Browsing by Author "Mirarab, Siavash"

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    A communal catalogue reveals Earth's multiscale microbial diversity
    Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J.; Prill, Robert J.; Tripathi, Anupriya; Gibbons, Sean M.; Ackermann, Gail; Navas-Molina, Jose A.; Janssen, Stefan; Kopylova, Evguenia; Vazquez-Baeza, Yoshiki; Gonzalez, Antonio; Morton, James T.; Mirarab, Siavash; Xu, Zhenjiang Zech; Jiang, Lingjing; Haroon, Mohamed F.; Kanbar, Jad; Zhu, Qiyun; Song, Se Jin; Kosciolek, Tomasz; Bokulich, Nicholas A.; Lefler, Joshua; Brislawn, Colin J.; Humphrey, Gregory; Owens, Sarah M.; Hampton-Marcell, Jarrad; Berg-Lyons, Donna; McKenzie, Valerie; Fierer, Noah; Fuhrman, Jed A.; Clauset, Aaron; Stevens, Rick L.; Shade, Ashley; Pollard, Katherine S.; Goodwin, Kelly D.; Jansson, Janet K.; Gilbert, Jack A.; Knight, Rob; Rivera, Jose L. Agosto; Al-Moosawi, Lisa; Alverdy, John; Amato, Katherine R.; Andras, Jason; Angenent, Largus T.; Antonopoulos, Dionysios A.; Apprill, Amy; Armitage, David; Ballantine, Kate; Barta, Jiri; Baum, Julia K.; Berry, Allison; Bhatnagar, Ashish; Bhatnagar, Monica; Biddle, Jennifer F.; Bittner, Lucie; Boldgiv, Bazartseren; Bottos, Eric M.; Boyer, Donal M.; Braun, Josephine; Brazelton, William; Brearley, Francis Q.; Campbell, Alexandra H.; Caporaso, J. Gregory; Cardona, Cesar; Carroll, JoLynn; Cary, S. Craig; Casper, Brenda B.; Charles, Trevor C.; Chu, Haiyan; Claar, Danielle C.; Clark, Robert G.; Clayton, Jonathan B.; Clemente, Jose C.; Cochran, Alyssa; Coleman, Maureen L.; Collins, Gavin; Colwell, Rita R.; Contreras, Monica; Crary, Benjamin B.; Creer, Simon; Cristol, Daniel A.; Crump, Byron C.; Cui, Duoying; Daly, Sarah E.; Davalos, Liliana; Dawson, Russell D.; Defazio, Jennifer; Delsuc, Frederic; Dionisi, Hebe M.; Dominguez-Bello, Maria Gloria; Dowell, Robin; Dubinsky, Eric A.; Dunn, Peter O.; Ercolini, Danilo; Espinoza, Robert E.; Ezenwa, Vanessa; Fenner, Nathalie; Findlay, Helen S.; Fleming, Irma D.; Fogliano, Vincenzo; Forsman, Anna; Freeman, Chris; Friedman, Elliot S.; Galindo, Giancarlo; Garcia, Liza; Alexandra Garcia-Amado, Maria; Garshelis, David; Gasser, Robin B.; Gerdts, Gunnar; Gibson, Molly K.; Gifford, Isaac; Gill, Ryan T.; Giray, Tugrul; Gittel, Antje; Golyshin, Peter; Gong, Donglai; Grossart, Hans-Peter; Guyton, Kristina; Haig, Sarah-Jane; Hale, Vanessa; Hall, Ross Stephen; Hallam, Steven J.; Handley, Kim M.; Hasan, Nur A.; Haydon, Shane R.; Hickman, Jonathan E.; Hidalgo, Glida; Hofmockel, Kirsten S.; Hooker, Jeff; Hulth, Stefan; Hultman, Jenni; Hyde, Embriette; Ibanez-Alamo, Juan Diego; Jastrow, Julie D.; Jex, Aaron R.; Johnson, L. Scott; Johnston, Eric R.; Joseph, Stephen; Jurburg, Stephanie D.; Jurelevicius, Diogo; Karlsson, Anders; Karlsson, Roger; Kauppinen, Seth; Kellogg, Colleen T. E.; Kennedy, Suzanne J.; Kerkhof, Lee J.; King, Gary M.; Kling, George W.; Koehler, Anson V.; Krezalek, Monika; Kueneman, Jordan G.; Lamendella, Regina; Landon, Emily M.; Lane-deGraaf, Kelly; LaRoche, Julie; Larsen, Peter; Laverock, Bonnie; Lax, Simon; Lentino, Miguel; Levin, Iris