Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

Alejandro Caro-Quintero, Jie Deng, Jennifer Auchtung, Ingrid Brettar, Manfred G Höfle, Joel Klappenbach, Konstantinos T Konstantinidis, Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea The ISME Journal. ,vol. 5, pp. 131- 140 ,(2011) , 10.1038/ISMEJ.2010.93

Donovan H. Parks, Michael Imelfort, Connor T. Skennerton, Philip Hugenholtz, Gene W. Tyson, CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Genome Research. ,vol. 25, pp. 1043- 1055 ,(2015) , 10.1101/GR.186072.114

A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, M. A. DePristo, The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data Genome Research. ,vol. 20, pp. 1297- 1303 ,(2010) , 10.1101/GR.107524.110

Rachel J. Whitaker, Dennis W. Grogan, John W. Taylor, Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Molecular Biology and Evolution. ,vol. 22, pp. 2354- 2361 ,(2005) , 10.1093/MOLBEV/MSI233

T. Frede Thingstad, Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems Limnology and Oceanography. ,vol. 45, pp. 1320- 1328 ,(2000) , 10.4319/LO.2000.45.6.1320

R. E. Lenski, J. E. Barrick, Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harbor Symposia on Quantitative Biology. ,vol. 74, pp. 119- 129 ,(2009) , 10.1101/SQB.2009.74.018

Gene W. Tyson, Jarrod Chapman, Philip Hugenholtz, Eric E. Allen, Rachna J. Ram, Paul M. Richardson, Victor V. Solovyev, Edward M. Rubin, Daniel S. Rokhsar, Jillian F. Banfield, Community structure and metabolism through reconstruction of microbial genomes from the environment Nature. ,vol. 428, pp. 37- 43 ,(2004) , 10.1038/NATURE02340

Frederick M. Cohan, Elizabeth B. Perry, A Systematics for Discovering the Fundamental Units of Bacterial Diversity Current Biology. ,vol. 17, ,(2007) , 10.1016/J.CUB.2007.03.032

Ruibang Luo, Binghang Liu, Yinlong Xie, Zhenyu Li, Weihua Huang, Jianying Yuan, Guangzhu He, Yanxiang Chen, Qi Pan, Yunjie Liu, Jingbo Tang, Gengxiong Wu, Hao Zhang, Yujian Shi, Yong Liu, Chang Yu, Bo Wang, Yao Lu, Changlei Han, David W Cheung, Siu-Ming Yiu, Shaoliang Peng, Zhu Xiaoqian, Guangming Liu, Xiangke Liao, Yingrui Li, Huanming Yang, Jian Wang, Tak-Wah Lam, Jun Wang, None, SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler GigaScience. ,vol. 1, pp. 30- 30 ,(2012) , 10.1186/2047-217X-1-18

C. Fraser, W. P. Hanage, B. G. Spratt, Recombination and the nature of bacterial speciation. Science. ,vol. 315, pp. 476- 480 ,(2007) , 10.1126/SCIENCE.1127573