Retrogenomic software and databases to solve evolutionary questions
Evolutionary Cell and Developmental Biology (Zoology)
Final Report Abstract
Over the last two decades, my group has been significantly involved in the development of the phylogenetic retrotransposon marker system, whereby interspecies comparisons of the presence/absence patterns of retrotransposons are fundamental to determining their evolutionary relationships to one another. With the current proliferation in genome sequencing projects and technologies, this marker system not only contributed to a new retrophylogenomic era, but also experienced new challenges. How does one exhaustively and unbiasedly extract phylogenomically informative transposed elements in a reasonable time? Furthermore, how do interested scientists keep up with this exceptional marker system at the multi-genome level without bioinformatics experience or high-end technical equipment? The answer is "2-n-way" and its associated tools. This user-friendly webapplication automatically generates multiple 2-way alignments and uses and compares combinations of them to extract an unlimited number of orthologous locations, and when pre-aligned with LAST or LASTZ and optimized via MUSCLE, does so in a few hours. Data that were generated during the development of 2-n-way provided, for example, insights into the evolution and demography of the extinct marsupial Tasmanian tiger and examined the true homoplasy of retrotransposon insertions in primates. To further evaluate the significance of genome-scale presence/absence data, we also developed novel computational tools that differentiate incomplete lineage sorting and ancestral hybridization, processes that contribute to confounding phylogenetic signals. The tools are currently being applied in several international genome projects and have generated data for many associated studies. The project produced a network of server-based applications and a set of analytical methods that are freely available and can be straightforwardly utilized by interested scientists, including students. We are currently integrating a statistical algorithm into the 2-n-way package that will automatically evaluate the resulting diagnostic markers for their significance in determining evolutionary relationships. The tools will be continually curated by our research group at the ZMBE in Münster and will deliver the initial cornerstone for an international computational competence center for presence/absence studies, including functional aspects such as exon gain or intron-loss. Currently, we are also integrating the Nanopore sequencing techniques (MinION genome and transcriptome analyses) so as to apply 2-n-way to many non-model organisms in retrophylogenomics and other functional and population genetics topics.
Publications
- Speciation network in Laurasiatheria: retrophylogenomic signals. Genome Res 27:997-1003, 2017
Churakov G, Zhang F, Grundmann N, Makalowski W, Noll A, Doronina L, Schmitz J
(See online at https://doi.org/10.1101/gr.210948.116) - The beaver’s phylogenetic lineage illuminated by retroposon reads. Sci Rep 7:43562, 2017
Doronina L, Matzke A, Churakov G, Stoll M, Huge A, Schmitz J
(See online at https://doi.org/10.1038/srep43562) - Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore. Nat Ecol & Evol, 2:182-192, 2018
Feigin CY, Newton AH, Doronina L, Schmitz J, Hipsley CA, Mitchell KJ, Gower G, Llamas B, Soubrier J, Heider TN, Menzies BR, Cooper A, O’Neill RJ, Pask AJ
(See online at https://doi.org/10.1038/s41559-017-0417-y) - The volcano rabbit in the phylogenetic network of lagomorphs. Genome Biol Evol 11:11-16, 2018
Doronina L, Churakov G, Shi J, Baertsch R, Clawson H, Schmitz J
(See online at https://doi.org/10.1093/gbe/evy257) - True homoplasy of retrotransposon insertions in primates. Sys Biol, 63:482-493, 2019
Doronina L, Reising O, Clawson H, Ray D, Schmitz J
(See online at https://doi.org/10.1093/sysbio/syy076) - The multi-comparative 2-n-way genome suite. Genome Res, 2020
Churakov G, Zhang F, Grundmann N, Makalowski W, Noll A, Doronina L, Schmitz J
(See online at https://doi.org/10.1101/gr.262261.120)
