DNA条形码现在是生物多样性工具包的标准部分。大约20年前，在几个小组中同时出现了这个想法，即DNA测序的进步可能使使用其基因组的小部分廉价有效地识别物种成为可能。尽管有早期的感染主义，但安大略省生物多样性研究所的保罗·赫伯特（Paul Hebert）和同事驱动的DNA条形码运动一直取得了失望。现在，为每个样品生成〜650 DNA字母的标准DNA条形码是常规的。在生命数据库的条形码中，已记录了超过260,000种的600万个DNA条形码（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.

对这些新的假定的物种斯坦三件事d out. One is that many are “cryptic”. This means that they were collected and initially identified as being members of a known species, but were found to be distinct based on their DNA barcode. So they must be very similar in morphology to known species. A second is that many are very small – tiny insects and the like. It looks like the biodiversity we have missed is in the vast majority of life that is best seen under a lens. Lastly, many of these species were found in areas where no new species are expected – in the back gardens (literally) of respected biodiversity scientists, in fields and parks where naturalists have been collecting for centuries. Many do come from undersampled tropical forests, but equally fruitful are urban shrubberies. New species are everywhere.

我们在线虫或round虫上工作。大多数线虫很小，生活在土壤和海泥中，难以识别。它们也非常丰富。您绝对需要一个好的指南，一个好的显微镜和很多耐心。玛丽·安妮·费利克斯（Marie-AnneFélix秀丽隐杆线虫。（严格来说，诺贝尔奖是给了人类使用的，他们使用C. elegans, but “the worm” was up there on the podium with them…)

Many of the nematodes she encountered were new species, but morphologically cryptic. She could tell them apart because they would not interbreed with any of the otherCaenorhabditisspecies she kept in culture. Through the efforts of Marie-Anne and the other collectors she inspired, there are now over 50 species ofCaenorhabditis在culture. Most of these species have not been formally named, but all are tiny worms (~1 mm long), see-through, and hard for humans to distinguish – except by DNA barcoding.

Formally naming these species is important, as it registers them in the matrix of scientific knowledge, and provides a hook on which to hang discoveries and comparisons. So the community ofCaenorhabditis多样性爱好者现在就是这样做的。Karin Kionkte（纽约大学），Marie-Anne及其同事在2011年发表了一篇激进论文，描述了15种新物种，其中包括每个[1]的诊断DNA条形码标记。本文包括最小的形态描述 - 仅确认该物种是Caenorhabditisand describing the male tail.

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…

其中之一Caenorhabditis物种 - 非正式地称为“C.sp。1” – was originally discovered living in the bracket fungusGanoderma applanatum沃尔特·萨德豪斯（Walter Sudhaus）的学生（柏林FreieUniversität）在一块木头上生长。从2013年开始，Dieter开始探索欧洲的林地，最终隔离了几种菌株C.sp。1, mostly from the same species of fungus. He then hooked up Walter Sudhaus in Germany and agreed to collaborate to describe the species. Karin Kiontke kindly supplied a sample of the original strain to Dieter for comparison, who then worked up a formal, morphological and ecological description ofC.sp。1, and we collaborated to provide DNA barcode data – the whole of the genome. Our paper “Caenorhabditismonodelphissp。n。：定义属的茎形态和基因组学Caenorhabditis”BMC Zoologyand formally describesC。SP.1及其整个基因组序列。

Microbiologists are now used to publishing full genome sequences along with descriptions of new bacterial species – since most bacteria have small genomes (less than 7 million DNA letters) this is quite easy to do nowadays. The tide is changing, though. A fungal species has been formally described with its genome sequence. And the genome of a strepsipteran insect (a wonderfully weird group of parasites) was published separately but simultaneously with its species description. We thinkC. monodelphisis the first time the whole genome of an animal has been a part of the species description. We think this is the “way to go” for the future: describe a species – describe its genome.

Why studyC. monodelphis?C. monodelphis是了解所有人的演变的关键物种Caenorhabditis。When we placed it on an evolutionary tree – using whole genome data from the many species we have sequenced as part of the CGP – we found it was sister to all other knownCaenorhabditis物种。这意味着我们可以使用它来估计所有人的祖先的基因组，因此是生物学Caenorhabditis可能看起来像 - 并回答（某些）模型物种的问题C. eleganscame to be just as it is.

Our analyses of the genome are still in their early stages, but we have already found some striking differences compared toC. elegans。For example, genes inC. monodelphishave nearly twice as many introns as do the same genes inC. elegans。Given our other data, we think this means that theCaenorhabditisancestor was intron-rich and that there has been extensive loss during the evolution ofC. elegans.但是我们不知道为什么C. elegans丢失了内含子 - 但是。分析所有其他基因组Caenorhabditiswill 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. elegansand the wealth of research associated with it.

Blaxter实验室已经有六个Caenorhabditis将其基因组作为最终DNA条形码发布的物种，我们很快将成为我们对所有目标进行测序的一半Caenorhabditis——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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Thanks to theBlaxter laband colleagues in the CGP for support. We exploited the twitter following of Sujai Kumar (@sujaik) to find out who else has published a genome alongside a eukaryotic species description.

基因组数据C. monodelphis(and for all the otherCaenorhabditis我们正在测序的物种）可以在浏览，查询和下载https://www.caenorhabditis.org。

麦角真菌的物种描述与其基因组一起

Chen L, Li XZ, Li CJ, Swoboda GA, Young CA, Sugawara K et al. Two distinctEpichloë物种与Achnatherum inebrians，醉酒的马草共生。Mycologia 2015：863-873。

链球动物的物种描述Mengenilla moldrzykiand its genome published in separate publications, but concurrently

Niehuis O, Hartig G, Grath S, Pohl H, Lehmann J, Tafer H et al. Genomic and Morphological Evidence Converge to Resolve the Enigma of Strepsiptera. Curr Biol 2012;22:1309-1313.

Pohl H, Niehuis O, Gloyna K, Misof B, Beutel R. A new species of Mengenilla (Insecta, Strepsiptera) from Tunisia. ZooKeys 2012;198:79-102.

Transcriptome data published alongside a species description

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.

参考：

[1] Kiontke KC，Felix M，Ailion M，Rockman MV，Braendle C，Penigault J＆Fitch DHA。系统发育和分子条形码Caenorhabditis，with numerous new species from rotting fruits. BMC Evolutionary Biology 2011; 11:339.

[2] Slos D, Sudhaus W, Stevens L, Bert W and Blaxter ML.Caenorhabditismonodelphissp。n。：定义属的茎形态和基因组学Caenorhabditis。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).