The Chironomus tentans draft genome annotation

If you use this data, please cite:
Kutsenko, A., Svensson, T., Nystedt, B. et al. The Chironomus tentans genome sequence and the organization of the Balbiani ring genes. BMC Genomics 15, 819 (2014). https://doi.org/10.1186/1471-2164-15-819

The dipteran Chironomus tentans (C. tentans) and its Balbiani ring (BR) genes serve as a model system for eukaryotic gene expression studies. Kutsenko, A. et al. (2014), reports the first draft genome of C. tentans, characterizing its gene expression machinery and the genomic architecture of its BR genes.

In brief, genomic DNA was extracted and sequenced, resulting in an assembly size of 213 Mb, which was likely an overestimate due to allelic variants. The estimated genome size is around 200 Mb, with low GC content (31%) and repeat fraction (15%) compared to other dipterans. Phylogenetic analysis places it as a sister clade to mosquitoes, diverging 150-250 million years ago. The assembled genome was relatively fragmented (scaffold NG50=65 Kbp), but was still found to be reasonably complete regarding gene content, with 97% of 248 highly conserved core eukaryotic genes being represented.

For transcriptome sequencing and genome annotation, poly (A)+ RNA was extracted from various tissues and developmental stages. This data was used as evidence for ab initio predictions of gene models and alternative splice variants, resulting in a draft annotation of 15,120 predicted genes. 
The C. tentans draft genome assembly can be downloaded here or from NCBI:
GenBank accession number: CBTT000000000.1
https://www.ncbi.nlm.nih.gov/assembly/GCA_000786525.1/

The draft genome annotation and the corresponding longest predicted proteins for each gene locus is provided here for download. Note that these preliminary annotations are provided as is, and incomplete, missing, or incorrect gene models are to be expected to some extent. 

Acknowledgements
We  acknowledge the Science for Life Laboratory and the National Genomics  Infrastructure (NGI) for sequencing service. Computations were mainly  performed on resources provided by SNIC through Uppsala  Multidisciplinary Center for Advanced Computational Science (UPPMAX).  Microscopy was performed at IFSU, Stockholm University. Ann-Charlotte  Sonnhammer at BILS is acknowledged for assistance concerning the initial  bioinformatics analysis. We thank Magnus Bjursell for initial support  in the project. This work was financed by grants from The Knut and Alice  Wallenberg Foundation through The Center for Metagenomic Sequence  analysis (CMS), The Granholm’s Foundation, The Carl Trygger’s Foundation  and The Swedish Research Council (VR).

若您引用此数据，请引用如下：

Kutsenko, A.，Svensson, T.，Nystedt, B. 等. Chironomus tentans 基因组序列及其 Balbiani 环基因的组织结构. BMC 丛刊 15，第 819 号（2014 年）. https://doi.org/10.1186/1471-2164-15-819

双翅目昆虫 Chironomus tentans（C. tentans）及其 Balbiani 环（BR）基因构成研究真核生物基因表达的一个模式系统。Kutsenko 等人（2014 年）报道了 C. tentans 的首个基因组草图，并对其基因表达机制及其 BR 基因的基因组结构进行了描述。

简而言之，通过提取和测序基因组 DNA，获得了 213 Mb 的组装大小，这可能是由于等位基因变异而高估的结果。估计的基因组大小约为 200 Mb，与其它双翅目昆虫相比，其 GC 含量（31%）和重复片段比例（15%）较低。系统发育分析将其定位为与蚊子同源的姐妹群，分歧于约 1.5 亿至 2.5 亿年前。组装的基因组相对破碎（支撑 NG50=65 Kbp），但在基因内容方面仍被认为是相对完整的，其中 248 个高度保守的核心真核生物基因中有 97% 得到了表征。

为了转录组测序和基因组注释，从各种组织和发育阶段中提取了 poly (A)+ RNA。这些数据被用作预测基因模型和选择性剪接变异的初始预测的证据，从而得出了 15,120 个预测基因的草图注释。

C. tentans 的基因组草图可以在以下链接或 NCBI 上下载：

GenBank 访问号：CBTT000000000.1

https://www.ncbi.nlm.nih.gov/assembly/GCA_000786525.1/

提供以下链接以下载基因组草图注释以及每个基因位点的最长预测蛋白。请注意，这些初步注释按现状提供，并可能存在不完整、缺失或错误的基因模型。

致谢

我们感谢 Science for Life Laboratory 和国家基因组学基础设施（NGI）提供的测序服务。计算主要在由瑞典国家计算基础设施（SNIC）通过乌普萨拉多学科先进计算科学中心（UPPMAX）提供的资源上完成。显微镜检查在斯德哥尔摩大学 IFSU 进行。我们感谢 Ann-Charlotte Sonnhammer 在 BILS 提供的初始生物信息学分析方面的协助。我们感谢 Magnus Bjursell 在项目初期提供的支持。本工作由 Knut 和 Alice Wallenberg 基金会通过元基因组序列分析中心（CMS）、Granholm 基金会、Carl Trygger 基金会和瑞典研究委员会（VR）提供的资金支持。