Botany Commons^™

Bioinformatic Workflows For Generating Complete Plastid Genome Sequences—An Example From Cabomba (Cabombaceae) In The Context Of The Phylogenomic Analysis Of The Water-Lily Clade, Michael Gruenstaeudl, Nico Gerschler, Thomas Borsch

Biological Sciences Faculty Publications

The sequencing and comparison of plastid genomes are becoming a standard method in plant genomics, and many researchers are using this approach to infer plant phylogenetic relationships. Due to the widespread availability of next-generation sequencing, plastid genome sequences are being generated at breakneck pace. This trend towards massive sequencing of plastid genomes highlights the need for standardized bioinformatic workflows. In particular, documentation and dissemination of the details of genome assembly, annotation, alignment and phylogenetic tree inference are needed, as these processes are highly sensitive to the choice of software and the precise settings used. Here, we present the procedure and …