Best Practices in Insect Genome Sequencing: What Works and What Doesn't.
Best Practices in Insect Genome Sequencing: What Works and What Doesn't.
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DOI：
10.1016/j.cois.2015.02.013
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发表时间：
2015-02-01
影响因子：
5.3
通讯作者：
Murali, Shwetha C.
中科院分区：
文献类型：
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作者：
Richards, Stephen;Murali, Shwetha C.
在过去的十年里，DNA测序成本的降低和核心实验室和公司的测序服务的激增，使许多昆虫学家能够实现昆虫物种的从头基因组测序和组装。然而，单独的序列生产不足以产生高质量的参考基因组，并且在许多情况下，不良的计划可能导致极其片段化的基因组组装，从而阻止高质量的基因注释和其他期望的分析。昆虫基因组的组装可能是有问题的，这是由于高多态性、不能繁殖基因组纯合性以及小的物理尺寸限制了能够从单个个体分离的DNA的量的组合。测序技术和组装策略的最新进展正在为昆虫基因组参考测序和组装带来一场革命。在这里，我们回顾了历史和新的基因组测序和组装策略，特别关注它们在节肢动物基因组中的应用。我们强调需要为组装软件的要求设计测序策略，以及能够返回传统组装方法的新长读技术。最后，我们比较和对比非常具有成本效益的短读基因组草图策略与长读方法，虽然需要额外的成本，但带来更高的成功可能性和接近成品基因组的归档组装质量的可能性。
The last decade of decreasing DNA sequencing costs and proliferating sequencing services in core labs and companies has brought the de-novo genome sequencing and assembly of insect species within reach for many entomologists. However, sequence production alone is not enough to generate a high quality reference genome, and in many cases, poor planning can lead to extremely fragmented genome assemblies preventing high quality gene annotation and other desired analyses. Insect genomes can be problematic to assemble, due to combinations of high polymorphism, inability to breed for genome homozygocity, and small physical sizes limiting the quantity of DNA able to be isolated from a single individual. Recent advances in sequencing technology and assembly strategies are enabling a revolution for insect genome reference sequencing and assembly. Here we review historical and new genome sequencing and assembly strategies, with a particular focus on their application to arthropod genomes. We highlight both the need to design sequencing strategies for the requirements of the assembly software, and new long-read technologies that are enabling a return to traditional assembly approaches. Finally, we compare and contrast very cost effective short read draft genome strategies with the long read approaches that although entailing additional cost, bring a higher likelihood of success and the possibility of archival assembly qualities approaching that of finished genomes.
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影响因子：
7.7
作者：
Voskoboynik A;Neff NF;Sahoo D;Newman AM;Pushkarev D;Koh W;Passarelli B;Fan HC;Mantalas GL;Palmeri KJ;Ishizuka KJ;Gissi C;Griggio F;Ben-Shlomo R;Corey DM;Penland L;White RA 3rd;Weissman IL;Quake SR
通讯作者：
Quake SR
影响因子：
64.8
作者：
Clark, Andrew G.;Eisen, Michael B.;MacCallum, Iain
通讯作者：
MacCallum, Iain
影响因子：
64.8
作者：
Dasmahapatra, Kanchon K.;Walters, James R.;Briscoe, Adriana D.;Davey, John W.;Whibley, Annabel;Nadeau, Nicola J.;Zimin, Aleksey V.;Hughes, Daniel S. T.;Ferguson, Laura C.;Martin, Simon H.;Salazar, Camilo;Lewis, James J.;Adler, Sebastian;Ahn, Seung-Joon;Baker, Dean A.;Baxter, Simon W.;Chamberlain, Nicola L.;Chauhan, Ritika;Counterman, Brian A.;Dalmay, Tamas;Gilbert, Lawrence E.;Gordon, Karl;Heckel, David G.;Hines, Heather M.;Hoff, Katharina J.;Holland, Peter W. H.;Jacquin-Joly, Emmanuelle;Jiggins, Francis M.;Jones, Robert T.;Kapan, Durrell D.;Kersey, Paul;Lamas, Gerardo;Lawson, Daniel;Mapleson, Daniel;Maroja, Luana S.;Martin, Arnaud;Moxon, Simon;Palmer, William J.;Papa, Riccardo;Papanicolaou, Alexie;Pauchet, Yannick;Ray, David A.;Rosser, Neil;Salzberg, Steven L.;Supple, Megan A.;Surridge, Alison;Tenger-Trolander, Ayse;Vogel, Heiko;Wilkinson, Paul A.;Wilson, Derek;Yorke, James A.;Yuan, Furong;Balmuth, Alexi L.;Eland, Cathlene;Gharbi, Karim;Thomson, Marian;Gibbs, Richard A.;Han, Yi;Jayaseelan, Joy C.;Kovar, Christie;Mathew, Tittu;Muzny, Donna M.;Ongeri, Fiona;Pu, Ling-Ling;Qu, Jiaxin;Thornton, Rebecca L.;Worley, Kim C.;Wu, Yuan-Qing;Linares, Mauricio;Blaxter, Mark L.;Ffrench-Constant, Richard H.;Joron, Mathieu;Kronforst, Marcus R.;Mullen, Sean P.;Reed, Robert D.;Scherer, Steven E.;Richards, Stephen;Mallet, James;McMillan, W. Owen;Jiggins, Chris D.
通讯作者：
Jiggins, Chris D.
影响因子：
56.9
作者：
SCHWARTZ, DC;LI, XJ;WANG, YK
通讯作者：
WANG, YK
影响因子：
46.9
作者：
通讯作者：
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