Evolutionary Genomics and Bioinformatics
How do processes like duplication, genomic rearrangements, and formation of novel genes shape genomes? Do these processes generate heritable differences in the phenotypes that we care about? To extend our understanding of these two questions, we combine large-scale sequencing data with statistical analysis to find the genetic basis of various traits in the nematode P. pacificus. Nematodes such as P. pacificus and C. elegans are excellent systems to study these two questions, because they are easy to maintain in the lab, have small genomes, and have a broad range of well established experimental protocols including genome editing (Witte et al. 2015, Rödelsperger 2018). Most importantly, nematodes exhibit numerous interesting morphological, developmental, and behavioral traits, of which the genetic basis and evolution is still poorly understood.
P. pacificus was among the first nematodes with a sequenced genome (Dieterich et al. 2007). Initial analysis showed that only 20% of the 20,000-30,000 P. pacificus genes have one-to-one orthologs in C. elegans. Furthermore, around one third of genes do not have homologs in any other sequenced nematode genome. Such genes are called orphan genes. Since most existing functional annotations are inferred from homologs in classical model organisms, basically no functional data exists for orphan genes. The largest fraction of all genes (45%) is composed of genes that have undergone lineage-specific duplications in either the C. elegans or the P. pacificus lineage. This demonstrates the tremendous impact of gene duplication and novel gene formation on the evolution and biology of Pristionchus nematodes. In individual cases we have shown that both classes of lineage-specific genes can control ecologically important traits and developmental decisions (Namdeo et al. 2018, Mayer et al. 2015).
How Do Novel Genes Arise?
One of our main goals is to understand the evolutionary dynamics and origin of orphan genes. We employ phylogenomics to address questions such as:
- Are orphan genes real or do they represent genomic artifacts?
- Are new genes gained and lost at a constant rate ?
- Do orphan genes evolve at a rapidly or do they experience evolutionary constraints ?
- How are orphan genes formed? Did they come from previously non-coding sequences or did they diverge so much from known protein coding genes that their homology has become undetectable?
In a first pilot study, we employed data from 14 RNA-seq experiments to show that 80% of orphan genes are expressed under standard laboratory conditions. Further, using analysis of selective constraints acting on protein coding sequences with regard to available genomic data of the sister species P. exspectatus and population scale sequencing data (Rödelsperger et al. 2014), we could show that up to 76% of orphan genes are under strong evolutionary constrained therefore represent truly protein-coding genes (Prabh and Rödelsperger. 2016). This demonstrated, that deeper taxon sampling is the key towards better understanding of the evolutionary dynamics and evolution of novel genes. Thus, we sequenced and compiled a collection of ten nematode genomes to deduce the age of novel genes based on their phylogenetic distribution, i.e. old genes are most likely shared across the entire phylogenetic range, whereas young genes may be species-specific or shared only among few genomes. Exploiting this age classification, we could contrast evolutionary processes between young and old genes. Thus, we found that new genes tend to arise at the chromosome arms, are initially only weakly expressed, evolve more rapidly, and tend to have a higher propensity of being lost (Prabh et al. 2018). Currently, we are studying how novel genes originate either by divergence from protein-coding sequences or by a de novo mechanism from non-coding sequences.
Evolution by Gene Duplication
In the preface of his visionary book “Evolution by Gene Duplication”, Susumu Ohno wrote: “Yet, being an effective policeman, natural selection is extremely conservative by nature. Had evolution been entirely dependent upon natural selection, from a bacterium only numerous forms of bacteria would have emerged. The creation of metazoans, vertebrates and finally mammals from unicellular organisms would have been quite impossible, for such big leaps in evolution required the creation of new gene loci with previously nonexistent functions.”. He postulated that only gene duplication could generate the redundancy that would allow organisms to accumulate formerly forbidden mutations. Moreover, since P. pacificus genes that have undergone lineage-specific duplications are so highly abundant, we are studying the role of gene duplication as a potential driver of phenotypic diversity. Previously, we observed that many developmental genes have undergone duplications possibly to increase the total gene dosage (Baskaran et al. 2015). However, when investigating duplication events at an intraspecies level, we found that in a majority of cases, one of the copies appears to be transcriptionally silent (Baskaran and Rödelsperger. 2015). Our basic goal is to study duplication processes at various time-scales asking the following questions:
- How does duplication affect gene dosage? Which genes can tolerate duplications?
