On identifiers from external databases and past releases

In release 11 we have updated a number of genomes, among them Schistosoma mansoni. The authors of the new S. mansoni annotation preserved identifiers where genes were unchanged, and otherwise assigned new identifiers. They kept a list of changes – updates, splits and merges – between the two versions, available here in full.

We have now imported this list into WormBase ParaSite. So, some genes will contain a note about the old identifier under “external references”, and you can also search by an old identifier and retrieve the new one.

Annotation authors do not always try to preserve gene identifiers, and e.g. in our other recent updates of H. contortus and F. hepatica, the identifiers are all new. We would like to describe a number of strategies that can be used to reach desired content in such cases, and go through a worked example.

Our search facility is best at suggesting and retrieving our gene identifiers e.g. WBGene00001135 and gene families e.g. hedgehog but will also retrieve a number of different identifiers from e.g. UniProt or GenBank. Do try it first, and let us know if the search is not returning something you would expect it to bring back.

FTP dumps from previous releases

Our Downloads section contains a link to our FTP site, with data for all previous releases of WormBase ParaSite. If all you require is e.g. a protein sequence for an old identifier, you are done – otherwise, you can use the sequence to search further.

BLAST

Given any sequence, you can retrieve a corresponding identifier by BLAST – perfect or near-perfect alignment across a large substring is almost always the right hit. Of course you might also find that your gene of interest has multiple copies, has been split in two in the new annotation, etc.

Other websites 🙂

Going through the UniProt search frequently gives good results when searching for gene families, and you might want to try the BLAST service at ENA or UniProt as an alternative to our BLAST.
We aim for you to able to retrieve all the data you need from WormBase ParaSite, but using multiple resources is very pragmatic and frequently optimal, and thus with every release, we reconcile our identifiers with a number of external sources. This process lets our gene pages link to corresponding pages in another resources in the External references section. To find a relevant WormBase ParaSite page given e.g. an INSDC or UniProt ID, you can use the previously described search facility.

Exonerate

Exonerate is a very fast tool for sequence alignment. It could come in handy if you need to achieve similar results to our online BLAST for a few hundred anonymous sequences. We hope you will not have to resort to it!

Example

Chalmers et al (2015) have identified ten tegumental surface proteins in S.mansoni as important in understanding the host immune response to adult schistosomes. Two of the ten genes – Smp_081920 and Smp_158960 – are absent from the new annotation.

Smp_158960 turns up in search results under a different identifier – it is now Smp_345020. Looking in the External references table reveals that Smp_158960 is the only previous identifier for Smp_345020, and checking view all locations link reveals that Smp_345020 is the only gene annotated with Smp_158960 as a previous identifier, so the mapping is one to one. We can guess that authors modified the gene structure and decided to give the gene a new identifier.

Searching Smp_081920 doesn’t return anything in search, and it took me a bit of time to figure out what happened.
I knew I could get the sequence from the FTP site, but it saved me some effort to discover that the identifier is still hanging on in UniProt, which gave me the protein sequence.
I have then used BLASTP, which gave me a full match with Smp_166350 on about 100bp: long enough for me to potentially trust but perhaps omitted by authors reconciling old and new identifiers.
I got certain I am looking at the same gene after comparing the exon structure of Smp_166350 with the structure of Smp_081920, conveniently still online at our friends’ place, Ensembl Metazoa. The two are very similar, except Smp_166350 has three additional non-coding exons.

I was skeptical of these non-coding exons and wanted to see some expression evidence for them.
I opened the JBrowse display in ParaSite and enabled some tracks across a few studies and developmental stages, and my skepticism grew. I saw high peaks in three non-coding exons and no reads aligned to what is claimed to be the coding region in tracks for cercariae and juveniles. Then, in tracks for adult worms but also in a track for miracidia, I saw the opposite: reads in the coding region, and no expression for that UTR.

My conclusion from this data would be that the gene Smp_081920 is now Smp_166350, but the structure of Smp_166350 is not completely correct: the UTRs are spurious, and they probably make another gene instead. I have submitted this conclusion to the annotation authors – it will be corrected in future versions of the annotation.

 

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Announcing WormBase ParaSite 11

We are pleased to announce the 11th release of WormBase ParaSite. We have added data, new functionality, and improved some of our per-release processes. Quite a few genomes are new or have been significantly updated.

Comments in ParaSite

By popular request we have added a comment-like space to our gene pages. You can mention your own results, point out an inconsistency, or make an observation about displayed data. We hope the comments will be of scientific content, even when taking a lighter form than communication through peer-reviewed journals.

