Combining UCEs and transcriptomes

Phylogenomic methods are incredibly popular, and there are various baits and probes for capturing different pieces of the insect genome for analysis. One of the next aspects of 'big data' will be to develop ways to combine all of these sources!

My previous post covered a method for visualizing data on tree tips -- specifically I showed a plot of the number of loci recovered after doing a quick combination of genomes, transcriptomes, and UCEs (using the Phyluce pipeline). I'm happy to write that our research paper on the combination of phylogenomic data has been published in Molecular Phylogenetics and Evolution. Bossert et al. 2019 report successful results when three types of datasets are combined for Apidae (the largest bee family).

Bossert et al. figure 1. Graphical summary of the workflow developed for combining genome, transcriptome, and UCE data, exemplified for the widely shared HIPK2 gene of the honey bee.

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Summary figure of the phylogeny of the bee family Apidae. The topology was in agreement with many of the previously published higher-level groupings. Despite widespread acknowledgement of a non-monophyletic Apinae, no taxonomic changes were proposed until now. Find the revised Apidae classification in Appendix A!

The trick to getting the transcriptomes to align without an excessive amount of error was to use the available genomes as a backbone. A transcriptome of the same length as a UCE in reality covers a longer region of the genome due to the fact that introns are excluded in these coding regions. By grabbing a long piece of the genome, exons at the ends of the transcriptome fragments could 'stretch out' and would not be misaligned with the ends of the UCEs.

Around the time our work came out, another group published a paper with a similar objective, using the Hemiptera UCE probe set. These authors had an alternative approach to combining transcriptomes and UCEs -- using  tblastx to search for homologous loci of UCEs in transcriptomes.

references:
Bossert, S., Murray, E.A., Almeida, E.A.B., Brady, S.G., Blaimer, B.B. & Danforth, B.N. (2019) Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae. Molecular Phylogenetics and Evolution, 130, 121-131. doi.org/10.1016/j.ympev.2018.10.012 
Kieran, T.J., Gordon, E.R., Forthman, M., Hoey-Chamberlain, R., Kimball, R.T., Faircloth, B.C., Weirauch, C. and Glenn, T.C. (2019) Insight from an ultraconserved element bait set designed for Hemipteran phylogenetics integrated with genomic resources. Molecular Phylogenetics and Evolution, 130, 297-303.