- Are both duplicate copies equal or is there an ancestral and a daughter copy?
- Are both copies functional?
- How does duplication change evolutionary rates?
In combination with functional studies such as gene knockouts (Markov et al. 2016), these genomic analyses reveal cases of neo- and sub-functionalization and may generate hypotheses about mechanisms that facilitate the retention of duplicate copies (Sieriebriennikov et al. 2018).
How do environment and genome determine phenotypes?
The influence of environmental factors on nematode development is highlighted by the fact that depending on the availability of food, young nematode larvae either develop into adults and produce progeny or develop into long-lived dauer larvae that can disperse in order to find a more suitable environment. Pristionchus nematodes display a second developmental plasticity that allows them to develop into two different morphs, which are specialized for either bacterial or predatory feeding. Previous studies have shown that pheromones controlling both developmental decisions are derived from primary metabolism such as fatty acid and carbon metabolism, suggesting that worms convey their nutritional status to themselves as well as to the environment. We apply an integrative approach involving genomic, transcriptomic, and metabolomic data to investigate how bacterial diet influences metabolism and development in P. pacificus, showing that bacterial diet induces differences in pheromone profiles, variable fractions of predatory morphs, and also behavioral differences. Our collection of over 1000 P. pacificus strains along with the ongoing work to characterize microbiomes and isolate bacteria from Pristionchus-associated environments (Meyer et al. 2017, Akduman et al. 2018) offers a platform to ask questions like:
- How does bacterial diet influence nematode development and other traits?
- Which genes respond to changes in bacterial diet?
- How broadly conserved are these interactions across different P. pacificus isolates ?
- What is the the optimal food for P. pacificus?
Nematodes like P. pacificus and C. elegans are excellent models to study the interactions between bacteria and their hosts, because they are easy to grow using monoxenic bacterial cultures as food source. In addition, worms as well as bacteria are genetically tractable, which can provide detailed mechanistic insights into the interaction between host and bacteria and their impact on development and behavior.
Decoding the P. pacificus Genome
How to associate genes with phenotypes?
It is relatively easy to sequence a genome. However, understanding the function and biological significance of individual genes, still takes an enormous amount of experimental work. One major part of our work is to contribute to the identification of links between genotype and phenotype. In close collaboration with other scientist from our department, we work on identifying the genetic basis for various traits. This involves the analysis of whole-genome sequenced mutant strains (Kieninger et al. 2016, Serobyan et al. 2016), as well as statistical analyses of the association between genotype and phenotype based on artificial crosses (Mayer et al. 1015, Moreno et al. 2016) and population-scale resequencing data (McGaughran et al. 2016, Falcke et al. 2018). While all three approaches start with a phenotypic observation first (forward genetics), the establishment of an efficient way to knock out genes in P. pacificus allows us to apply reverse genetic approaches to test if the candidate genes that were identified based on knowledge from C. elegans, can also control a given phenotype in P. pacificus (Moreno et al. 2017, Markov et al. 2016). Characterizing the identified loci at a within-and cross-species level can give further insights into the evolution of associated traits.
Can we guess putative functions of genes based on expression profiles?
Given that for most P. pacificus genes no clear one-to-one ortholog exists in C. elegans, inference of gene function based on conservation is inherently difficult. To further characterize P. pacificus genes, we perform gene expression profiling of developmental processes (Baskaran et al. 2015), different tissues (Lightfoot et al. 2016), and varying environmental conditions (Sanghvi et al. 2016) to make first guesses of potential functions of orphan genes and to test how conserved expression profiles are between C. elegans and P. pacificus.
- Neel Prabh (PhD student / Orphan Genes)
- Praveen Baskaran (PhD student / Gene Duplication)
- Kevin Menden (Student Research Assistant / Antisense Transcription)
Rödelsperger, C., Ebbing, A., Sharma, D. R., Okumura, M., Sommer, R. J. & H. C. Korswagen (2021): Spatial transcriptomics of nematodes identifies sperm cells as a source of genomic novelty and rapid evolution. Mol. Biol. Evol., 38, 229-243.
Akduman, N., Rödelsperger, C. & Sommer, R.J. (2018): Culture-based analysis of Pristionchus-associated microbiota from beetles and figs for studying nematode-bacterial interactions. PLoS One. DOI: 10.1371/journal.pone.0198018.
