School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong.
School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong.
PLoS Biol. 2020 Sep 29;18(9):e3000636. doi: 10.1371/journal.pbio.3000636. eCollection 2020 Sep.
The Myriapoda, composed of millipedes and centipedes, is a fascinating but poorly understood branch of life, including species with a highly unusual body plan and a range of unique adaptations to their environment. Here, we sequenced and assembled 2 chromosomal-level genomes of the millipedes Helicorthomorpha holstii (assembly size = 182 Mb; shortest scaffold/contig length needed to cover 50% of the genome [N50] = 18.11 Mb mainly on 8 pseudomolecules) and Trigoniulus corallinus (assembly size = 449 Mb, N50 = 26.78 Mb mainly on 17 pseudomolecules). Unique genomic features, patterns of gene regulation, and defence systems in millipedes, not observed in other arthropods, are revealed. Both repeat content and intron size are major contributors to the observed differences in millipede genome size. Tight Hox and the first loose ecdysozoan ParaHox homeobox clusters are identified, and a myriapod-specific genomic rearrangement including Hox3 is also observed. The Argonaute (AGO) proteins for loading small RNAs are duplicated in both millipedes, but unlike in insects, an AGO duplicate has become a pseudogene. Evidence of post-transcriptional modification in small RNAs-including species-specific microRNA arm switching-providing differential gene regulation is also obtained. Millipedes possesses a unique ozadene defensive gland unlike the venomous forcipules found in centipedes. We identify sets of genes associated with the ozadene that play roles in chemical defence as well as antimicrobial activity. Macro-synteny analyses revealed highly conserved genomic blocks between the 2 millipedes and deuterostomes. Collectively, our analyses of millipede genomes reveal that a series of unique adaptations have occurred in this major lineage of arthropod diversity. The 2 high-quality millipede genomes provided here shed new light on the conserved and lineage-specific features of millipedes and centipedes. These findings demonstrate the importance of the consideration of both centipede and millipede genomes-and in particular the reconstruction of the myriapod ancestral situation-for future research to improve understanding of arthropod evolution, and animal evolutionary genomics more widely.
多足类动物包括千足虫和蜈蚣，是生命中一个引人入胜但却知之甚少的分支，其中包括一些具有非常不寻常的身体结构和一系列独特的环境适应能力的物种。在这里，我们对千足虫 Helicorthomorpha holstii（组装大小= 182Mb；覆盖基因组 50%所需的最短支架/连续体长度[N50]= 18.11Mb，主要在 8 个假染色体上）和 Trigoniulus corallinus（组装大小= 449Mb，N50= 26.78Mb，主要在 17 个假染色体上）进行了测序和组装。揭示了在其他节肢动物中未观察到的千足虫独特的基因组特征、基因调控模式和防御系统。千足虫的重复含量和内含子大小是导致其基因组大小差异的主要因素。鉴定了紧密的 Hox 和第一个松散的后生动物 ParaHox 同源盒簇，并且还观察到一个包括 Hox3 的多足动物特异性基因组重排。Argonaute（AGO）蛋白用于加载小 RNA 在两种千足虫中都被复制，但与昆虫不同的是，AGO 副本已成为假基因。还获得了小 RNA 中转录后修饰的证据，包括物种特异性 microRNA 臂切换，提供了差异基因调控。千足虫拥有一种独特的 ozadene 防御腺，与蜈蚣的有毒螯肢不同。我们确定了与 ozadene 相关的基因集，这些基因在化学防御以及抗微生物活性中发挥作用。宏观同线性分析显示，这两种千足虫与后口动物之间存在高度保守的基因组块。总的来说，我们对千足虫基因组的分析表明，在这个主要的节肢动物多样性谱系中发生了一系列独特的适应。这里提供的这两个高质量的千足虫基因组为深入了解千足虫和蜈蚣的保守和谱系特异性特征提供了新的线索。这些发现表明，考虑蜈蚣和千足虫的基因组，特别是重建多足动物的祖先情况，对于未来的研究提高对节肢动物进化和动物进化基因组学的理解具有重要意义。
