DOI: 10.5061/dryad.70rxwdc7b
title: Re-annotated genomes for plastomes and mitogenomes

description: Diatoms are pivotal in global oxygen, carbon dioxide, and silica cycling,
 contributing significantly to photosynthesis and serving as fundamental
 components in aquatic ecosystems. Recent advancements in genomic
 sequencing have shed light on their evolutionary dynamics, revealing
 evolutionary complex genomes influenced by symbiotic relationships and
 horizontal gene transfer events. By analyzing 120 plastome and 70
 mitogenome publicly available sequences, this paper aims to elucidate the
 evolutionary dynamics of diatoms across diverse lineages. In comparing
 genomic events between plastomes and mitogenomes, gene losses and
 pseudogenes were more frequently observed in plastomes, while they were
 less commonly found in mitogenomes. Overall, gene losses were abundant in
 the plastomes of Astrosyne radiata, Toxarium undulatum, and Proboscia sp.
 Frequently lost and pseudogenized genes were acpP, ilv, serC, tsf, tyrC,
 ycf42 and bas1. In mitogenomes, mttB, secY and tatA genes were lost
 repeatedly across several diatom taxa. Analysis of nucleotide substitution
 rates indicated that, in general, mitogenomes were evolving at a more
 rapid rate compared to plastomes. This is contrary to what was observed in
 synteny analyses where plastomes exhibited greater structural
 rearrangements compared to mitogenomes with the exception of the genera
 Coscinodiscus and one group of species within Thalassiosira. 
description: Genomes deposited in NCBI GenBank may contain annotation errors
 or missing gene data, which can lead to misinterpretations regarding gene
 losses and gains. In fact, this was the case for every one of the
 published organellar genomes we analyzed. To address this, the authors
 included a confirmatory step to verify whether genes were actually absent
 or simply missing due to annotation issues. Thus, all genomes were
 re-annotated using multiple reference genomes to ensure annotation
 completeness.
description: # Re-annotated genomes
 [https://doi.org/10.5061/dryad.70rxwdc7b](https://doi.org/10.5061/dryad.70rxwdc7b) ## Description of the data and file structure #### Genome Annotation and Validation Process #### Background Genomes deposited in public databases such as NCBI GenBank often contain annotation errors or missing gene information. These inaccuracies can lead to incorrect conclusions about gene presence, loss, or gain in the studied organisms. In fact, during our analysis, every published organellar genome we examined showed some level of annotation inconsistency or incompleteness. #### Problem with Existing Annotations A common issue, particularly with diatom genomes in NCBI, is incomplete or poor annotation. This often happens because the reference genomes used during the original annotation process themselves lacked certain genes. Consequently, errors propagate and result in genomes that do not fully represent the true gene content. #### Our Approach: Confirmatory Re-Annotation To address these issues and ensure reliable genomic data, we implemented a confirmatory step: * Re-annotation of all genomes analyzed in this study. * Used multiple reference genomes known to have complete gene sets to guide the re-annotation. * This approach allowed us to distinguish genes that are truly absent from those simply missing due to annotation errors. * As a result, previously unannotated genes were identified and added, improving the completeness and accuracy of the genome annotations. #### Methodology **Data Acquisition**: Downloaded FASTA files of the organellar genome sequences from NCBI for all strains included in this study. **Annotation**: Performed re-annotation using the GeSeq tool (Tillich et al., 2017), which supports annotation based on multiple reference genomes and custom settings. #### Summary By incorporating multiple complete reference genomes during re-annotation and confirming gene presence, our workflow improves the reliability of gene annotations in diatom organellar genomes. This careful validation helps prevent misinterpretation caused by missing or erroneous gene annotations in public databases. #### **File: 75\_MT\_Reannotation.zip** **Description:** Re-annotated mitogenomes using GeSeq in Chlorobox #### File: 125\_CP\_Reannotation.zip **Description:** Re-annotated plastomes using GeSeq in Chlorobox ## Code/software GeSeq in Chlorobox (web server) [https://chlorobox.mpimp-golm.mpg.de/geseq.html](https://chlorobox.mpimp-golm.mpg.de/geseq.html)  ## Access information Other publicly accessible locations of the data: * N/A Data was derived from the following sources: * GeSeq in Chlorobox (web server) [https://chlorobox.mpimp-golm.mpg.de/geseq.html](https://chlorobox.mpimp-golm.mpg.de/geseq.html)  #### File naming convention/scheme: **Mitogenomes (ingroups):** *[total no. of ingroup taxa] MTs Reannotation-2_[Genus]**[species]*[NCBI accession no.]_[source: GenBank].gb **Mitogenomes (outgroups):** *Outgroups MT-[Genus]**[species]-MT*[Genus]*[species]*[NCBI accession no.]_[source: GenBank].gb **Plastomes (ingroups):** *[total no. of ingroup taxa] CP Re-annotation_[Genus]**[species]*[NCBI accession no.]_[source: GenBank].gb **Plastomes (outgroups):** *Outgroups CP-Reannotation_[Genus]**[species]*[NCBI accession no.]_[source: GenBank].gb