Microplitis demolitor Official Gene Set iyMicDemo2.1a_OGSv2.0

Interpretive summary:Microplitis demolitor is a wasp species that contains viral DNA in its genome. Scientists want to know more about this virus for many reasons. For example, it might help the wasp lay its eggs in other insect species. But, it’s challenging to find the viral DNA with the tools most scientists use, so they have to find and describe it on their own. The authors of this dataset found the viral DNA locations in the Microplitis demolitor genome, and also described the viral genes. Now, scientists know where the virus DNA is so they can perform better experiments to understand the wasp.Technical abstract:Official Gene Sets are essential genome annotation resources for genome projects. They define annotations, which ascribe function to a genome; and declare the community-recognized annotation set for a genome assembly. Often, they integrate data curated by a genome database and/or community curators.Studies in Microplitis demolitor often focus on the endogenized, beneficial Bracovirus that integrated into the wasp's genome ~100 million years ago. Due to this long divergence from free living viruses and the simplistic nature of viral genes, it is difficult to identify these genes with traditional annotation measures. The accurate and complete annotation of the viral gene set is imperative for future experimental and evolutionary research.The Microplitis demolitor Official Gene Set iyMicDemo2.1a_OGSv2.0 is based on genome assembly iyMicDemo2.1a (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_026212275.2/), and derives from the following datasets:1. New manually curated annotations by Kelly Tims and Dr. Gaelen Burke on genome assembly GCF_000572035.2, lifted over to the new genome assembly, iyMicDemo2.1a/GCF_026212275.2, via the LiftOff software v1.6.3 (https://github.com/agshumate/Liftoff/releases/tag/1.6.3), using the -exclude_partial and -polish options.2. Manually curated annotations from Microplitis demolitor Official Gene Set v1.0 on genome assembly Mdem2 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000572035.2/). These manual annotations were lifted over to the new genome assembly, iyMicDemo2.1a, via the LiftOff software v1.6.3 (https://github.com/agshumate/Liftoff/releases/tag/1.6.3), using the -exclude_partial and -polish options.3. NCBI Annotation Release GCF_026212275.2-RS_2023_02 from RefSeq's Eukaryotic Genome Annotation Pipeline v10.1 (https://www.ncbi.nlm.nih.gov/refseq/annotation_euk/Microplitis_demolitor/GCF_026212275.2-RS_2023_02/)USDA-ARS NAL staff used the gff3_merge program from the GFF3toolkit software package v2.1.0 (https://github.com/NAL-i5K/GFF3toolkit/releases/tag/v2.1.0) to merge the above four datasets. Overlapping annotations from the dataset with the lower number listed above replaced annotations from the dataset with the higher number (e.g. newer manual annotations have precedence over computationally predicted annotations from RefSeq. USDA-ARS NAL staff then performed QA/QC on the dataset and added metadata).In addition, we provide two supporting datasets for the Official Gene Set:Proviral segments.Proviral segments are linear forms of the circular, dsDNA segments that are packaged within Microplitis demolitor bracovirus (MdBV) virions produced within wasp ovaries. The proviral segment boundaries were manually identified as reported in Burke et al. 2014 and 2018. Illumina short-read DNA sequencing data was generated from sequencing DNAs isolated from MdBV virions and mapped to the iyMicdemo2.1a assembly. Bigwig tracks of these data were viewed in the i5K Jbrowse genome browser to identify regions of high coverage corresponding to proviral segments. Additionally, boundaries were determined using the presence of sequence motifs known to flank proviral segments as previously outlined in Burke et al. 2014.Replication units.Replication units are regions of DNA amplified in copy number compared to surrounding genomic DNA regions in the calyx cells of wasp ovaries where MdBV is produced. The Replication Units house proviral segments singly or in clusters. Replication units were first identified in Burke et al. 2015 on a previous genome assembly by mapping Illumina sequence reads generated from DNA isolated from wasp ovaries to the genome reference and identifying regions of high coverage. The boundaries of replication units are sometimes associated with specific sequence motifs. The sequences corresponding to replication unit boundaries in the iyMicDemo2.1a genome assembly were identified using a combination of blast and manual curation looking for the same sequences present at replication unit boundaries as previously identified.We have provided the full Official Gene Set iyMicDemo2.1a_OGSv2.0 in the file iyMicDemo2.1a_OGSv2.0.tar.gz. We have also provided a subset of the Official Gene Set with only the manual annotations in the file iyMicDemo2.1a_OGSv2.0_manual-annotations.tar.gz.These datasets, and tools to interact with it, are also available at the i5k Workspace@NAL (https://i5k.nal.usda.gov). These updated annotations should facilitate continued research on Microplitis demolitor via curated annotations on the improved, newer genome assembly.

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  "fn": "Burke, Gaelen R.",
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[
  "Microplitis demolitor",
  "genome annotation",
  "i5k",
  "insects"
]

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