Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors.
Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors.
复制标题
DOI：
10.1101/gr.275894.121
复制
发表时间：
2022-05
期刊：
影响因子：
7
通讯作者：
Yaffe, Eitan
中科院分区：
文献类型：
--
作者：
Shalon, Nitan;Relman, David A.;Yaffe, Eitan
具有环状基因组的可移动遗传元件在微生物群落的进化中发挥着关键作用。它们的圆形基因组对应于宏基因组图中的圆形行走，然而，来自自然微生物群落的组装产生的图形充满了虚假循环，使圆形基因组的准确重建变得复杂。我们提出了 DomCycle，一种基于所谓的“主导”图循环的识别来重建可能的循环基因组的算法。在实施过程中，我们利用配对读取来弥合组装间隙，并通过核苷酸水平分析来仔细检查循环，从而使该方法对错误组装工件具有鲁棒性。我们使用模拟和真实测序数据验证了该方法。将 DomCycle 应用到来自不同自然环境的 32 个公开可用的 DNA 鸟枪序列数据集，重建了数百个循环移动基因组。聚类揭示了 20 个高度流行且神秘的质粒，它们具有具有最近共同祖先的克隆群体结构。这种方法有助于研究通过水平基因转移进化的微生物群落。
Mobile genetic elements with circular genomes play a key role in the evolution of microbial communities. Their circular genomes correspond to circular walks in metagenome graphs, and yet, assemblies derived from natural microbial communities produce graphs riddled with spurious cycles, complicating the accurate reconstruction of circular genomes. We present DomCycle, an algorithm that reconstructs likely circular genomes based on the identification of so-called “dominant” graph cycles. In the implementation, we leverage paired reads to bridge assembly gaps and scrutinize cycles through a nucleotide-level analysis, making the approach robust to misassembly artifacts. We validated the approach using simulated and real sequencing data. Application of DomCycle to 32 publicly available DNA shotgun sequence data sets from diverse natural environments led to the reconstruction of hundreds of circular mobile genomes. Clustering revealed 20 highly prevalent and cryptic plasmids that have clonal population structures with recent common ancestors. This method facilitates the study of microbial communities that evolve through horizontal gene transfer.
登录
查看更多内容
影响因子：
14.9
作者：
Galata V;Fehlmann T;Backes C;Keller A
通讯作者：
Keller A
影响因子：
4.5
作者：
Lanza VF;de Toro M;Garcillán-Barcia MP;Mora A;Blanco J;Coque TM;de la Cruz F
通讯作者：
de la Cruz F
基于完整基因组序列分析，水平基因转移有助于哈维氏弧菌 345 的毒力和抗生素耐药性
影响因子：
4.4
作者：
Deng, Yiqin;Xu, Haidong;Feng, Juan
通讯作者：
Feng, Juan
影响因子：
17.1
作者：
Conlan S;Thomas PJ;Deming C;Park M;Lau AF;Dekker JP;Snitkin ES;Clark TA;Luong K;Song Y;Tsai YC;Boitano M;Dayal J;Brooks SY;Schmidt B;Young AC;Thomas JW;Bouffard GG;Blakesley RW;NISC Comparative Sequencing Program;Mullikin JC;Korlach J;Henderson DK;Frank KM;Palmore TN;Segre JA
通讯作者：
Segre JA
影响因子：
64.8
作者：
Methe, Barbara A.;Nelson, Karen E.;Pop, Mihai;Creasy, Heather H.;Giglio, Michelle G.;Huttenhower, Curtis;Gevers, Dirk;Petrosino, Joseph F.;Abubucker, Sahar;Badger, Jonathan H.;Chinwalla, Asif T.;Earl, Ashlee M.;FitzGerald, Michael G.;Fulton, Robert S.;Hallsworth-Pepin, Kymberlie;Lobos, Elizabeth A.;Madupu, Ramana;Magrini, Vincent;Martin, John C.;Mitreva, Makedonka;Muzny, Donna M.;Sodergren, Erica J.;Versalovic, James;Wollam, Aye M.;Worley, Kim C.;Wortman, Jennifer R.;Young, Sarah K.;Zeng, Qiandong;Aagaard, Kjersti M.;Abolude, Olukemi O.;Allen-Vercoe, Emma;Alm, Eric J.;Alvarado, Lucia;Andersen, Gary L.;Anderson, Scott;Appelbaum, Elizabeth;Arachchi, Harindra M.;Armitage, Gary;Arze, Cesar A.;Ayvaz, Tulin;Baker, Carl C.;Begg, Lisa;Belachew, Tsegahiwot;Bhonagiri, Veena;Bihan, Monika;Blaser, Martin J.;Bloom, Toby;Bonazzi, Vivien R.;Brooks, Paul;Buck, GregoryA.;Buhay, Christian J.;Busam, Dana A.;Campbell, Joseph L.;Canon, Shane