Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome.
Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome.
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萤火虫 Pyrocoelia pectoralis 基因组的长读序列组装
DOI：
10.1093/gigascience/gix112
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发表时间：
2017-12-01
期刊：
影响因子：
9.2
通讯作者：
Hu J
中科院分区：
文献类型：
--
作者：
Fu X;Li J;Tian Y;Quan W;Zhang S;Liu Q;Liang F;Zhu X;Zhang L;Wang D;Hu J
摘要背景萤火虫是甲目鞘翅目或有翼甲虫中的一类昆虫，因其生物发光而成为最广为人知和最受欢迎的昆虫物种之一。然而，由于其生存环境的大规模破坏，萤火虫面临灭绝的危险。为了提高人们对萤火虫的认识，有效地保护萤火虫，我们测定了陆生萤火虫胸围鳞翅目昆虫的全基因组序列。根据这一发现，我们在PacBio Sequel平台上利用单分子实时(SMRT)测序技术开发了陆地萤火虫Pyrocoelia ectoraris(E.Oliv.，1883；鞘翅目：Lampyridae)的高度可靠的基因组资源。总共产生了57.8G的长片段并组装成一个760.4 Mb的基因组，这接近估计的基因组大小，覆盖了98.7%的完整昆虫和0.7%的部分昆虫基准通用单拷贝同源基因。K-mer分析表明，该基因组是高度杂合性的。然而，我们的长读组件显示了连续性，重叠群N50的长度为3.04 Mb，最长的重叠群长度为13.69 Mb。此外，还检测到135 589个SSR和341Mb重复序列。共有23092个基因被预测，88.44%的基因被注释了一个或多个相关功能。结论我们构建了高质量的萤火虫基因组，这不仅为萤火虫的保护和生物多样性提供了深入的认识，而且为研究它们的有性交流、生物发光和进化机制提供了丰富的信息。
Abstract Background Fireflies are a family of insects within the beetle order Coleoptera, or winged beetles, and they are one of the most well-known and loved insect species because of their bioluminescence. However, the firefly is in danger of extinction because of the massive destruction of its living environment. In order to improve the understanding of fireflies and protect them effectively, we sequenced the whole genome of the terrestrial firefly Pyrocoelia pectoralis. Findings Here, we developed a highly reliable genome resource for the terrestrial firefly Pyrocoelia pectoralis (E. Oliv., 1883; Coleoptera: Lampyridae) using single molecule real time (SMRT) sequencing on the PacBio Sequel platform. In total, 57.8 Gb of long reads were generated and assembled into a 760.4-Mb genome, which is close to the estimated genome size and covered 98.7% complete and 0.7% partial insect Benchmarking Universal Single-Copy Orthologs. The k-mer analysis showed that this genome is highly heterozygous. However, our long-read assembly demonstrates continuousness with a contig N50 length of 3.04 Mb and the longest contig length of 13.69 Mb. Furthermore, 135 589 SSRs and 341 Mb of repeat sequences were detected. A total of 23 092 genes were predicted; 88.44% of genes were annotated with one or more related functions. Conclusions We assembled a high-quality firefly genome, which will not only provide insights into the conservation and biodiversity of fireflies, but also provide a wealth of information to study the mechanisms of their sexual communication, bio-luminescence, and evolution.
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影响因子：
3.7
作者：
Kumar S;Jones M;Koutsovoulos G;Clarke M;Blaxter M
通讯作者：
Blaxter M
影响因子：
7
作者：
Kielbasa, Szymon M.;Wan, Raymond;Frith, Martin C.
通讯作者：
Frith, Martin C.
DOI：
10.1073/pnas.1003379107
发表时间：
2010-07-06
影响因子：
11.1
作者：
Kirkness, Ewen F.;Haas, Brian J.;Pittendrigh, Barry R.
通讯作者：
Pittendrigh, Barry R.
影响因子：
48
作者：
Chin, Chen-Shan;Peluso, Paul;Schatz, Michael C.
通讯作者：
Schatz, Michael C.
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium