DNA barcoding is now a standard part of the biodiversity toolkit. Nearly 20 years ago, the idea arose – simultaneously in several groups – that advances in DNA sequencing might make it possible to identify species cheaply and efficiently using small parts of their genomes. Despite early scepticisms, the DNA barcoding movement, driven by Paul Hebert and colleagues at the Biodiversity Institute of Ontario, has been a runaway success. It is now routine to generate a standard DNA barcode of ~650 DNA letters for every specimen. Over 6 million DNA barcodes from over 260,000 species have been logged in the Barcode of Life database (https://www.boldsystems.org/).

Having all the data in the central Barcode of Life database is a revelation: while 260,000 recognised, named species have DNA barcodes attached to them, there are nearly 500,000 different clusters (sets of sequences similar to each other but distinct from anything else) of DNA barcodes in the database. The quarter-million extra clusters are likely to be real, new species – organisms that have not yet been formally named. The huge number of undescribed species is not a huge surprise to biodiversity scientists, but is challenging to biodiversity science.

这些有关这些新推定物种的三件事脱颖而出。一个是许多是“神秘的”。这意味着它们是被收集的，最初被确定为已知物种的成员，但根据其DNA条形码而发现它们是不同的。因此，它们在形态上必须与已知物种非常相似。第二个是很多很小的 - 微小的昆虫等。看来我们错过的生物多样性是在绝大多数生活中最好看到的生物多样性。最后，其中许多物种是在没有新物种的地区发现的 - 在尊敬的生物多样性科学家的后花园中，在博物学家已经收集了几个世纪的田地和公园中。许多确实来自不足的热带森林，但同样富有成果的是城市灌木。新物种无处不在。

We work on nematodes, or roundworms. Most nematodes are tiny, live hidden in the soil and marine muds, and are difficult to identify. They are also extraordinarily abundant. You definitely need a good guide, a good microscope, and a lot of patience. Marie-Anne Félix, at the Institute of Biology of the Ecole Normale Supérieure in Paris, started a tiny revolution a decade ago when she went looking for relatives of the most famous of nematodes, the Nobel prize-winningCaenorhabditis elegans。(Strictly, the Nobel prizes were given to the humans who made huge discoveries usingC. elegans, but “the worm” was up there on the podium with them…)

她遇到的许多线虫都是新物种，但在形态上神秘。她可以告诉他们，因为他们不会与其他任何一个Caenorhabditis她保留在文化中的物种。通过玛丽·安妮（Marie-Anne）和她启发的其他收藏家的努力，现在有50多种Caenorhabditis在文化中。这些物种中的大多数尚未正式命名，但所有这些物种都是微小的蠕虫（长约1毫米），透明，并且很难使人类区分 - 除了DNA条形码外。

正式命名这些物种很重要，因为它以科学知识的矩阵进行了记录，并提供了一个可以悬挂发现和比较的钩子。所以社区的Caenorhabditisdiversity enthusiasts is now doing just that. Karin Kionkte (New York University), Marie-Anne and colleagues published a radical paper in 2011, describing 15 new species, including a diagnostic DNA barcode marker for each [1]. This paper included minimal morphological descriptions – simply affirming that the species wereCaenorhabditis并描述男性尾巴。

A single DNA barcode marker may not always be enough to define taxa, and is by definition from a gene that is found in all species and so unlikely to tell us anything about novel biology. Much more useful would be a catalogue of “all” the genes of a species, conserved ones as well as new ones, in the context of the whole genome… In the decade or so since the first major publications on DNA barcoding, the technology of DNA sequencing has been transformed. It is cheaper and faster than ever before. So we decided to sequence the whole genomes – all 100 million DNA letters – of all theCaenorhabditisspecies we could. We called this idea theCaenorhabditisGenomes Project (CGP), invited Marie-Anne and others to join, and started sequencing…

One of theseCaenorhabditisspecies – informally called “C.sp。1” – was originally discovered living in the bracket fungusganoderma applanatumgrowing on a stump of wood by a student of Walter Sudhaus (Freie Universität Berlin). From 2013 onwards, Dieter began exploring the woodlands of Europe, eventually isolating several more strains ofC.sp。1，主要来自相同的真菌。然后，他将沃尔特·苏德豪斯（Walter Sudhaus）连接在德国，并同意合作描述该物种。Karin Kiontke友善地向Dieter提供了原始菌株的样本，以进行比较，然后他们进行了正式，形态学和生态描述C.sp。1，我们合作提供了DNA条形码数据 - 整个基因组。我们的论文”Caenorhabditis monodelphissp。n.: defining the stem morphology and genomics of the genusCaenorhabditis” was published inBMC Zoology和formally describesC。sp。1 along with its entire genome sequence.

