We are pleased to announce the 14th release of WormBase ParaSite, bringing a new S. mediterranea assembly, and 8 other new and updated genomes.
New and updated genomes
We are happy to announce these new genomes of flatworms:
- Schmidtea mediterranea (PRJNA379262) , a high quality assembly and annotation of the model planarian
- Schistosoma bovis (PRJNA451066) , the genome of a liver fluke that, it was recently discovered, can form viable hybrids with S. haematobium
- Opisthorchis felineus (PRJNA413383), a parasite of fish and fish-eating mammals, responsible for opistorchiasis in Siberia
There is also an annotation update for Mesocestoides corti (PRJEB510) created with recently sequenced RNASeq data. It supports 5076 new genes and 8367 revised structures of the previous AUGUSTUS-only annotation.
If flatworm genomics is relevant to your work, be sure to also visit PlanMine, run by the authors of the Schmidtea genome. It contains many different assemblies from a number of free-living flatworms, phylogenetic data, and more.
Please note that we are deprecating the assembly SmedGD_c1.3 for Schmidtea mediterranea (PRJNA12585), corresponding to Robb et al. (2007), and intend to remove it once we are confident that no new research is being based on this assembly. Do let us know if you rely on it, or if there are good reasons for us to keep both Schmidteas around.
There are two new clade IV genomes, potentially relevant to agricultural research: Ditylenchus dipsaci (PRJNA498219), a plant pest, and an updated genome of an entomopathogenic nematode Steinernema carpocapsae (PRJNA202318).
There are also two genomes of free-living clade V nematodes. First is the genome of Halicephalobus mephisto (PRJNA528747), an extremophile found in deep rock fracture water in several gold mines in South Africa. We also have a genome of Mesorhabditis belari (PRJEB30104), an animal exhibiting an interesting pattern of reproduction: the eggs only mature after being activated by the males, which nevertheless do not pass on any genetic material.
Finally, we update WormBase core genomes to the WormBase version WS271.
Comparative genomics: bringing smaller trees
We remove altogether 7 genomes from our comparative genomics analysis for which there is a clearly better alternative genome of the same species.
We are hoping that this will make our results more robust overall, and their interpretation easier.
If you still need the old results, ortholog and paralog files from the last release are available through our FTP site. Apart from the previous S. mediterranea (PRJNA12585), we do not plan to remove any other genomes from our portal.
Our collaborators, the Functional Genomics group at the European Bioinformatics Institute, continue to process all public RNASeq studies through their plaform, RNASeq-er.
New data that has been produced in the last months, and more inclusive curation, helped us bring the total of studies processed on our site to 201, across 48 different species. This includes 30 studies for S. mediterranea, now aligned to the new assembly.
The total amount of studies RNASeq-er has data for is, as of July 2019, 639. Apart from 201 we have the results for, there are also 301 unannotated C. elegans or P. pacificus studies, which we skipped to reduce toil involved. The other 137 studies miss metadata or were consciously excluded, either because they did not have sufficiently many replicates, used a non-standard protocol like small miRNA-seq or Ribo-Seq, or because the authors asked us to suppress it.
Do contact us if you would like us to include a particular study, or if you have metadata that we are missing. It would be particularly helpful if you could let us know of any additional publications relating to our studies, as they are not always linked to archive records.
There are no major changes to this aspect of our service since we rolled it out in the last release: you can browse through a list of studies by following a link on the species page, and access per-gene results on the gene page through the tab on the left.
We have improved how expression data is organized within the JBrowse track selector, separating studies into categories. If you usually access the gene expression studies through the “Gene expression” tab, have a look at how the studies are organized in the track selector (example link, S. mansoni) – it provides an interesting alternative way of viewing the results.
Differential expression result files should now be slightly more convenient, and we hope that you will be able to open the files without trouble in any popular spreadsheet software. We are also providing complete results for each contrast – useful if you want to apply your own filtering criteria.
There is currently a slight non-uniformity in our count and TPM results, as RNASeq-er are switching between two different quantification methods. Either HTSeq (previous) or FeatureCounts (new) are used to quantify aligned reads within each study.