Genome annotation of Oikopleura dioica from different geographical locations: Okinawa, Osaka, and Barcelona. Genome browser is currently hosted on oikobrowser.jnicolaus.com
This repository contains genome annotations of O. dioica for the purpose of incremental improvements by hands.
3 different fasta genome and GTF annotation sets that was used in the scrambling paper (Plessy and Mansfield et al., 2023) https://www.biorxiv.org/content/10.1101/2023.05.09.539028v1. The procedure of the genome annotation is detailed on the Bliznina et al., 2021 paper https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07512-6.
These are:
OKI.I69/v2/OKI.I69.v2.0.gtfOkinawaBar2_p4/v1/Bar2_p4.Flye.v1.0.gtfBarcelonaOSKA2016v1.9/v2/OSKA2016v1.9.v2.0.gtfOsaka
- I have created other versions which incorporate CAGE data from https://github.com/oist/LuscombeU-CAGE_libraries/ to add 5' UTRs as follows:
./OKI.I69/v2.1/OKI2018_I69_5primeutr_v2.1.gtfv2.0 + 5' UTR./Bar2_p4/v1.1/Bar2_p4_5primeutr_v1.1.gtfv1.0 + 5' UTR./Bar2_p4/v4/Bar2_p4_5primeutr_v4.0.gtfv1.0 + 5' UTR complemented with liftoff results from Norway (http://oikoarrays.biology.uiowa.edu/Oiko/)- This modifies the original annotation by adding gene models that do not overlap in the same strand with v1.0
./OSKA2016v1.9/v2.1/OSKA2016_5primeutr_v2.1.gtfv2.0 + 5' UTR
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Version X.2 is the version with 5' UTR with the addition of
gene_nameattribute obtained from eggnog using the longest transcript assigned to respectivegene_idusing the following parameters:-m diamond ---evalue 0.001 --score 60 --pident 40 --query_cover 20 --subject_cover 20 --itype proteins --tax_scope auto --target_orthologs all --go_evidence non-electronic --pfam_realign none --report_orthologs -
Version X.3 is the version with 5' UTR (CAGE) and 3' UTR (Canonical polyA site), supplemented with valid liftoff gene models, and genes split according to CAGE peaks and liftoff gene models using the package
github.com/oist/LuscombeU_annotationpolish. GTF was created using AGAT, gff3 files were sanitised using AGAT.
I have also added Liftoff results from Norwegian O. dioica which is located under the resource directory in each genome. They were done using the parameters -flank 0.5 and -polish.
Index files are required for fasta files and were created using samtools faidx.
Conservation tracks under /resources/conservation_tracks were computed using cactus, cactus-hal2maf and halPhyloP using default settings for 4 different species including Osaka, Barcelona, Norway and Okinawa.
Synteny was calculated across species using LAST.
- Clone the repository and create a new branch for your changes.
- To add a new gene that was not annotated before, add a new gene annotation to the GFF3 file.
- To fix a gene model that was previously annotated wrongly, remove the old gene annotation and add the new gene model.
To add new genes, please add an identifier so that we know that the gene was edited manually.
More info on gff3 and gtf file formats: https://www.ensembl.org/info/website/upload/gff3.html https://asia.ensembl.org/info/website/upload/gff.html?redirectsrc=//www.ensembl.org%2Finfo%2Fwebsite%2Fupload%2Fgff.html
Johannes Nicolaus Wibisana of The Luscombe Unit of the Okinawa Institute of Science and Technology is maintaining this repository. For questions please email [email protected].