New species and updates

We are updating three flatworm genomes:

The new assembly of S. mansoni is very complete and accurate, and the gene models were manually annotated over the course of several months.

This is the list of our new or updated nematode genomes:

Parasites:

Free-living:

We are also publishing a fix from the authors to their annotation of Ascaris suum and Parascaris univalens. The gene models submitted to us in the previous release suffered from a systematic error, which resulted in much shorter proteins. We regret the error.

Additionally, the release includes genomes from the WS265 release of WormBase, including the newest WormBase core species, Trichuris muris.

In total 17 genomes were added or changed, bringing the total to 148 genomes across 124 species.

Analyses

We ran all our usual tertiary annotation pipelines that identify repeats, low complexity regions, non-coding RNAs, protein domains, predicted GO terms, and more, as well as our comparative genomics pipeline, where we expect an improvement especially around recently updated branches.

We have revisited our cross-references pipeline. This pipeline lets us support discovery of what is currently known about each gene, and provide rich descriptions, through inferring links between our genes and entities from other resources. We have updated these cross-references for all our genomes, and added new references: to UniParc and RNAcentral. You can either find these references on the gene pages, or use BioMart to retrieve them in bulk.

RNASeq data

We have configured our JBrowse track displays to include tracks with aligned reads produced by the RNASeq-er project. RNASeq-er processes all RNASeq datasets published in ENA, so there are many tracks to choose from: currently 11735, from 492 studies across 74 species.

Use case 1 : discover public datasets

Browsing our displays could be an alternative to searching a primary source like the European Nucleotide Archive, benefiting from an additional filter: they include  only the runs that RNASeq-er successfully aligned and passed through QC.

For more than half the species, the only RNASeq data available is what was produced while preparing the genome.

For other species, there have been additional studies, for example see the JBrowse display of tapeworm Echinococcus multilocularis. Apart from a few studies from the same lab in the United Kingdom where the genome was sequenced, the display contains runs sequenced in China and Japan as part of BioProjects PRJNA254535 and PRJDB3524.

The WormBase ParaSite species with most RNASeq data present is unsurprisingly C. elegans, with 6446 runs across 245 studies.

Use case 2 : compare expression across tracks

Consider the gene Smp_169190 in Schistosoma mansoni. Lu et al (2018, preprint) compared expression in developmental stages, and found Smp_169190 to be differentially expressed in the cercarial life stage.

This link here  takes you to two of the tracks used in Lu et al’s metaanalysis. These are ERR022872, showing RNA sequenced from cercaria, and a track ERR506086, with RNA sequenced from an an adult worm. The two tracks differ in expression dramatically in gene Smp_169190.

You can also see the expression in other life stages. A search for “cercaria” shows quite a few tracks, that will probably be similar to ERR022872. Similar search for “miracidia” yields a track SRR922067 and an interesting result: miracidia don’t express Smp_169190, but there is high expression for two of the nearby TAL genes.

Genomes we don’t have in WormBase ParaSite

The work on the version 11 of WormBase ParaSite is ongoing! We now have a list of assemblies of new species, and improved genomes of existing species, that we plan to publish. As well as including data submitted to us directly, we also surveyed the archives and have made an effort to include all assemblies of taxa Nematoda and Platyhelminthes  available in NCBI and ENA that have been annotated with gene structures.

We seem to be doing well in our attempts to reflect the sequencing efforts of relatives of Caenorhabdhitis elegans – the order Rhabditida makes up 43 of our 100 Nematoda genomes. This good coverage seems to extend to other nematodes relevant to answering basic biology questions, for nematodes causing disease in humans and livestock, and for parasites of plants.

The situation is very different for our other phylum of interest, Platyhelminthes, which is more diverse, and has historically been harder for biologists to study due to complex life cycles of these animals. The phylum doesn’t have a clear model organism like C. elegans, but many species, like the flukes F. hepatica and S. mansoni, are subject to active research.

In particular, phylum Platyhelminthes has a class Turbellaria of free-living marine worms, full of ancient, evolutionarily unique and remarkable organisms, like this Pseudobiceros bedfordi : a large colorful flatworm that feeds on ascidians and small crustaceans.

 

Some species of this class are studied due to their unusual properties. We are tracking research in the area, and currently have two genomes of TurbellariaMacrostomum lignano and Schmidtea mediterranea.

M.lignano is a tiny worm living in shore sands of Adriatic sea, and is used as a model organism for a number of evolutionary studies. We’ll be publishing an update to this genome, sequenced in 2017 by University Medical Center Groningen.