I.; Liancourt, Pierre; Liang, Wenju; Linz, Alexandra M.; Lipson, David A.; Liu, Yongqin; Lladser, Manuel E.; Lozada, Mariana; Spirito, Catherine M.; MacCormack, Walter P.; MacRae-Crerar, Aurora; Magris, Magda; Martin-Platero, Antonio M.; Martin-Vivaldi, Manuel; Margarita Martinez, L.; Martinez-Bueno, Manuel; Marzinelli, Ezequiel M.; Mason, Olivia U.; Mayer, Gregory D.; McDevitt-Irwin, Jamie M.; McDonald, James E.; McGuire, Krista L.; McMahon, Katherine D.; McMinds, Ryan; Medina, Monica; Mendelson, Joseph R., III; Metcalf, Jessica L.; Meyer, Folker; Michelangeli, Fabian; Miller, Kim; Mills, David A.; Minich, Jeremiah; Mocali, Stefano; Moitinho-Silva, Lucas; Moore, Anni; Morgan-Kiss, Rachael M.; Munroe, Paul; Myrold, David; Neufeld, Josh D.; Ni, Yingying; Nicol, Graeme W.; Nielsen, Shaun; Nissimov, Jozef I.; Niu, Kefeng; Nolan, Matthew J.; Noyce, Karen; O'Brien, Sarah L.; Okamoto, Noriko; Orlando, Ludovic; Castellano, Yadira Ortiz; Osuolale, Olayinka; Oswald, Wyatt; Parnell, Jacob; Peralta-Sanchez, Juan M.; Petraitis, Peter; Pfister, Catherine; Pilon-Smits, Elizabeth; Piombino, Paola; Pointing, Stephen B.; Pollock, F. Joseph; Potter, Caitlin; Prithiviraj, Bharath; Quince, Christopher; Rani, Asha; Ranjan, Ravi; Rao, Subramanya; Rees, Andrew P.; Richardson, Miles; Riebesell, Ulf; Robinson, Carol; Rockne, Karl J.; Rodriguezl, Selena Marie; Rohwer, Forest; Roundstone, Wayne; Safran, Rebecca J.; Sangwan, Naseer; Sanz, Virginia; Schrenk, Matthew; Schrenzel, Mark D.; Scott, Nicole M.; Seger, Rita L.; Seguin-Orlando, Andaine; Seldin, Lucy; Seyler, Lauren M.; Shakhsheer, Baddr; Sheets, Gabriela M.; Shen, Congcong; Shi, Yu; Shin, Hakdong; Shogan, Benjamin D.; Shutler, Dave; Siegel, Jeffrey; Simmons, Steve; Sjoling, Sara; Smith, Daniel P.; Soler, Juan J.; Sperling, Martin; Steinberg, Peter D.; Stephens, Brent; Stevens, Melita A.; Taghavi, Safiyh; Tai, Vera; Tait, Karen; Tan, Chia L.; Tas, Neslihan; Taylor, D. Lee; Thomas, Torsten; Timling, Ina; Turner, Benjamin L.; Urich, Tim; Ursell, Luke K.; van der Lelie, Daniel; Van Treuren, William; van Zwieten, Lukas; Vargas-Robles, Daniela; Thurber, Rebecca Vega; Vitaglione, Paola; Walker, Donald A.; Walters, William A.; Wang, Shi; Wang, Tao; Weaver, Tom; Webster, Nicole S.; Wehrle, Beck; Weisenhorn, Pamela; Weiss, Sophie; Werner, Jeffrey J.; West, Kristin; Whitehead, Andrew; Whitehead, Susan R.; Whittingham, Linda A.; Willerslev, Eske; Williams, Allison E.; Wood, Stephen A.; Woodhams, Douglas C.; Yang, Yeqin; Zaneveld, Jesse; Zarraonaindia, Iratxe; Zhang, Qikun; Zhao, Hongxia (2017-11-23)
    Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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    One thousand plant transcriptomes and the phylogenomics of green plants