Baskaran, P., Rödelsperger, C., Prabh, N., Serobyan, V., Markov, G. V., Hirsekorn, A. & Dieterich, C. (2015): Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus. BMC Evol Biology, DOI: 10.1186/s12862-015-0466-2.
Baskaran, P. & Rödelsperger, C. (2015): Microevolution of Duplications and Deletions and Their Impact on Gene Expression in the Nematode Pristionchus pacificus. PLoS One, DOI: 10.1371/journal.pone.0131136.
Baskaran, P., Jaleta, T.G., Streit, A. & Rödelsperger, C. (2017): Duplications and Positive Selection Drive the Evolution of Parasitism-Associated Gene Families in the Nematode Strongyloides papillosus. Genome Biol Evol. 9, 790-801. DOI: 10.1093/gbe/evx040.
Dieterich, C., Clifton, S.W., Schuster, L.N., Chinwalla, A., Delehaunty, K., Dinkelacker, I., Fulton, L., Fulton, R., Godfrey, J., Minx, P., Mitreva, M., Roeseler, W., Tian, H., Witte, H., Yang, S.P., Wilson, R.K. & Sommer, R.J. (2008): The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. Nat Genet. 40, 1193-8. DOI: 10.1038/ng.227.
Falcke. J.M., Bose, N., Artyukhin, A.B., Rödelsperger, C., Markov, G.V., Yim, J.J., Grimm, D., Claassen, M.H., Panda. O., Baccile, J.A., Zhang, Y.K., Le, H.H., Jolic, D., Schroeder, F.C., Sommer, R.J. (2018): Linking Genomic and Metabolomic Natural Variation Uncovers Nematode Pheromone Biosynthesis. Cell Chem Biol. 25: DOI: 10.1016/j.chembiol.2018.04.004.
Kieninger, M.R., Ivers, N.A., Rödelsperger, C., Markov, G.V., Sommer, R.J. & Ragsdale EJ (2016): The Nuclear Hormone Receptor NHR-40 Acts Downstream of the Sulfatase EUD-1 as Part of a Developmental Plasticity Switch in Pristionchus. Curr Biol. 26, 2174-9. DOI: 10.1016/j.cub.2016.06.018.
Lightfoot, J.W., Chauhan, V.M., Aylott, J.W. & Rödelsperger, C. (2016): Comparative transcriptomics of the nematode gut identifies global shifts in feeding mode and pathogen susceptibility. BMC Res Notes. 9:142, DOI: 10.1186/s13104-016-1886-9.
Mayer, M. G., Rödelsperger, C., Witte H., Riebesell, M. & Sommer, R. J. (2015): An orphan gene regulates intraspecific competition in nematodes by copy number variation. PLoS Genetics, 11, DOI: 10.1371/journal.pgen.1005146.
Markov, G.V., Meyer, J.M., Panda, O., Artyukhin, A.B., Claaßen, M., Witte, H., Schroeder, F.C. & Sommer, R.J. (2016): Functional Conservation and Divergence of daf-22 Paralogs in Pristionchus pacificus Dauer Development. Mol Biol Evol. 33, 2506-14. DOIi: 10.1093/molbev/msw090.
McGaughran, A., Rödelsperger, C., Grimm, D.G., Meyer, J.M., Moreno, E., Morgan, K., Leaver, M., Serobyan, V., Rakitsch, B., Borgwardt, K.M. & Sommer, R.J. (2016): Genomic Profiles of Diversification and Genotype-Phenotype Association in Island Nematode Lineages. Molecular Biology and Evolution, 33 (9):2257-72, DOI: 10.1093/molbev/msw093.
Meyer, J.M., Markov, G.V., Baskaran, P., Herrmann, M., Sommer, R.J., Rödelsperger, C. (2016): Draft Genome of the Scarab Beetle Oryctes borbonicus on La Réunion Island. Genome Biol Evol. 8(7):2093-105, DOI: 10.1093/gbe/evw133.
Meyer, J.M., Baskaran P., Quast C., Susoy V., Rödelsperger C., Glöckner F.O. & Sommer R.J. (2017): Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes borbonicus on La Réunion Island. Environ Microbiol. 19, 1476-1489. DOI: 10.1111/1462-2920.13697.