S. mediterranea is a freshwater species, important for research in stem cells and regeneration. ParaSite currently hosts the original published version of the Schmidtea genome, from 2014. Another group has since published  a new and improved assembly. We are hopeful that the authors will annotate this version of the genome with gene structures soon, so that we can include it in ParaSite.

Do reach out to us if you have a potential submission, know of a published genome that could be included in ParaSite, or to tell us about ongoing research about Nematoda or Platyhelminthes that should be on our radar.

Announcing WormBase ParaSite 10

We are pleased to announce the tenth release of WormBase ParaSite. We have included genomes of four new species, bringing the total number of genomes to 138, representing 118 distinct species, and updated the assemblies or annotations of an additional four. This includes results of recent efforts to sequence Ascaridae genomes (Wang et al, 2017): a much improved assembly of Ascaris suum, with an N50 of 4.6Mb up from 290.6kb, and a newly sequenced Parascaris univalens. The other three new genomes are of particular interest to the study of nematode reproduction. These are two species of the genus Diploscapter, D. coronatus (Hiraki et al, 2017) and D. pachys (Fradin et al, 2017), which have managed to stay adaptable and maintain genetic variation throughout their long evolutionary history as parasites; and the free-living Caenorhabditis nigoni (Yin et al, 2018), a parthenogenic cousin of hermaphroditic C. briggsae.

The assembly and annotation of Echinococcus canadensis are now in line with the paper introducing the genome (Maldonado et al, 2017). We also have included a tidy-up update of the assembly of Schistosoma haematobium. For the WormBase core species, we have updated the annotations to WS263. As with each release, we have updated our comparative genomics data – recalculating the orthologues and paralogues for all species – and the protein features pipeline, annotating genes with protein domains and inferred GO terms using the latest version InterProScan.

What would you like to learn about in our BSP workshop?

We’re looking forward to presenting a workshop at the upcoming BSP Spring meeting in Aberystwyth. To help us prepare, we’d love to know what our users would find most useful for us to cover. Please fill in our quick survey (one question only!): https://www.surveymonkey.co.uk/r/8LYF2YW

 

Announcing WormBase ParaSite Release 9

We are pleased to announce the ninth release of WormBase ParaSite.  In this release, we have included genomes for two new species (Ditylenchus destructor – PRJNA312427 and Taenia saginata – PRJNA71493) and an additional alternative genome for one species (Taenia asiatica – PRJNA299871).  This brings the total number of genomes to 134, representing 114 species.  Additionally, all WormBase core species have been updated to release WS258.

As part of this release, we have introduced a new genome browser: JBrowse (example for S. mansoni).  This offers a fast and interactive experience for all genomes.  Custom tracks can be attached directly from a local computer, without needing to upload any data.  This makes JBrowse ideal for visualising large data files, without the need to download or install any additional software.  Other features include combination tracks for visualising multiple files as a single track, and sequence search tracks for locating short sequence motifs within the genome.

Parasitic Nematodes: Bridging the Divide workshop abstract solicitation

As part of the 21st International C.elegans conference, we would like to solicit contributions to the workshop on parasitic nematodes.

We are pleased to invite student and postdoc abstract submissions for 5 minute lightning talks to be presented at the NSF-sponsored, 3rd Parasitic Nematodes: Bridging the Divide workshop. We encourage submissions that address the broad theme of C. elegans as a model for parasitic nematode biology, including work relating to human, animal, and plant parasitic nematodes and from both a basic biology standpoint or a translational perspective. The platform provided by this workshop represents a unique opportunity for early-career scientists to interact with other researchers at the intersection of C. elegans biology and parasitology. These five minute talks will be presented on the first day of the 21st International C. elegans Meeting. The presenting authors must be available during any of the limited number of possible time slots available. Abstract submissions are due on May 12th at 5pm PST and presenting authors will be notified of decisions by May 19th. Instructions for logistics and formatting of lightning talk presentations will follow acceptance.

Abstract Format: Abstracts should be limited to 2,500 characters in total, including the title, authors, author affiliations, main body, and spaces. Abstracts should be sent to the workshop e-mail address (parasiteworkshop@gmail.com) as a single PDF file with subject heading “Lightning Talk Abstract”. A notification of receipt will follow submission. Accepted abstracts will appear online in a Worm Breeder’s Gazette article and titles will be listed on the International Worm Meeting website.

Workshop Date: Wednesday, June 21, 2017
Workshop Time: 2:30pm- 5:30pm
Workshop Location: Sunset Village Grand Horizon Ballroom

Lightning Talk Abstract Submission Deadline: May 12, 2017 (5pm PST)
Notification of Acceptance: May 19, 2017