    Leebens-Mack, James H.; Barker, Michael S.; Carpenter, Eric J.; Deyholos, Michael K.; Gitzendanner, Matthew A.; Graham, Sean W.; Grosse, Ivo; Li, Zheng; Melkonian, Michael; Mirarab, Siavash; Porsch, Martin; Quint, Marcel; Rensing, Stefan A.; Soltis, Douglas E.; Soltis, Pamela S.; Stevenson, Dennis W.; Ullrich, Kristian K.; Wickett, Norman J.; DeGironimo, Lisa; Edger, Patrick P.; Jordon-Thaden, Ingrid E.; Joya, Steve; Liu, Tao; Melkonian, Barbara; Miles, Nicholas W.; Pokorny, Lisa; Quigley, Charlotte; Thomas, Philip; Villarreal, Juan Carlos; Augustin, Megan M.; Barrett, Matthew D.; Baucom, Regina S.; Beerling, David J.; Benstein, Ruben Maximilian; Biffin, Ed; Brockington, Samuel F.; Burge, Dylan O.; Burris, Jason N.; Burris, Kellie P.; Burtet-Sarramegna, Valerie; Caicedo, Ana L.; Cannon, Steven B.; Cebi, Zehra; Chang, Ying; Chater, Caspar; Cheeseman, John M.; Chen, Tao; Clarke, Neil D.; Clayton, Harmony; Covshoff, Sarah; Crandall-Stotler, Barbara J.; Cross, Hugh; dePamphilis, Claude W.; Der, Joshua P.; Determann, Ron; Dickson, Rowan C.; Di Stilio, Veronica S.; Ellis, Shona; Fast, Eva; Feja, Nicole; Field, Katie J.; Filatov, Dmitry A.; Finnegan, Patrick M.; Floyd, Sandra K.; Fogliani, Bruno; Garcia, Nicolas; Gateble, Gildas; Godden, Grant T.; Goh, Falicia (Qi Yun); Greiner, Stephan; Harkess, Alex; Heaney, James Mike; Helliwell, Katherine E.; Heyduk, Karolina; Hibberd, Julian M.; Hodel, Richard G. J.; Hollingsworth, Peter M.; Johnson, Marc T. J.; Jost, Ricarda; Joyce, Blake; Kapralov, Maxim V.; Kazamia, Elena; Kellogg, Elizabeth A.; Koch, Marcus A.; Von Konrat, Matt; Konyves, Kalman; Kutchan, Toni M.; Lam, Vivienne; Larsson, Anders; Leitch, Andrew R.; Lentz, Roswitha; Li, Fay-Wei; Lowe, Andrew J.; Ludwig, Martha; Manos, Paul S.; Mavrodiev, Evgeny; McCormick, Melissa K.; McKain, Michael; McLellan, Tracy; McNeal, Joel R.; Miller, Richard E.; Nelson, Matthew N.; Peng, Yanhui; Ralph, Paula E.; Real, Daniel; Riggins, Chance W.; Ruhsam, Markus; Sage, Rowan F.; Sakai, Ann K.; Scascitella, Moira; Schilling, Edward E.; Schlosser, Eva-Marie; Sederoff, Heike; Servick, Stein; Sessa, Emily B.; Shaw, A. Jonathan; Shaw, Shane W.; Sigel, Erin M.; Skema, Cynthia; Smith, Alison G.; Smithson, Ann; Stewart, C. Neal, Jr.; Stinchcombe, John R.; Szovenyi, Peter; Tate, Jennifer A.; Tiebel, Helga; Trapnell, Dorset; Villegente, Matthieu; Wang, Chun-Neng; Weller, Stephen G.; Wenzel, Michael; Weststrand, Stina; Westwood, James H.; Whigham, Dennis F.; Wu, Shuangxiu; Wulff, Adrien S.; Yang, Yu; Zhu, Dan; Zhuang, Cuili; Zuidof, Jennifer; Chase, Mark W.; Pires, J. Chris; Rothfels, Carl J.; Yu, Jun; Chen, Cui; Chen, Li; Cheng, Shifeng; Li, Juanjuan; Li, Ran; Li, Xia; Lu, Haorong; Ou, Yanxiang; Sun, Xiao; Tan, Xuemei; Tang, Jingbo; Tian, Zhijian; Wang, Feng; Wang, Jun; Wei, Xiaofeng; Xu, Xun; Yan, Zhixiang; Yang, Fan; Zhong, Xiaoni; Zhou, Feiyu; Zhu, Ying; Zhang, Yong; Ayyampalayam, Saravanaraj; Barkman, Todd J.; Nam-Phuong Nguyen; Matasci, Naim; Nelson, David R.; Sayyari, Erfan; Wafula, Eric K.; Walls, Ramona L.; Warnow, Tandy; An, Hong; Arrigo, Nils; Baniaga, Anthony E.; Galuska, Sally; Jorgensen, Stacy A.; Kidder, Thomas I.; Kong, Hanghui; Lu-Irving, Patricia; Marx, Hannah E.; Qi, Xinshuai; Reardon, Chris R.; Sutherland, Brittany L.; Tiley, George P.; Welles, Shana R.; Yu, Rongpei; Zhan, Shing; Gramzow, Lydia; Theissen, Gunter; Wong, Gane Ka-Shu (2019-10-31)
    Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.