After we got the Heliconius melpomene genome, I thought it’d be easy to find out about one’s favourite gene on our genome browser or on ENSEMBL. Unfortunately, orthologous gene names for Heliconius don’t seem to have made it through to the public databases.
However, I recently went to a talk by Rob Waterhouse, who runs a website called OrthDB which classifies genes into orthologous groups. http://www.orthodb.org/ This provides one method for finding a Heliconius gene by name. OrthoDB obtained the Heliconius melpomene data from ENSEMBL, and then classified them into their orthologous groups, so you can search for gene names really easily there, and easily find genes, gene names, and their synonyms used in related species.
In the course of his work incorporating the Heliconius genome into OrthoDB, Rob Waterhouse also ran an analysis to find orthologous gene groups that really should be in the Heliconius genome (on the basis that they’re in most other related species), but that were not found by the method Jamie Walters used to annotate the genome, Maker. He forwarded this list to Jamie, but I don’t think any use was made of it. As he’s shared it with me too, I thought I’d make it public for those who are interested. I’ve attached it here.
Copy of HMELP.missing.orthologues
nice, OrthoDB has been quite useful for us, in our search of novel genes for Nymphalidae butterflies that we can use for making phylogenies.
We created some software to harvest data from OrthoDB. We have a very simple script for filtering by species or gene name.
This is cool, Carlos! This should be really useful. Question, if we want to test for GOs of a subset of genes in a little known genome, say Heliconius, how would we go about this using (perhaps) OrthoDB and the Heliconius Genome Consortium data?
Certainly PyPhyloGenomics can be used to find those “lost genes” in the H. melpomene genome.
From your list of genes, I see that many can be found in the Bombyx mori CDS and genome files.
Pseudocode using PyPhyloGenomics to do the job:
> extract geneIDS of B. mori, those starting with "BGIBMGA"
> use these IDs to pull the CDS sequences from silkcds.fa
> BLAST these CDS sequences against the Heliconius_melpomene_genomev2.fas
> parse the output BLAST table
> pull out the matching sequences from the Heliconius genome
I can work out the real code and let you know about the results if you want.
Hi friends, I m a PhD student in the University of Costa Rica and I will be working with Heliconius cydno, sapho and sara genomics. I have a question… Have any of you the paper where H, cydno and H. pachinus are synonymized? As well as H. sapho and H. hewitsony. I really need access to that paper because I am studying gene introgression!
Thanks for you valuable help!
The reference you’re seeking is:
Lamas, G., C. Callaghan, M. M. Casagrande, O. Mielke, T. Pyrcz, R. Robbins and A. Viloria. 2004. Hesperioidea – Papilionoidea. Association for Tropical Lepidoptera/Scientific Publishers, Gainesville, Florida.
The complete checklist can be viewed here:
and is accessed from this page:
However, I should say that most Heliconius workers continue using H. pachinus and H. hewitsoni as good species, in part because they are really distinctive. The Pacific slope H. pachinus for example is partially reproductively isolated from H. cydno galanthus on the Atlantic side of Costa Rica (M. Kronforst and Larry Gilbert) and is therefore perhaps a semi-species or good species.
These species delimitations are justified in part by using what Neil Rosser and I call the “relaxed biological species” definition, meaning that some hybridization is allowed in sympatry. This seems necessary because many species exchange genes with closely related species, albeit occasionally. For details of Rosser et al.’s modification of Lamas’s checklist, see:
Rosser N, Phillimore AB, Huertas B, Willmott KR, & Mallet J. 2012. Testing historical explanations for gradients in species richness in heliconiine butterflies of tropical America. Biological Journal of the Linnean Society 105: 479-497. DOI: 10.1111/j.1095-8312.2011.01814.x
I’ve realized that the suggested changes from Lamas 2004 we made in the Rosser et al. 2012 paper are not easily accessible. They are available as Table 1 in the 44 MB supplementary information word document at:
or as a 29 MB PDF at:
I’m sorry, we really need to make all this sort of stuff clearer in future.
Hi, what a surprise! You must be Jim Mallet, aren’t you? We met last year in San José, Costa Rica in a dinner with Larry Gilbert and others, do you remember me? I talked with you while we were waiting to pay the bill. Thank you very much for your answer! In fact I believe there is not a formal paper which support the thesis of H. cydno and H. pachinus been the same species and to H. sapho and H. hewitsony am I wrong? I am now in my PhD. Thesis and I will look for some DNA evidence, either way they are the same or not! I have to see the results first! What do you think?? I m very excited with this project and if it is OK with you I will be asking you for advices! Thanks again… Luis Ricardo Murillo Hiller
I think I didn’t answer this. I don’t really care whether pachinus and cydno are the same or different species. There’s really too little overlap zone (it would today be somewhere near downtown San Jose!) to use the “bimodal hybrid zone” argument of Jiggins et al. 1996 pp 233-4 (http://www.ucl.ac.uk/taxome/jim/pap/jig96.pdf) or Jiggins & Mallet 2000). Similarly, I don’t think there’s any known overlap between sapho and hewitsoni. Lamas 2004 lumped them, but the tradition among Heliconiologists is to keep them separate because the “look different enough”, and might be expected to maintain integrity if they were to come into sympatry. If you use a phylogenetic definition and can find some mtDNA differences, then you might call them different species, but I don’t think you can rule out simple isolation by distance as an explanation.