A genome database for a Japanese population of the larvacean Oikopleura dioica.
A genome database for a Japanese population of the larvacean Oikopleura dioica.
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日本幼虫 Oikopleura dioica 群体的基因组数据库。
DOI：
10.1111/dgd.12689
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
T.A.
中科院分区：
文献类型：
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作者：
Wang;K.;Tomura;R.;Chen;W.;Kiyooka;M.;Ishizaki;H.;Aizu;T.;Minakuchi;Y.;Seki;Yutaka Suzuki;M.;Omotezako;T.;Suyama;R.;Masunaga;A.;Plessy;C.;Luscombe;N.M.;Dantec;C.;Lemaire;P.;Itoh;T.;Toyoda;A.;Nishida;H.;and Onuma;T.A.
Oikopleura dioicaa幼虫是一种浮游脊索动物，是一种属于脊椎动物近亲的被膜动物。其简单透明的体型、不变的胚胎细胞谱系和短短5天的生命周期使其成为发育生物学研究的一种有前途的模式生物。基因组浏览器OikoBase成立于2013年，使用的是挪威的O.Dieoica。然而，其他种群的基因组信息是不可用的，尽管许多研究人员已经研究了当地种群。在本研究中，我们使用Illumina和PacBio RSII技术对在我实验室培养了3年的日本西南部种群Ofo.dioica的基因组进行了测序。将日本血吸虫基因组组装成576个骨架序列，总长度为56.6 Mb，N50长度为1.5 Mb。在命名为OSKA2016的基因组组装中预测了总共18,743个基因模型(转录本模型)。此外，使用RNA-seq数据汇编了19,277份非冗余记录。与OikoBase相比，OSKA2016的全球序列相似性仅为86.5%，突显了这两个遥远的全球生物种群之间的序列差异。基因组组装、转录本组装和转录本模型被整合到八角(https://www.aniseed.cnrs.fr/))中，用于基因组浏览和BLAST搜索。对从男性或女性特定基因组文库中获得的读数的图谱在OSKA2016中产生了男性特定的支架，并显示超过2.6亿Mb的序列包括在男性特定的Y区域中。来自两个不同种群的基因组和转录组资源将成为使用这种模式生物的发育生物学、进化生物学和分子生态学的有用数据集。
The larvaceanOikopleura dioicais a planktonic chordate and is a tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of 5 days make it a promising model organism for the study of developmental biology. The genome browser OikoBase was established in 2013 using NorwegianO. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome ofO. dioicafrom a southwestern Japanese population that was cultured in our laboratory for 3 years. The genome of JapaneseO. dioicawas assembled into 576 scaffold sequences with a total length and N50 length of 56.6 and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named OSKA2016. In addition, 19,277 non‐redundant transcripts were assembled using RNA‐seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distantO. dioicapopulations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and BLAST searches. Mapping of reads obtained from male‐ or female‐specific genome libraries yielded male‐specific scaffolds in the OSKA2016 and revealed that over 2.6 Mb of sequence were included in the male‐specific Y‐region. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism.