Abstract
The model organism Pristionchus pacificus and the genus Pristionchus, Kreis, 1932 have been intensively studied in the last decade with contemporary work focusing on the development, evolution, ecology, behavior, neurobiology, and genomics of this group of organisms. In particular, mechanistic studies on the development and evolution of mouth-form plasticity, predation and associated self-recognition processes enabled unique insight into life history strategies and the evolution of novelty. These studies include a comparative research agenda making use of the 39 available species of Pristionchus, all of which can be studied in living cultures. Sampling efforts revealed that Asia represents a biodiversity hotspot for Pristionchus worms. However, previous samplings have a bias towards northern and island areas, largely for logistic reasons. Here, we report on two extensive sampling trips to the Yunnan and Shaanxi provinces in Mainland China. We report the isolation of nine new Pristionchus species by morphology, morphometrics, mating experiments and genome-wide sequence analysis.
References
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 Evolutionary Biology, 15, 185.
https://doi.org/10.1186/s12862-015-0466-2
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. Nature Genetics, 40, 1193–1198.
https://doi.org/10.1038/ng.227
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792–1797.
https://doi.org/10.1093/nar/gkh340
Ekseth, O.K., Kuiper M. & Mironov, V. (2014) orthAgogue: an agile tool for the rapid prediction or orthology relations. Bioinformatics, 30, 734–736.
https://doi.org/10.1093/bioinformatics/btt582
Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B.W., Nusbaum, C., Lindblad-Toh, K., Friedman, N. & Regev, A. (2011) Full length transcriptomics assembly from RNA-seq data without a reference genome. Nature Biotechnology, 29, 644–652.
https://doi.org/10.1038/nbt.1883
Herrmann, M., Mayer, W.E. & Sommer, R.J. (2006a) Nematodes of the genus Pristionchus are closely associated with scarab beetles and the Colorado potato beetle in Western Europe. Zoology, 109, 96–108.
https://doi.org/10.1016/j.zool.2006.03.001
Herrmann, M., Mayer, W.E. & Sommer, R.J. (2006b) Sex, bugs and Haldane’s rule: the nematode genus Pristionchus in the United States. Frontiers in Zoology, 3, 14.
https://doi.org/10.1186/1742-9994-3-14
Herrmann, M., Mayer, W.E., Hong, R.L., Kienle, S., Minasaki, R. & Sommer, R.J. (2007) The nematode Pristionchus pacificus (Nematoda: Diplogastridae) is associated with the Oriental beetle Exomala orientalis (Coleoptera: Scarabaeidae) in Japan. Zoological Science, 24, 883–889.
https://doi.org/10.2108/zsj.24.883
Herrmann, M., Weiler, C., Rödelsperger, C., Kanzaki, N. & Sommer, R.J. (2016) Two new Pristionchus species (Nematoda: Diplogastridae) from Taiwan are part of a species-cluster representing the closest known relatives of the model organism P. pacificus. Zoological Studies, 55, 48.
https://doi.org/10.6620/ZS.2016.55-48
Herrmann, M., Kanzaki, N., Weiler, C., Yoshida, K., Rödelsperger, C. & Sommer, R.J. (2019) Two new Species of Pristionchus (Nematoda: Diplogastridae) include the Gonochoristic Sister Species of P. fissidentatus. Journal of Nematology, 51, 1–14.
https://doi.org/10.21307/jofnem-2019-024
Hooper, D.J. (1986) Handling, fixing, staining and mounting nematodes. In: Southey, J.F. (Ed.), Laboratory methods for work with plant and soil nematodes. Her Majesty’s Stationally Office, London, pp. 59–80.
