Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago
Recent studies have shown that environmental DNA is found almost everywhere. Flower petal surfaces are an attractive tissue to use for investigation of the dispersal of environmental DNA in nature as they are isolated from the external environment until the bud opens and only then can the petal surface accumulate environmental DNA. Here, we performed a crowdsourced experiment, the “Ohanami Project”, to obtain environmental DNA samples from petal surfaces of Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago during spring 2015. C. × yedoensis is the most popular garden cherry species in Japan and clones of this cultivar bloom simultaneously every spring. Data collection spanned almost every prefecture and totaled 577 DNA samples from 149 collaborators. Preliminary amplicon-sequencing analysis showed the rapid attachment of environmental DNA onto the petal surfaces. Notably, we found DNA of other common plant species in samples obtained from a wide distribution; this DNA likely originated from the pollen of the Japanese cedar. Our analysis supports our belief that petal surfaces after blossoming are a promising target to reveal the dynamics of environmental DNA in nature. The success of our experiment also shows that crowdsourced environmental DNA analyses have considerable value in ecological studies.
KeywordsCrowdsourcing Cherry blossom Environmental DNA Amplicon sequencing
We thank all the Ohanami Project collaborators (Supplementary material 5) for their help with sampling. We also thank the NGS Field 4th Meeting organizers who encouraged us to publish this manuscript. We thank Dr. Hiroshi Mori of National Institute of Genetics for helpful comments. We would also like to show our gratitude to Halna Tsunekawa for graphical design of the project website and the logo. Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics.
TO, TK, YS, RY, KA, and WI led the project. NS, YS, and RY performed library construction and sequencing. TO, TK, AD, SH, TH, KK, TK, SK, MM, WN, SN, NS, HS, Y-hT, YT, YT, MT, KY, YS, and KA performed data analysis. TO developed the data management system and submitted data to the public repository. TK, TO, and WI wrote the manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare no conflict of interest associated with this manuscript.
- Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc Accessed 17 Feb 2017
- Howe J (2006) The rise of Crowdsourcing. Wired 2006. https://www.wired.com/2006/06/crowds/. Accessed 17 Feb 2017
- Iketani H, Ohta S, Kawahara T, Katsuki T, Mase N, Sato Y, Yamamoto T (2007) Analyses of clonal status in ‘Somei-yoshino’and confirmation of genealogical record in other cultivars of Prunus × yedoensis by microsatellite markers. Breed Sci 57:1–6. https://doi.org/10.1270/jsbbs.57.1 CrossRefGoogle Scholar
- Japan Meteorological Agency (2015) Forecast of cherry blossom blooming date. http://www.data.jma.go.jp/sakura/data/sakura004_03.html. Accessed 17 Feb 2017
- Kato S, Matsumoto A, Yoshimura K, Katsuki T, Iwamoto K, Tsuda Y, Ishio S, Nakamura K, Moriwaki K, Shiroishi T, Gojobori T, Yoshimaru H (2012) Clone identification in Japanese flowering cherry (Prunus subgenus Cerasus) cultivars using nuclear SSR markers. Breed Sci 62:248–255. https://doi.org/10.1270/jsbbs.62.248 CrossRefPubMedPubMedCentralGoogle Scholar
- Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79:5112–5120. https://doi.org/10.1128/AEM.01043-13 CrossRefPubMedPubMedCentralGoogle Scholar
- Lindstrom K (2007) From experimental to chronometric seasonality—the establishment of seasons as a national symbol in modern Japan. In: Palang H, Sooväli H, Printsmann A (eds) Seasonal landscapes. Springer, Dordrecht, pp 225–229. https://doi.org/10.1007/1-4020-4990-0_9
- Shirahata Y (2000) Hanami to sakura: Nihon teki naru mono saikō [Hanami and Sakura: Reconsideration of what Japanese style is]. PHP Institute, KyotoGoogle Scholar
- Yamagishi J, Sato Y, Shinozaki N, Ye B, Tsuboi A, Nagasaki M, Yamashita R (2016) Comparison of boiling and robotics automation method in DNA extraction for metagenomic sequencing of human oral microbes. PloS One 11:e0154389. https://doi.org/10.1371/journal.pone.0154389 CrossRefPubMedPubMedCentralGoogle Scholar