Moreno, E., McGaughran, A., Rödelsperger, C., Zimmer, M. & Sommer, R.J. (2016): Oxygen-induced social behaviours in Pristionchus pacificus have a distinct evolutionary history and genetic regulation from Caenorhabditis elegans. Proc Biol Sci., 283, 20152263. DOI: 10.1098/rspb.2015.2263.
Moreno, E., Sieriebriennikov, B., Witte, H., Rödelsperger, C., Lightfoot, J.W. & Sommer, R.J. Regulation of hyperoxia-induced social behaviour in Pristionchus pacificus nematodes requires a novel cilia-mediated environmental input. Sci Rep. 7, 17550. DOI: 10.1038/s41598-017-18019-0.
Namdeo, S., Moreno, E., Rödelsperger, C., Baskaran. P,, Witte, H. & Sommer, R.J. (2018): Two independent sulfation processes regulate mouth-form plasticity in the nematode Pristionchus pacificus. Development. 145. DOI: 10.1242/dev.166272.
Prabh,N. & Rödelsperger, C. (2016): Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs? BMC Bioinformatics. 17, 226, DOI: 10.1186/s12859-016-1102-x.
Prabh, N. Röseler, W., Witte, H., Eberhardt, G., Sommer, R.J. & Rödelsperger C. 2018: Deep taxon sampling reveals the evolutionary dynamics of novel gene families in Pristionchus nematodes. Genome Research. DOI: 10.1101/gr.234971.118.
Rödelsperger, C., Streit, A., Sommer, R. J. (2013): Structure, function and evolution of the nematode genome. In: eLS. Chichester: John Wiley & Sons, Ltd., DOI: 10.1002/9780470015902.a0024603.
Rödelsperger, C., Neher, R. A., Weller, A., Eberhardt, G., Witte, H., Mayer, W., Dieterich, C. & Sommer, R. J. (2014): Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data. Genetics, 196, 1153-1165.
Rödelsperger, C., Menden, K., Serobyan, V., Witte, H. & Baskaran, P. (2016): First insights into the nature and evolution of antisense transcription in nematodes. BMC Evol. Biol., 16: 165. DOI: 10.1186/s12862-016-0740-y
Rödelsperger, C., Meyer, J.M., Prabh, N., Lanz, C., Bemm, F. & Sommer, R.J. (2017): Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus. Cell Rep. 21, 834-844. DOI: 10.1016/j.celrep.2017.09.077.
Rödelsperger, C. (2018): Comparative Genomics of Gene Loss and Gain in Caenorhabditis and Other Nematodes. Methods Mol Biol. 1704, 419-432. DOI: 10.1007/978-1-4939-7463-4_16.
Rödelsperger, C., Röseler, W., Prabh, N., Yoshida K., Weiler C., Herrmann M. & Sommer R.J. (2018): Phylotranscriptomics of Pristionchus Nematodes Reveals Parallel Gene Loss in Six Hermaphroditic Lineages. Current Biology. 28. DOI: 10.1016/j.cub.2018.07.041
Sanghvi, G.V., Baskaran, P., Röseler, W., Sieriebriennikov, B., Rödelsperger, C., Sommer, R.J. (2016): Life History Responses and Gene Expression Profiles of the Nematode Pristionchus pacificus Cultured on Cryptococcus Yeasts. PLoS One. 11. DOI: 10.1371/journal.pone.0164881.
Serobyan, V., Xiao, H., Namdeo, S., Rödelsperger, C., Sieriebriennikov, B., Witte, H., Röseler, W. & Sommer, R.J. (2016): Chromatin remodelling and antisense-mediated up-regulation of the developmental switch gene eud-1 control predatory feeding plasticity. Nat Commun. 7, 12337. DOI: 10.1038/ncomms12337.
Sieriebriennikov, B., Prabh, N., Dardiry, M., Witte, H., Röseler, W., Kieninger, M.R., Rödelsperger, C. & Sommer, R.J. (2018): A Developmental Switch Generating Phenotypic Plasticity Is Part of a Conserved Multi-gene Locus. Cell Rep. 23, 2835-2843. DOI: 10.1016/j.celrep.2018.05.008.
Witte, H., Moreno, E., Rödelsperger, C., Kim, J., Kim, J.-S., Streit A. & Sommer, R. J. (2015): Gene inactivation using the CRISPR/Cas9 system in the nematode Pristionchus pacificus. Dev Genes & Evol., 225, 55-62.