R.;Cantarel, Brandi L.;Chain, Patrick S.;Chen, I-Min A.;Chen, Lei;Chhibba, Shaila;Chu, Ken;Ciulla, Dawn M.;Clemente, Jose C.;Clifton, Sandra W.;Conlan, Sean;Crabtree, Jonathan;Cutting, Mary A.;Davidovics, Noam J.;Davis, Catherine C.;DeSantis, Todd Z.;Deal, Carolyn;Delehaunty, Kimberley D.;Dewhisrst, Floyd E.;Deych, Elena;Ding, Yan;Dooling, David J.;Dugan, Shannon P.;Dunne, W. Michael, Jr.;Durkin, A. Scott;Edgar, Robert C.;Erlich, Rachel L.;Farmer, Candace N.;Farrell, Ruth M.;Faust, Karoline;Feldgarden, Michael;Felix, Victor M.;Fisher, Sheila;Fodor, Anthony A.;Forney, Larry;Foster, Leslie;Di Francesco, Valentina;Friedman, Jonathan;Friedrich, Dennis C.;Fronick, Catrina C.;Fulton, Lucinda L.;Gao, Hongyu;Garcia, Nathalia;Giannoukos, Georgia;Giblin, Christina;Giovanni, Maria Y.;Goldberg, Jonathan M.;Goll, Johannes;Gonzalez, Antonio;Griggs, Allison;Gujja, Sharvari;Haas, Brian J.;Hamilton, Holli A.;Harris, Emily L.;Hepburn, Theresa A.;Herter, Brandi;Hoffmann, Diane E.;Holder, Michael E.;Howarth, Clinton;Huang, Katherine H.;Huse, Susan M.;Izard, Jacques;Jansson, Janet K.;Jiang, Huaiyang;Jordan, Catherine;Joshi, Vandita;Katancik, JamesA.;Keitel, WendyA.;Kelley, Scott T.;Kells, Cristyn;Kinder-Haake, Susan;King, Nicholas B.;Knight, Rob;Knights, Dan;Kong, Heidi H.;Koren, Omry;Koren, Sergey;Kota, Karthik C.;Kovar, Christie L.;Kyrpides, Nikos C.;La Rosa, Patricio S.;Lee, Sandra L.;Lemon, Katherine P.;Lennon, Niall;Lewis, Cecil M.;Lewis, Lora;Ley, Ruth E.;Li, Kelvin;Liolios, Konstantinos;Liu, Bo;Liu, Yue;Lo, Chien-Chi;Lozupone, Catherine A.;Lunsford, R. Dwayne;Madden, Tessa;Mahurkar, Anup A.;Mannon, Peter J.;Mardis, Elaine R.;Markowitz, Victor M.;Mavrommatis, Konstantinos;McCorrison, Jamison M.;McDonald, Daniel;McEwen, Jean;McGuire, Amy L.;McInnes, Pamela;Mehta, Teena;Mihindukulasuriya, Kathie A.;Miller, Jason R.;Minx, Patrick J.;Newsham, Irene;Nusbaum, Chad;O'Laughlin, Michelle;Orvis, Joshua;Pagani, Ioanna;Palaniappan, Krishna;Patel, Shital M.;Pearson, Matthew;Peterson, Jane;Podar, Mircea;Pohl, Craig;Pollard, Katherine S.;Priest, Margaret E.;Proctor, Lita M.;Qin, Xiang;Raes, Jeroen;Ravel, Jacques;Reid, Jeffrey G.;Rho, Mina;Rhodes, Rosamond;Riehle, Kevin P.;Rivera, Maria C.;Rodriguez-Mueller, Beltran;Rogers, Yu-Hui;Ross, Matthew C.;Russ, Carsten;Sanka, Ravi K.;Sankar, Pamela;Sathirapongsasuti, J. Fah;Schloss, Jeffery A.;Schloss, Patrick D.;Schmidt, Thomas M.;Scholz, Matthew;Schriml, Lynn;Schubert, Alyxandria M.;Segata, Nicola;Segre, Julia A.;Shannon, William D.;Sharp, Richard R.;Sharpton, Thomas J.;Shenoy, Narmada;Sheth, Nihar U.;Simone, Gina A.;Singh, Indresh;Smillie, Chris S.;Sobel, Jack D.;Sommer, Daniel D.;Spicer, Paul;Sutton, Granger G.;Sykes, Sean M.;Tabbaa, Diana G.;Thiagarajan, Mathangi;Tomlinson, Chad M.;Torralba, Manolito;Treangen, Todd J.;Truty, Rebecca M.;Vishnivetskaya, Tatiana A.;Walker, Jason;Wang, Lu;Wang, Zhengyuan;Ward, Doyle V.;Warren, Wesley;Watson, Mark A.;Wellington, Christopher;Wetterstrand, Kris A.;White, James R.;Wilczek-Boney, Katarzyna;Wu, Yuan Qing;Wylie, Kristine M.;Wylie, Todd;Yandava, Chandri;Ye, Liang;Ye, Yuzhen;Yooseph, Shibu;Youmans, Bonnie P.;Zhang, Lan;Zhou, Yanjiao;Zhu, Yiming;Zoloth, Laurie;Zucker, Jeremy D.;Birren, Bruce W.;Gibbs, Richard A.;Highlander, Sarah K.;Weinstock, George M.;Wilson, Richard K.;White, Owen
通讯作者：
White, Owen