Jungle Genomics - overcoming the Linnean shortfall with Nanopore sequencing in biodiversity hotspots
Final Report Abstract
The loss of habitats at dramatic scales requires that taxonomists increase significantly the speed of species discovery. In the first project phase, we developed a monograph-pipeline based on type material of all described names for a taxonomic group, which can be used to distinguish genetically distinct species from synonyms and results in a comprehensive monograph. We focussed on the gourd family (Cucurbitaceae) and started with the genus Cucumis, with important crop species like melon (C. melo) and cucumber (C. sativus). We obtained leaf fragments of all published names in the genus from different herbaria across Europe and extracted DNA of those old samples to perform phylogeny estimation and revise species concepts. A newly designed bait set for Cucurbitaceae and a target-enrichment-sequencing approach enabled us to obtain genomic data and develop a novel data-analysis-pipeline for efficient and fast production of extensive phylogenomic matrices. Combining the phylogenomic results with distribution data from GBIF and morphological data from herbarium specimens allowed us to produce an online monograph available on our constantly updated website (www.cucurbit.de) as a common basis for systematists, plant breeders, ecologists, and conservationists. However, we also realized that our approach has limitations since it cannot contribute to discovery of new species which have never been named. In the second phase of the project we therefore developed a Nanopore-based field sequencing approach to be able to integrate plant species discovery in our existing pipeline. Nanopore-sequencing allows to rapidly screen unidentified material in collections and, importantly, directly in the field. In this way, we can drastically speed up plant species discovery. To test our field genomics protocol, we collaborated with colleagues in the biodiversity hotspot Madagascar. Starting again with type material from herbaria, we built a genomic reference database for the 70 described Malagasy cucurbit species and during three field trips used Nanopore sequencing to screen ca. 500 samples directly in the forest. Querying our reference database on-site allowed us to guide collecting efforts towards the new species, which made the field work more efficient. In a collaboration project, a Malagasy PhD student is currently finalizing a full monograph for the Cucurbitaceae of Madagascar based on our newly produced genomic dataset. In combination with our family-wide data for Cucurbitaceae, this new Malagasy dataset allows to infer comprehensive phylogeny estimates and analyse the biogeographic history, and diversification rates of Malagasy cucurbits for the first time. In addition to the genus-level dataset for Cucumis and the Malagasy cucurbit dataset, we also produced a dataset for the entire order Cucurbitales, which contributed to the recently published new phylogeny of the angiosperms (PAFTOL-project led by Royal Botanical Gardens Kew). Our simple jungle-genomics approach allows inclusion and training of local scientists, which increases the success rate of fieldwork and helps to make taxonomists in developing countries more independent from foreign support. The project has already produced considerable publication output in high-impact journals including Nature and Nature Genetics.
Publications
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A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits. Nature Genetics, 51(11), 1607-1615.
Zhao, Guangwei; Lian, Qun; Zhang, Zhonghua; Fu, Qiushi; He, Yuhua; Ma, Shuangwu; Ruggieri, Valentino; Monforte, Antonio J.; Wang, Pingyong; Julca, Irene; Wang, Huaisong; Liu, Junpu; Xu, Yong; Wang, Runze; Ji, Jiabing; Xu, Zhihong; Kong, Weihu; Zhong, Yang; Shang, Jianli; ... & Huang, Sanwen
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DNA extraction from old herbarium material of Veronica subgen. Pseudolysimachium (Plantaginaceae). Ukrainian Botanical Journal, 75(6), 564-575.
Höpke, J.; Brewer, G.; Dodsworth, S.; Ortiz, E.M. & Albach, D.C.
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Origin and domestication of Cucurbitaceae crops: insights from phylogenies, genomics and archaeology. New Phytologist, 226(5), 1240-1255.
Chomicki, Guillaume; Schaefer, Hanno & Renner, Susanne S.
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Biogeography and integrative taxonomy of Epipterygium (Mniaceae, Bryophyta). TAXON, 69(6), 1150-1171.
Hanusch, Maximilian; Ortiz, Edgardo M.; Patiño, Jairo & Schaefer, Hanno
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Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae. Scientific Reports, 10(1).
Bellot, Sidonie; Mitchell, Thomas C. & Schaefer, Hanno
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Tecunumania stothertiae (Cucurbitaceae): a new species from western Ecuador and a new generic record for South America. Phytotaxa, 446(3), 199-204.
CORNEJO, XAVIER; SCHAEFER, HANNO & NEE, MICHAEL H.
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Captus: Assembly of phylogenomic datasets from high-throughput sequencing data
Ortiz, E.M.
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Enhancing photosynthesis at high light levels by adaptive laboratory evolution. Nature Plants, 7(5), 681-695.
Dann, Marcel; Ortiz, Edgardo M.; Thomas, Moritz; Guljamow, Arthur; Lehmann, Martin; Schaefer, Hanno & Leister, Dario
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Zehneria palmatiloba, a new species of Cucurbitaceae from Atlantic Central Africa. Phytotaxa, 496(2), 170-178.
LACHENAUD, OLIVIER & SCHAEFER, HANNO
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Biogeography of Zehneria (Cucurbitaceae) and a New Species from India. Systematic Botany, 47(3), 738-747.
Ranjan, Vinay; Kumar, Anant; Krishna, Gopal & Schaefer, Hanno
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Genomanalysen der Europäischen Stechpalme (Ilex aquifolium). In: Die Stechpalme im Gebiet der Bayerischen Voralpen: Vorkommen und Genetik. Forstliche Forschungsberichte München Nr. 223
Ortiz, E.M.; G. Shigita; A. Höwener & H. Schaefer
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NanoAmp: Species identification via Nanopore sequencing of barcoded amplicons
Ortiz, E.M.
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Transcriptomic data reveals nuclear-mitochondrial discordance in Gomphocerinae grasshoppers (Insecta: Orthoptera: Acrididae). Molecular Phylogenetics and Evolution, 170(c(2022, 5)), 107439.
Hawlitschek, Oliver; Ortiz, Edgardo M.; Noori, Sajad; Webster, Kathleen C.; Husemann, Martin & Pereira, Ricardo J.
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A novel phylogenomics pipeline reveals complex pattern of reticulate evolution in Cucurbitales. American Geophysical Union (AGU).
Ortiz Edgardo M., Höwener Alina; Shigita Gentaro, Raza Mustafa; Maurin Olivier, Zuntini Alexandre; Forest Félix, Baker William J. & Schaefer Hanno
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Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines. BMC Ecology and Evolution, 23(1).
Raza, Mustafa; Ortiz, Edgardo M.; Schwung, Lea; Shigita, Gentaro & Schaefer, Hanno
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Phylogenomics and the rise of the angiosperms. Nature, 629(8013), 843-850.
Zuntini, Alexandre R.; Carruthers, Tom; Maurin, Olivier; Bailey, Paul C.; Leempoel, Kevin; Brewer, Grace E.; Epitawalage, Niroshini; Françoso, Elaine; Gallego-Paramo, Berta; McGinnie, Catherine; Negrão, Raquel; Roy, Shyamali R.; Simpson, Lalita; Toledo Romero, Eduardo; Barber, Vanessa M. A.; Botigué, Laura; Clarkson, James J.; Cowan, Robyn S.; Dodsworth, Steven; ... & Baker, William J.
