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Friday 24 February 2012
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Taxon diversity analysis for environmental insect samples using illumina hi-seq platform

LI Yiyuan, LIU Shanlin

Classic DNA barcoding protocols have been optimized for individual processing of biological samples. Next Generation Sequencing (NGS) technologies are considered as a potential solution to overcoming hurdles in data collection with accurate analysis of environmental samples of mixed taxa. Among current NGS platforms, Illumina sequencers have the potential to provide an efficient solution to analyzing environmental samples at much lower cost per sequence read.

In this study, we first sequenced mixed amplicons for the standard barcode region obtained from insect samples collected by Malaise traps. Additionally, we developed a PCR-independent protocol to overcome taxonomic bias introduced by PCR amplifications. Our results show that the improved sequence length and the large sequencing capacity currently available on Illumina NGS has ensured its application to environmental biodiversity analysis, with several technical advantages: higher sensitivity for taxa with low abundance, higher recovery ratio for true positives, lower running cost per sample, and the capability to eliminate PCR bias. The application of Illumina platforms in bioassessment is promising, yet modifications of protocols in collection, preservation, and molecular lab work seem critical for this implementation.

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Editorial board
  • BRANDNER Melissa
    • University of Nordland
    • Bodø (Norway)
  • BROCHMANN Christian
    • National Centre for Biosystematics
    • Oslo (Norway)
  • CHARITON Anthony
    • CSIRO Land and Water
    • Lucas Heights NA (Australia)
  • DEAGLE Bruce
    • University of Victoria
    • Victoria (Canada)
  • Eric Coissac
    • LECA
    • Grenoble (France)
  • KASAPIDIS Panagiotis
    • Hellenic Center for Marine Research
    • Irakleion, Crete (Greece)
  • PAWLOWSKI Jan
    • Université de Genève
    • Genève 4 (Switzerland)
  • TABERLET Pierre
    • LECA,
    • Grenoble (France)
  • WILLERSLEV Eske
    • Centre for GeoGenetics
    • Copenhagen (Denmark)
  • ZINGER Lucie
    • IBENS
    • Paris (France)
Editorial
  • Vodka, Bison and Metabarcoding

    31 July 2015, by BRANDNER Melissa

    The start of last month saw the occurrence of the Fifth Metabarcoding Spring School held in Białowieża National Park , Poland. A variety of scientists attended from all over the globe to learn, share and inspire with unique stories of metabarcoding.
    The scientists at the Mammal Research Institute PAS in Białowieża National Park hosted this year’s workshop. And our hats go off to them for the organizational skills, warmth and hospitality. During the week, experienced metabarcoders gave lectures on their trials and tribulations in the field of metabarcoding, sparking conversations between the attendees. The end of the first day saw flash talks from all participants of the event, creating an icebreaker and showing the wide variety of applications for metabarcoding, including, dietary studies, environmental health, fundamental ecology and exploration of rare and ancient habitats.
    Pierre Taberlet (who is rumoured to run 8000 PCR a day!) taught technical aspects such as DNA extraction in (...)

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