Kanzaki, N. (2013) Simple methods for morphological observation of nematodes. Nematological Research, 43, 15–17.
https://doi.org/10.3725/jjn.43.15
Kanzaki, N. & Giblin-Davis, R.M. (2015) Diplogastrid systematics and phylogeny. In: Sommer, R.J. (Ed.), Pristionchus pacificus—a nematode model for comparative and evolutionary biology Brill, Leiden. pp.43–76.
https://doi.org/10.1163/9789004260306_004
Kanzaki, N., Ragsdale, E., Herrmann, M. & Sommer, R.J. (2012a) Two new species of Pristionchus (Rhabditida: Diplogastridae) P. fissidentatus n. sp. from Nepal and La Réunion island and P. elegans n. sp. from Japan. Journal of Nematology, 44, 80–90. [PMC free article, PubMed, Google Scholar]
Kanzaki, N., Ragsdale, E. J., Herrmann, M., Mayer, W.E. & Sommer, R.J. (2012b) Description of three Pristionchus species (Nematoda: Diplogastridae) from Japan that form a cryptic species complex with the model organism P. pacificus. Zoological Science, 29, 403–417.
https://doi.org/10.2108/zsj.29.403
Kanzaki, N., Ragsdale, E.J., Herrmann, M., Mayer, W.E., Tanaka, R. & Sommer, R.J. (2012c) Parapristionchus giblindavisi n. gen., n. sp. (Rhabditida: Diplogastridae) isolated from stag beetles (Coleoptera: Lucanidae) in Japan. Nematology,14: 933–947.
https://doi.org/10.1163/156854112X635878
Kanzaki, N., Ragsdale, E.J., Herrmann, M., Röseler, W. & Sommer, R.J. (2013a) Two new species of Pristionchus (Nematoda: Diplogastridae) support the biogeographic importance of Japan for the evolution of the genus Pristionchus and the model system P. pacificus. Zoological Science, 30, 680–692.
https://doi.org/10.2108/zsj.30.680
Kanzaki, N., Ragsdale, E.J., Herrmann, M., Roeseler, W. & Sommer, R.J. (2013b) Pristionchus bucculentus n. sp. (Rhabditida: Diplogastridae) isolated from a shining mushroom beetle (Coleoptera: Scaphidiidae) in Hokkaido, Japan. Journal of Nematology, 45, 78–86.
Kanzaki, N., Ragsdale, E.J., Herrmann, M., Susoy, V., & Sommer, R.J. (2013c) Two androdioecious and one dioecious new species of Pristionchus (Nematoda: Diplogastridae): new reference points for the evolution of reproductive mode. Journal of Nematology, 45, 172–194.
Kanzaki, N., Ragsdale, E.J., Herrmann, M., & Sommer, R.J. (2014) Two new and two recharacterized species resulting from a radiation of Pristionchus (Nematoda: Diplogastridae) in Europe. Journal of Nematology, 46, 60–74.
Kanzaki, N., Herrmann, M., Yoshida ,K., Weiler, C., Rödelsperger, C. & Sommer, R.J. (2018) Samplings of Millipedes in Japan and Scarab Beetles in Hong Kong result in five new Species of Pristionchus (Nematoda: Diplogastridae). Journal of Nematology, 50, 4.
https://doi.org/10.21307/jofnem-2018-044
Kreis, H.A. (1932) Beiträge zur Kenntnis pflanzenparasitischer Nematoden. Zeitschrift für Parasitenkunde, 5, 184–194.
https://doi.org/10.1007/BF02120641
Li, P., Dai, C., Bao, H., Chen, L., Gao, D., Wang, G., Wang, J., Wang, H., Yedid, G. & Zhang, K. (2015) A new species of Pristionchus (Rhabditida: Diplogastridae) and its bacterial symbiont from Yixing, China. Journal of Nematology, 47, 190–197.
Morgan, K., McGaughran, A., Villate, L., Herrmann, M., Witte, H., Bartelmes, G., Rochat, J. & Sommer, R.J. (2012) Multi locus analysis of Pristionchus pacificus on La Réunion Island reveals an evolutionary history shaped by multiple introductions, constrained dispersal events and rare out-crossing. Molecular Ecology, 21, 250–266.
https://doi.org/10.1111/j.1365-294X.2011.05382.x
Ragsdale, E., Kanzaki, N., Roeseler, W., Herrmann, M. & Sommer, R.J. (2013) Three new species of Pristionchus (Nematoda: Diplogastridae) show morphological divergence through evolutionary intermediates of a novel feeding polymorphism. Zoological Journal of the Linnean Society, 168, 671–698.
