We’re delighted to announce the release of WormBase ParaSite 15, our biggest release yet!
This release sees the addition of assemblies of 19 new species:
- 5 Panagrolaimus/Propanagrolaimus species, including the Antarctic nematode Panagrolaimus davidi, from Schiffer et al., 2019.
- 10 new Caenorhabditis species from Stevens et al., 2019 and Stevens et al, 2020.
- Setaria digitata, a filarial parasite of ungulates, from Rashanthy Nadarajah and colleagues of the University of Colombo.
- The large liver fluke Fasciola gigantica, from The Genome Institute.
- The lung fluke Paragonimus westermani, from Oey et al., 2019.
- The cestode Echinococcus oligarthrus, from Moldanado et al., 2019
Genome and annotation updates
We have also incorporated alternative or updated assemblies/gene models for a further 8 species:
- An alternative (PacBio) assembly from Sun-Yat Sen University for Angiostrongylus cantonensis (PRJNA350391, Xu et al, 2019).
- An alternative Hymenolepis diminuta assembly from The University of Warmia and Mazury (PRJEB30942, Nowak et al., 2019).
- An alternative (PacBio) Steinernema feltiae assembly (PRJNA353610, Fu et al., 2020).
- An alternative (PacBio) Schistosoma japonicum assembly from Fudan University (PRJNA520774, Luo et al., 2019).
- Schistosoma haematobium (PRJNA78265) has been updated to reflect an assembly update in INSDC (GCA_000699445.2, Stroehlein et al., 2019). Gene ID mappings from the previous assembly (GCA_000699445.1) are available in the GFF file, and on gene pages.
- A handful of curated gene models have been added to the Fasciola hepatica (PRJEB25283) annotation, submitted by Emily Robb of Queens’ University Belfast.
- Curated gene models for the P-glycoprotein repertoire have been added to the Parascaris univalens (PRJNA386823) annotation, submitted by Alexander Gerhard of The Free University of Berlin.
- The Haemonchus contortus (PRJEB506) annotation has been updated to reflect ongoing curation by Steve Doyle and colleagues at the Wellcome Sanger Institute.
We have imported phenotype data from the recent Schistosoma mansoni RNAi screen by Wang et al., 2020. You can browse the data from S. mansoni gene pages (see the “phenotype” link in the left hand menu). Please let us know if you have any feedback or suggestions for other RNAi studies that you’d like to see in WormBase ParaSite.
Other changes to note
- The Ancylostoma ceylanicum (PRJNA72583) annotation has been updated to incorporate some missing gene models.
- Caenorhabditis sp. 34 has been renamed to Caenorhabditis inopinata.
- In response to feedback from the community, we now present two alternative Steinernema carpocapsae assemblies: GCA_000757645.1, as described by Dillman et al., 2015 and GCA_000757645.3, as described by Serra et al. (2019). The Serra annotation has been updated to incorporate UTRs, which were omitted in WormBase ParaSite 14. IDs for genes on the X chromosome have also been updated to follow the naming convention of the rest of the gene set. ID mappings between WBPS14 GCA_000757645.3 and WBPS15 GCA_000757645.3 are available on gene pages and in the GFF file. A mapping between gene IDs in GCA_000757645.1 and GCA_000757645.3 is available on the WBPS FTP site.
- IsoSeq data for the heartworm Dirofilaria immitis is available on JBrowse, submitted by Nic Wheeler and colleagues of the University of Wisconsin-Madison.
- We have added the alternative Necator americanus gene set, described by Logan et al., 2020, as a JBrowse track.