微生物学家现在被用来发布完整的基因组序列以及对新细菌物种的描述 - 由于大多数细菌的基因组小（少于700万个DNA字母），因此现在很容易做到这一点。不过，潮流正在发生变化。真菌物种已与其基因组序列进行了正式描述。链球菌昆虫的基因组（一群奇特的寄生虫群）分别出版，但与其物种描述同时出版。我们认为C. monodelphis是动物的整个基因组首次成为物种描述的一部分。我们认为这是未来的“要走之路”：描述一个物种 - 描述其基因组。

为什么学习C. monodelphis?C. monodelphisis a key species for understanding the evolution of allCaenorhabditis。当我们将其放在进化树上时 - 使用我们测序的许多物种的整个基因组数据作为CGP的一部分 - 我们发现它是所有其他已知的姐妹Caenorhabditisspecies. This means we can use it to estimate what the genome, and thus the biology, of the ancestor of allCaenorhabditismight have looked like – and answer (some of) the question of how the model speciesC. eleganscame to be just as it is.

我们对基因组的分析仍处于早期阶段，但是与C. elegans。例如,基因C. monodelphishave nearly twice as many introns as do the same genes inC. elegans。鉴于我们的其他数据，我们认为这意味着Caenorhabditisancestor was intron-rich and that there has been extensive loss during the evolution ofC. elegans.But we don’t know whyC. eleganshas lost introns – yet. Analysis of all the other genomes inCaenorhabditiswill allow us to test ideas of what drivers and mechanisms are at work, and these drivers and mechanisms may turn out to be true of many other species too. This is precisely what we hope the CGP will provide: an essential evolutionary context forC. elegans以及与之相关的大量研究。

The Blaxter lab already have another sixCaenorhabditisspecies to publish with their genomes as the ultimate DNA barcode, and we will soon be half-way to our goal of sequencing allCaenorhabditis——只要Marie-Anne, Dieter and their colleagues don’t keep on discovering new species. Doubtless they will, and that will keep us (happily) busy [3].

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感谢Blaxter实验室和colleagues in the CGP for support. We exploited the twitter following of Sujai Kumar (@sujaik）找出其他人在真核物种描述旁边发表了一个基因组。

Genomic data forC. monodelphis（以及其他Caenorhabditisspecies we are sequencing) are available to browse, query and download athttps://www.caenorhabditis.org。

A species description of a ergot fungus alongside its genome

Chen L，Li XZ，Li CJ，Swoboda GA，Young CA，Sugawara K等。两个不同的Epichloëspecies symbiotic with Achnatherum inebrians, drunken horse grass. Mycologia 2015:863-873.

A species description of the strepsipteranMengenilla Moldrzyki和its genome published in separate publications, but concurrently

Niehuis O，Hartig G，Grath S，Pohl H，Lehmann J，Tafer H等。基因组和形态学证据融合以解决链球菌的谜。Curr Biol 2012; 22：1309-1313。

Pohl H，Niehuis O，Gloyna K，Misof B，BeutelR。来自突尼斯的一种新物种Mengenilla（昆虫，链球菌）。Zookeys 2012; 198：79-102。

与物种描述一起发布的转录组数据

Edmunds SC, Hunter CI, Smith V, Stoev P, Penev L. Biodiversity research in the “big data” era: GigaScience and Pensoft work together to publish the most data-rich species description. GigaScience 2013;2:14.

References:

[1] Kiontke KC, Felix M, Ailion M, Rockman MV, Braendle C, Penigault J & Fitch DHA. A phylogeny and molecular barcodes forCaenorhabditis,腐烂的水果有许多新物种。BMC进化生物学2011;11：339。

[2] Slos D, Sudhaus W, Stevens L, Bert W and Blaxter ML.Caenorhabditis monodelphissp。n.: defining the stem morphology and genomics of the genusCaenorhabditis.BMC Zoology 2017; 2:4.

[3] Blaxter ML. Imagining Sisyphus happy: DNA barcoding and the unnamed majority. Philos Trans R Soc Lond B Biol Sci 2016; 5:371(1702).