripts. Reads were mapped to predicted coding sequences using Bowtie2 () within the RSEM package (). Though expression data doesn’t accurately always reflect protein levels in the venom (), it does in Protobothrops (, ). Therefore, we used the number of fragments per kilobase mapped (FPKM) as a measure of protein abundance. Mapped read counts for each sample, as estimated by RSEM, can be found in , online. Proteomic analysis was conducted as described previously (, ). […]

Pipeline specifications

Software tools Bowtie2, RSEM
Application RNA-seq analysis
Organisms Protobothrops mucrosquamatus