Diplonema papillatum Genome sequencing and assembly

Diplonemid flagellates are among the most abundant and species-rich of known marine eukaryotes, colonizing all habitats, depth, and geographic regions of the world ocean. However, little is known about their biology and ecological role.In this study, we determined the nuclear genome sequence of the model diplonemid Diplonema papillatum to provide a reference genome for the clade.The ~280-Mb genome assembly contains nearly 38,000 predicted protein-coding genes, likely co-transcribed in groups of up to 100. Gene clusters are separated by long repetitive regions that include numerous transposable elements, which also reside within introns. Analysis of gene family evolution reveals that the last common diplonemid ancestor underwent considerable metabolic expansions, mostly via horizontal gene transfer.In addition to serving as a reference genome for the specious diplonemid clade, the D.papillatum nuclear genome sequence will allow systematic functional and cell-biological studies in D. papillatum, because we have recently put in place genetic-manipulation methodologies for this species. Further, genome information will be critical for comparative studies of gene complement evolution in the sister group of kinetoplastids that includes human-pathogenic taxa. It will become possible to demonstrate by phylogenetic analyses including D. papillatum sequences that genes previously thought to be confined to kinetoplastids were in fact emerged already present in the common ancestor of the two groups.

双滴鞭毛虫（Diplonemid flagellates）是目前已知海洋真核生物中丰度最高、物种多样性最丰富的类群之一，它们栖息于全球海洋的各类生境、不同深度区域与所有地理海域。然而，学界对其生物学特性与生态功能却知之甚少。本研究针对模式双滴鞭毛虫（Diplonema papillatum）完成了核基因组测序，旨在为该演化支提供参考基因组。该约280 Mb的基因组组装结果包含近38000个预测蛋白编码基因，这些基因大概率以最多100个为一组进行共转录。基因簇之间由长重复区域分隔，这类区域包含大量转座因子（transposable elements），且转座因子也存在于内含子中。基因家族演化分析显示，双滴鞭毛虫的最后共同祖先经历了显著的代谢功能扩张，这一过程主要通过水平基因转移（horizontal gene transfer）实现。除了为物种多样的双滴演化支提供参考基因组外，乳突双滴鞭毛虫（D. papillatum）的核基因组序列还将支持针对该物种的系统性功能与细胞生物学研究——因为我们近期已建立了该物种的遗传操作体系。此外，该基因组信息对于开展动质体目（Kinetoplastids）姊妹群的基因组分演化比较研究也至关重要，而动质体目包含多种可致病的人类病原体类群。通过纳入乳突双滴鞭毛虫序列的系统发育分析（phylogenetic analyses），我们将得以证实：此前被认为仅存在于动质体目的基因，实际上早已存在于这两个类群的共同祖先之中。