Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians.
Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians.
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DOI：
10.1186/s40851-018-0102-2
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发表时间：
2018
影响因子：
2.7
通讯作者：
Agata K
中科院分区：
文献类型：
--
作者：
An Y;Kawaguchi A;Zhao C;Toyoda A;Sharifi-Zarchi A;Mousavi SA;Bagherzadeh R;Inoue T;Ogino H;Fujiyama A;Chitsaz H;Baharvand H;Agata K
Planarians是一种非寄生性的扁形动物（扁形虫），以其再生能力和组织良好的大脑而闻名。摘要日本三角涡虫是广泛分布于东亚地区的典型真涡虫种。已经开发了广泛的细胞和分子实验方法，以确定该物种中数千个基因的功能，使该涡虫成为再生生物学和神经生物学的良好实验模型。然而，没有基因组水平的信息是可用的D。japonica，迄今为止已经鉴定出很少的基因调控网络。为了获得该物种的全基因组信息并研究其基因调控网络，我们从实验室培育的无性克隆株中提取了200个真涡虫的基因组DNA，并通过第二代测序对476 Gb的数据进行了测序。Kmer频率绘图和fosmid序列分析表明，使用第二代测序短读段难以组装的复杂基因组。为了应对这一挑战，我们开发了一种新的组装策略，并改进了从头基因组组装，产生了1.56 Gb的基因组序列（DjGenome ver1.0，包括202，925个支架和N50长度27，741 bp），其覆盖组装的转录组中所有19，543个基因的99.4%，尽管基因组是片段化的，因为80%的基因组由重复序列组成（基因组频率≥ 2）。通过比较两个真涡虫属之间的基因组，我们确定了保守的非编码元件（CNEs），这是基因调控元件的指示。利用非洲爪蟾进行的转基因实验表明，Djndk基因中的一个CNE可能是一个调控元件，这表明ndk基因的调控和脑形成机制在脊椎动物和无脊椎动物之间可能是保守的。基因组草图和CNE分析将有助于解决基因调控网络的Planarians。基因组数据库可在http://www.planarian.jp上获得。本文的在线版本（10.1186/s40851-018-0102-2）包含补充材料，可供授权用户使用。
Planarians are non-parasitic Platyhelminthes (flatworms) famous for their regeneration ability and for having a well-organized brain. Dugesia japonica is a typical planarian species that is widely distributed in the East Asia. Extensive cellular and molecular experimental methods have been developed to identify the functions of thousands of genes in this species, making this planarian a good experimental model for regeneration biology and neurobiology. However, no genome-level information is available for D. japonica, and few gene regulatory networks have been identified thus far. To obtain whole-genome information on this species and to study its gene regulatory networks, we extracted genomic DNA from 200 planarians derived from a laboratory-bred asexual clonal strain, and sequenced 476 Gb of data by second-generation sequencing. Kmer frequency graphing and fosmid sequence analysis indicated a complex genome that would be difficult to assemble using second-generation sequencing short reads. To address this challenge, we developed a new assembly strategy and improved the de novo genome assembly, producing a 1.56 Gb genome sequence (DjGenome ver1.0, including 202,925 scaffolds and N50 length 27,741 bp) that covers 99.4% of all 19,543 genes in the assembled transcriptome, although the genome is fragmented as 80% of the genome consists of repeated sequences (genomic frequency ≥ 2). By genome comparison between two planarian genera, we identified conserved non-coding elements (CNEs), which are indicative of gene regulatory elements. Transgenic experiments using Xenopus laevis indicated that one of the CNEs in the Djndk gene may be a regulatory element, suggesting that the regulation of the ndk gene and the brain formation mechanism may be conserved between vertebrates and invertebrates. This draft genome and CNE analysis will contribute to resolving gene regulatory networks in planarians. The genome database is available at: http://www.planarian.jp. The online version of this article (10.1186/s40851-018-0102-2) contains supplementary material, which is available to authorized users.
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影响因子：
2.5
作者：
Hayashi, Tetsutaro;Shibata, Norito;Agata, Kiyokazu
通讯作者：
Agata, Kiyokazu
影响因子：
12.3
作者：
Buels R;Yao E;Diesh CM;Hayes RD;Munoz-Torres M;Helt G;Goodstein DM;Elsik CG;Lewis SE;Stein L;Holmes IH
通讯作者：
Holmes IH
影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
3.7
作者：
Egger B;Steinke D;Tarui H;De Mulder K;Arendt D;Borgonie G;Funayama N;Gschwentner R;Hartenstein V;Hobmayer B;Hooge M;Hrouda M;Ishida S;Kobayashi C;Kuales G;Nishimura O;Pfister D;Rieger R;Salvenmoser W;Smith J;Technau U;Tyler S;Agata K;Salzburger W;Ladurner P
通讯作者：
Ladurner P
影响因子：
7
作者：
Cantarel, Brandi L.;Korf, Ian;Yandell, Mark
通讯作者：
Yandell, Mark