https://doi.org/10.1111/zoj.12041
Ragsdale, E.J., Kanzaki, N. & Herrmann, M. (2015) Taxonomy and natural history: the genus Pristionchus. In: Sommer, R.J. (Ed.), Pristionchus pacificus—a nematode model for comparative and evolutionary biology. Brill, Leiden, pp. 77–120.
https://doi.org/10.1163/9789004260306_005
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 Reports, 21, 834–844.
https://doi.org/10.1016/j.celrep.2017.09.077
Rödelsperger, C., Röseler, W., Prabh, N., Yoshida, K., Weiler, C., Herrmann, M. & Sommer, R.J. (2018) Phylotransciptomics of Pristionchus nematodes reveals parallel gene loss in six hermaphroditic lineages. Current Biology, 28: 3123–3127.
https://doi.org/10.1016/j.cub.2018.07.041
Schlager, B., Wang, X., Braach, G. & Sommer, R.J. (2009) Molecular cloning of a dominant roller mutant and establishment of DNA-mediated transformation in the nematode model Pristionchus pacificus. Genesis, 47, 300–304.
https://doi.org/10.1002/dvg.20499
Sommer, R.J. (2009) The future of evo-devo: model systems and evolutionary theory. Nature Revue Genetics, 10, 416–422.
https://doi.org/10.1038/nrg2567
Sommer, R.J. (2015) Integrative evolutionary biology and mechanistic approaches in comparative biology. In: Sommer, R.J. (Ed.), Pristionchus pacificus—a nematode model for comparative and evolutionary biology. Brill, Leiden, pp. 19–41.
https://doi.org/10.1163/9789004260306_003
Sommer, R.J., Carta, L.K., Kim, S.Y. & Sternberg, P.W. (1996) Morphological, genetic and molecular description of Pristionchus pacificus n. sp. (Nematoda: Neodiplogastridae). Fundamental and Applied Nematology, 19, 511–521.
Sommer, R.J., Dardiry, M., Lenuzzi, M., Namdeo, S., Renahan, T., Sieriebriennikov, B. & Werner, M. (2017) The genetics of phenotypic plasticity in nematode feeding structures. Open Biology, 7, 160332.
https://doi.org/10.1098/rsob.160332
Stamatakis, A. (2014) RaxML version 8: atool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313.
https://doi.org/10.1093/bioinformatics/btu033
Sudhaus, W. & Fürst von Lieven, A. (2003) A phylogenetic classification and catalogue of the Diplogastridae (Secernentea, Nematoda). Journal of Nematode Morphology and Systematics, 6, 43–90.
Susoy, V., Ragsdale, E.J., Kanzaki, N. & Sommer, R.J. (2015) Rapid diversification associated with a macroevolutionary pulse of developmental plasticity. eLIFE, 4, e05463.
https://doi.org/10.7554/eLife.05463
Susoy, V., Herrmann, M., Kanzaki, N., Kruger, M., Nguyen, C.N., Rödelsperger, C., Röseler, W., Weiler, C., Giblin-Davis, R.M., Ragsdale, E.J. & Sommer, R.J. (2016) Large-scale diversification without genetic isolation in nematode symbionts of figs. Science Advance, 2, e1501031.
https://doi.org/10.1126/sciadv.1501031
Tian, H., Schlager, B., Xiao, H. & Sommer, R.J. (2008) Wnt signaling induces vulva development in the nematode Pristionchus pacificus. Current Biology, 18, 142–146.
https://doi.org/10.1016/j.cub.2007.12.048
Weadick, C.J. & Sommer, R.J. (2016) Mating system transitions drive lifespan evolution in Pristionchus nematodes. American Naturalist, 187, 517–529.
https://doi.org/10.1086/685283
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. Development, Genes & Evolution, 225, 55–62. https://doi.org/10.1007/s00427-014-0486-8
Yoshida, K., Herrmann, M., Kanzaki, N., Weiler, C., Rödelsperger, C. & Sommer, R.J. (2018) Two new species of Pristionchus (Nematoda: Diplogastridae) from Taiwan and the definition of the pacificus species-complex sensu stricto. Journal of Nematology, 50, 355–368.