Literature DB >> 29460198

Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis 'Somei-yoshino' across the Japanese archipelago.

Tazro Ohta1, Takeshi Kawashima2, Natsuko O Shinozaki3, Akito Dobashi4, Satoshi Hiraoka5, Tatsuhiko Hoshino6, Keiichi Kanno7, Takafumi Kataoka8, Shuichi Kawashima9, Motomu Matsui10, Wataru Nemoto11, Suguru Nishijima12,13,14, Natsuki Suganuma15, Haruo Suzuki16, Y-H Taguchi17, Yoichi Takenaka18, Yosuke Tanigawa19, Momoka Tsuneyoshi20, Kazutoshi Yoshitake21, Yukuto Sato22, Riu Yamashita22, Kazuharu Arakawa23, Wataru Iwasaki10.   

Abstract

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.

Entities:  

Keywords:  Amplicon sequencing; Cherry blossom; Crowdsourcing; Environmental DNA

Mesh:

Substances:

Year:  2018        PMID: 29460198     DOI: 10.1007/s10265-018-1017-x

Source DB:  PubMed          Journal:  J Plant Res        ISSN: 0918-9440            Impact factor:   2.629


  13 in total

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Journal:  BMC Bioinformatics       Date:  2010-06-23       Impact factor: 3.169

6.  DNA fingerprinting study on the intraspecific variation and the origin of Prunus yedoensis (Someiyoshino).

Authors:  H Innan; R Terauchi; N T Miyashita; K Tsunewaki
Journal:  Jpn J Genet       Date:  1995-04

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8.  Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes.

Authors:  Junya Yamagishi; Yukuto Sato; Natsuko Shinozaki; Bin Ye; Akito Tsuboi; Masao Nagasaki; Riu Yamashita
Journal:  PLoS One       Date:  2016-04-22       Impact factor: 3.240

9.  Database indexing for production MegaBLAST searches.

Authors:  Aleksandr Morgulis; George Coulouris; Yan Raytselis; Thomas L Madden; Richa Agarwala; Alejandro A Schäffer
Journal:  Bioinformatics       Date:  2008-06-21       Impact factor: 6.937

10.  Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

Authors:  Ebrahim Afshinnekoo; Cem Meydan; Shanin Chowdhury; Dyala Jaroudi; Collin Boyer; Nick Bernstein; Julia M Maritz; Darryl Reeves; Jorge Gandara; Sagar Chhangawala; Sofia Ahsanuddin; Amber Simmons; Timothy Nessel; Bharathi Sundaresh; Elizabeth Pereira; Ellen Jorgensen; Sergios-Orestis Kolokotronis; Nell Kirchberger; Isaac Garcia; David Gandara; Sean Dhanraj; Tanzina Nawrin; Yogesh Saletore; Noah Alexander; Priyanka Vijay; Elizabeth M Hénaff; Paul Zumbo; Michael Walsh; Gregory D O'Mullan; Scott Tighe; Joel T Dudley; Anya Dunaif; Sean Ennis; Eoghan O'Halloran; Tiago R Magalhaes; Braden Boone; Angela L Jones; Theodore R Muth; Katie Schneider Paolantonio; Elizabeth Alter; Eric E Schadt; Jeanne Garbarino; Robert J Prill; Jane M Carlton; Shawn Levy; Christopher E Mason
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  1 in total

Review 1.  Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review.

Authors:  Pritam Banerjee; Kathryn A Stewart; Gobinda Dey; Caterina M Antognazza; Raju Kumar Sharma; Jyoti Prakash Maity; Santanu Saha; Hideyuki Doi; Natasha de Vere; Michael W Y Chan; Pin-Yun Lin; Hung-Chun Chao; Chien-Yen Chen
Journal:  AoB Plants       Date:  2022-07-02       Impact factor: 3.138

  1 in total

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