MinION: Democratising biodiversity research by misusing a portable long-read sequencer for short-read barcoding

Many animal species on Earth are awaiting discovery and description, but finding all these unknown species is a monumental task. Here, we discuss how the MinION, an affordable, portable sequencer could speed up the process of discovering new species and propose this tool for large-scale biodiversity discovery across the planet. Ourexpanding on what we discuss here published today inBMC Biology

Most undescribed biodiversity consists of countless of small organisms that belong to millions of species. This makes it hard to find new and rare species in samples that often comprise thousands of organisms (such as bulk insect samples). One solution is using DNA sequences to sort specimens into putative species using high-throughput methods (“反向工作流程”)。不幸的是,这通常需要昂贵的集中测序设施,在地球上最多的一些生物多样性地区无法使用。

…the MinION, an affordable handheld portable sequencer, powered by USB, that offers fast sequencing even in difficult environments

In comes the MinION, an affordable (~1000 USD) handheld portable sequencer, powered by USB, that offers fast sequencing even indifficult environments(例如,在储备中的鼠标狐猴Madagascar, reptiles in anEcuadorian rainforest,Chironomid Midges和Ants新加坡, plants species in a威尔士国家公园).

We are这里applying MinION sequencing to obtain DNA barcode amplicons for成千上万的昆虫标本atminimal cost同时仅使用非常基本的实验室设备。为了展示我们的工作流程,我们对菲利达科(“ scuttle Flies”)的DNA条形码进行了测序,这是一个多样的双翅目家族,在Kibale国家公园(乌干达)的一个不适陷阱中,它们都在8周的时间内收集了8周。我们发现> 650种。这超过了目前针对整个非洲地区描述的黑蝇物种数量。这些结果使我们推测非洲可能仅是100,000种phoridae的家园。超过90%可能属于一个属,Megaselia

Study workflow for species discovery

通过将一个流循环的条形码容量从500增加到3,500个标本,可以在此规模上使用奴才的具有成本效益的物种发现。这需要对我们的三个更改previously proposed protocol。首先是使用更简单的库准备方法(1D vs 1d2). The second was greatly improving an existing bioinformatics pipeline that accommodates and corrects for the numerous测序错误of MinION sequencers (10-15%). The third was dual use of the same flowcell: amplicon coverage is assessed during the first use and weak amplicons are re-sequenced during the second use.

Phorid fly specimens collected in one Malaise trap in one week
Megaseliasepsioides(Diptera: Phoridae), a new species discovered in this study

我们更新的工作流程可在大型样本中发现有效的物种,但它也突出显示了哪些物种密切相关。我们通过描述一个新物种来证明这些优势Megaseliasepsioides(Diptera:Phoridae)。条形码数据迅速突出显示M. sepsioides作为感兴趣的分类单元,我们能够有效地记录新物种的分子和形态明显性。

We conclude that the MinION sequencer is now ready for large-scale barcoding using easily amplified barcodes. A complete MinION barcoding lab can be established for

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