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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

1
Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, 14195 Berlin, Germany
2
Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, 14195 Berlin, Germany
3
Berlin Center for Genomics in Biodiversity Research (BeGenDiv), 14195 Berlin, Germany
*
Author to whom correspondence should be addressed.
Received: 1 May 2018 / Revised: 11 June 2018 / Accepted: 19 June 2018 / Published: 21 June 2018
(This article belongs to the Special Issue Open Science Phyloinformatics: Resources, Methods, and Analyses)
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Abstract

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 results of sequencing, assembling, annotating and quality-checking of three complete plastid genomes of the aquatic plant genus Cabomba as well as subsequent gene alignment and phylogenetic tree inference. We accompany our findings by a detailed description of the bioinformatic workflow employed. Importantly, we share a total of eleven software scripts for each of these bioinformatic processes, enabling other researchers to evaluate and replicate our analyses step by step. The results of our analyses illustrate that the plastid genomes of Cabomba are highly conserved in both structure and gene content. View Full-Text
Keywords: bioinformatics; Cabomba; genome assembly; phylogenomics; plastid genome; standardization; workflow bioinformatics; Cabomba; genome assembly; phylogenomics; plastid genome; standardization; workflow
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Gruenstaeudl, M.; Gerschler, N.; Borsch, T. 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. Life 2018, 8, 25.

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