A draft nuclear-genome assembly of the acoel flatworm Praesagittifera naikaiensis
A draft nuclear-genome assembly of the acoel flatworm Praesagittifera naikaiensis
复制标题
DOI：
10.1093/gigascience/giz023
复制
发表时间：
2019-04-01
期刊：
影响因子：
9.2
通讯作者：
Satoh, Noriyuki
中科院分区：
文献类型：
--
作者：
Arimoto, Asuka;Hikosaka-Katayama, Tomoe;Satoh, Noriyuki
研究背景：体腔是原始的两侧性动物，具有非常简单的柔软身体，其中许多器官，包括肠道，都不发达。它们为研究基本两侧体计划形成、全身再生以及与光合微藻共生所涉及的分子和发育机制提供了平台。由于基因组信息是必不可少的，为未来的研究，acoel生物学，我们测序和组装的核基因组的一个acoel，Praesagittiferaaikaiensis。结果：为了避免来自共生微藻的序列污染，从没有藻类的胚胎中提取DNA。使用Illumina（配对末端和配对文库）和PacBio测序的组合实现了超过290 x的测序覆盖率。还获得了胚胎、幼虫和成虫的RNA测序和Iso-Seq数据。首先，组装了一个初步的类似于17-磷酸酶对（kb）的线粒体基因组，其从核序列组装中删除。结果，核基因组装配草图长度类似于656 Mb，支架N50为117 kb，重叠群N50为57 kb。虽然近似70%的组装序列可能由包括DNA转座子和反转录转座子的重复序列组成，但基因组草图估计包含22，143个蛋白质编码基因，其中近似99%由相应的转录本证实。我们无法在acoel基因组中找到水平转移的微藻基因。基准通用单拷贝同源分析表明，77%的保守单拷贝基因是完整的。Pfam结构域分析为转录因子和信号分子提供了一套基本的基因家族。结论：我们目前的测序和组装的P. naikaiensis核基因组与其他后生动物的基因组，提供了基础信息，为未来的研究基因和基因组属性的这个动物群体。这些研究可能有助于阐明简单两侧对称动物的起源和进化。
Background: Acoels are primitive bilaterians with very simple soft bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in the formation of the basic bilaterian body plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel, Praesagittifera naikaiensis. Findings: To avoid sequence contamination derived from symbiotic microalgae, DNA was extracted from embryos that were free of algae. More than 290x sequencing coverage was achieved using a combination of Illumina (paired-end and mate-pair libraries) and PacBio sequencing. RNA sequencing and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary similar to 17-kilobase pair (kb) mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nuclear genome assembly was similar to 656 Mb in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb. Although similar to 70% of the assembled sequences were likely composed of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein-coding genes, similar to 99% of which were substantiated by corresponding transcripts. We could not find horizontally transferred microalgal genes in the acoel genome. Benchmarking Universal Single-Copy Orthologs analyses indicated that 77% of the conserved single-copy genes were complete. Pfam domain analyses provided a basic set of gene families for transcription factors and signaling molecules. Conclusions: Our present sequencing and assembly of the P. naikaiensis nuclear genome are comparable to those of other metazoan genomes, providing basic information for future studies of genic and genomic attributes of this animal group. Such studies may shed light on the origins and evolution of simple bilaterians.