Plastid phylogenomics of water lilies, with a focus on partitioning strategies and the development of bioinformatic tools
Final Report Abstract
This project aimed to conduct a molecular evolutionary analysis of the water lilies and related plant species by sequencing and comparing the complete plastid genomes of these study plants. To carry out the genomic comparisons, large-scale DNA sequencing, bioinformatics data processing of the genomic sequence data, and the development of novel, customized software tools were conducted. Using leaf samples of live plants grown ex situ at the botanical garden of the ’Botanischer Garten und Botanisches Museum Berlin’, a total of 23 novel plastid genomes were sequenced, primarily from plants that have so far not been included in similar analyses. Several results were obtained through these analyses. First, the plant family that includes the water lilies may not be a single lineage in evolutionary terms when considered under its current taxonomic circumscription; while some genes indicate such a single origin for this family, other genes do not. Second, the precise way of subdividing the genomic sequence data may affect the evolutionary reconstructions of, and thus our conclusions on, the target lineage; however, interactions of this effect with genomic areas of low sequencing coverage may exist, and a software tool that assists in the evaluation of this interaction was developed. Third, the precise choice of software for selecting optimal parameter values for evolutionary analysis may affect the evolutionary reconstructions of, and thus our conclusions on, the target lineage; however, indications of incorrect sequence annotations among many archived plastid genomes were found using a software tool developed to that end, and these incorrect annotations would need to be corrected before the impact of software choice can be accurately tested. In summary, this research project generated novel genomic DNA sequence data of several so far understudied plant taxa and tackled three evolutionary research questions by conducting genomic data analysis as well as developing and applying novel bioinformatics software tools. A total of four peer-reviewed publications were generated during the course of this project, which summarize the project results and place them into perspective compared to similar investigations.
Publications
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Why the monophyly of Nymphaeaceae currently remains indeterminate: an assessment based on gene-wise plastid phylogenomics. Plant Systematics and Evolution, 305(9), 827-836.
Gruenstaeudl, Michael
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annonex2embl : automatic preparation of annotated DNA sequences for bulk submissions to ENA. Bioinformatics, 36(12), 3841-3848.
Gruenstaeudl, Michael
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PACVr: plastome assembly coverage visualization in R. BMC Bioinformatics, 21(1).
Gruenstaeudl, Michael & Jenke, Nils
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airpg: automatically accessing the inverted repeats of archived plastid genomes. BMC Bioinformatics, 22(1).
Mehl, Tilman & Gruenstaeudl, Michael
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Depth and evenness of sequence coverage are associated with assembly quality, genome structure, and choice of sequencing platform in archived plastid genomes. Cold Spring Harbor Laboratory.
Jenke, Nils & Gruenstaeudl, Michael
