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
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...
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MDPI AG
2018-06-01
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| Series: | Life |
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| Online Access: | http://www.mdpi.com/2075-1729/8/3/25 |
| _version_ | 1828117112642600960 |
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| author | Michael Gruenstaeudl Nico Gerschler Thomas Borsch |
| author_facet | Michael Gruenstaeudl Nico Gerschler Thomas Borsch |
| author_sort | Michael Gruenstaeudl |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T13:08:54Z |
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| id | doaj.art-1b7f60014af549b095ea4f38a21a8594 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-04-11T13:08:54Z |
| publishDate | 2018-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-1b7f60014af549b095ea4f38a21a85942022-12-22T04:22:38ZengMDPI AGLife2075-17292018-06-01832510.3390/life8030025life8030025Bioinformatic Workflows for Generating Complete Plastid Genome Sequences—An Example from Cabomba (Cabombaceae) in the Context of the Phylogenomic Analysis of the Water-Lily CladeMichael Gruenstaeudl0Nico Gerschler1Thomas Borsch2Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, 14195 Berlin, GermanyInstitut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, 14195 Berlin, GermanyInstitut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, 14195 Berlin, GermanyThe 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.http://www.mdpi.com/2075-1729/8/3/25bioinformaticsCabombagenome assemblyphylogenomicsplastid genomestandardizationworkflow |
| spellingShingle | Michael Gruenstaeudl Nico Gerschler Thomas Borsch 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 bioinformatics Cabomba genome assembly phylogenomics plastid genome standardization workflow |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | bioinformatics Cabomba genome assembly phylogenomics plastid genome standardization workflow |
| url | http://www.mdpi.com/2075-1729/8/3/25 |
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