VTechWorks staff will be away for the Thanksgiving holiday beginning at noon on Wednesday, November 27, through Friday, November 29. We will resume normal operations on Monday, December 2. Thank you for your patience.

Browsing by Author "Koren, Sergey"

Now showing 1 - 5 of 5
  • Thumbnail Image
    Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation
    Miller, Jason R.; Koren, Sergey; Dilley, Kari A.; Puri, Vinita; Brown, David M.; Harkins, Derel M.; Thibaud-Nissen, Françoise; Rosen, Benjamin D.; Xiao-Guang, Chen; Tu, Zhijian Jake; Sharakhov, Igor V.; Sharakhova, Maria V.; Sebra, R.; Stockwell, T. B.; Bergman, N. H.; Sutton, G. G.; Phillippi, A. M.; Pieemarini, P. M.; Shabman, R. S. (2018-03)
    The 50-year old Aedes albopictus C6/36 cell line is a resource for the detection, amplification, and analysis of mosquito-borne viruses including Zika, dengue, and chikungunya. The cell line is derived from an unknown number of larvae from an unspecified strain of Aedes albopictus mosquitoes. Toward improved utility of the cell line for research in virus transmission, we present an annotated assembly of the C6/36 genome.
  • Thumbnail Image
    Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
    Waterhouse, Robert M.; Aganezov, Sergey; Anselmetti, Yoann; Lee, Jiyoung; Ruzzante, Livio; Reijnders, Maarten J. M. F.; Feron, Romain; Bérard, Sèverine; George, Phillip; Hahn, Matthew W.; Howell, Paul I.; Kamali, Maryam; Koren, Sergey; Lawson, Daniel; Maslen, Gareth; Peery, Ashley; Phillippy, Adam M.; Sharakhova, Maria V.; Tannier, Eric; Unger, Maria F.; Zhang, Simo V.; Alekseyev, Max A.; Besansky, Nora J.; Chauve, Cedric; Emrich, Scott J.; Sharakhov, Igor V. (2020-01-02)
    Background New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies. Results We evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi. Conclusions Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.
  • Thumbnail Image
    Genomic insights into the Ixodes scapularis tick vector of Lyme disease
    Gulia-Nuss, Monika; Nuss, Andrew B.; Meyer, Jason M.; Sonenshine, Daniel E.; Roe, R. Michael; Waterhouse, Robert M.; Sattelle, David B.; de la Fuente, Jose; Ribeiro, Jose M.; Megy, Karine; Thimmapuram, Jyothi; Miller, Jason R.; Walenz, Brian P.; Koren, Sergey; Hostetler, Jessica B.; Thiagarajan, Mathangi; Joardar, Vinita S.; Hannick, Linda I.; Bidwell, Shelby; Hammond, Martin P.; Young, Sarah; Zeng, Qiandong; Abrudan, Jenica L.; Almeida, Francisca C.; Ayllon, Nieves; Bhide, Ketaki; Bissinger, Brooke W.; Bonzon-Kulichenko, Elena; Buckingham, Steven D.; Caffrey, Daniel R.; Caimano, Melissa J.; Croset, Vincent; Driscoll, Timothy; Gilbert, Don; Gillespie, Joseph J.; Giraldo-Calderon, Gloria I.; Grabowski, Jeffrey M.; Jiang, David; Khalil, Sayed M. S.; Kim, Donghun; Kocan, Katherine M.; Koci, Juraj; Kuhn, Richard J.; Kurtti, Timothy J.; Lees, Kristin; Lang, Emma G.; Kennedy, Ryan C.; Kwon, Hyeogsun; Perera, Rushika; Qi, Yumin; Radolf, Justin D.; Sakamoto, Joyce M.; Sanchez-Gracia, Alejandro; Severo, Maiara S.; Silverman, Neal; Simo, Ladislav; Tojo, Marta; Tornador, Cristian; Van Zee, Janice P.; Vazquez, Jesus; Vieira, Filipe G.; Villar, Margarita; Wespiser, Adam R.; Yang, Yunlong; Zhu, Jiwei; Arensburger, Peter; Pietrantonio, Patricia V.; Barker, Stephen C.; Shao, Renfu; Zdobnov, Evgeny M.; Hauser, Frank; Grimmelikhuijzen, Cornelis J. P.; Park, Yoonseong; Rozas, Julio; Benton, Richard; Pedra, Joao H. F.; Nelson, David R.; Unger, Maria F.; Tubio, Jose M. C.; Tu, Zhijian Jake; Robertson, Hugh M.; Shumway, Martin; Sutton, Granger; Wortman, Jennifer R.; Lawson, Daniel; Wikel, Stephen K.; Nene, Vishvanath M.; Fraser, Claire M.; Collins, Frank H.; Birren, Bruce; Nelson, Karen E.; Caler, Elisabet; Hill, Catherine A. (Springer Nature, 2016-02)
    Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing similar to 57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.
  • Thumbnail Image
    Improved reference genome of Aedes aegypti informs arbovirus vector control
    Matthews, Benjamin J.; Dudchenko, Olga; Kingan, Sarah B.; Koren, Sergey; Antoshechkin, Igor; Crawford, Jacob E.; Glassford, William J.; Herre, Margaret; Redmond, Seth N.; Rose, Noah H.; Weedall, Gareth D.; Wu, Yang; Batra, Sanjit S.; Brito-Sierra, Carlos A.; Buckingham, Steven D.; Campbell, Corey L.; Chan, Saki; Cox, Eric; Evans, Benjamin R.; Fansiri, Thanyalak; Filipovic, Igor; Fontaine, Albin; Gloria-Soria, Andrea; Hall, Richard; Joardar, Vinita S.; Jones, Andrew K.; Kay, Raissa G. G.; Kodali, Vamsi K.; Lee, Joyce; Lycett, Gareth J.; Mitchell, Sara N.; Muehling, Jill; Murphy, Michael R.; Omer, Arina D.; Partridge, Frederick A.; Peluso, Paul; Aiden, Aviva Presser; Ramasamy, Vidya; Rasic, Gordana; Roy, Sourav; Saavedra-Rodriguez, Karla; Sharan, Shruti; Sharma, Atashi; Smith, Melissa Laird; Turner, Joe; Weakley, Allison M.; Zhao, Zhilei; Akbari, Omar S.; Black, William C.; Cao, Han; Darby, Alistair C.; Hill, Catherine A.; Johnston, J. Spencer; Murphy, Terence D.; Raikhel, Alexander S.; Sattelle, David B.; Sharakhov, Igor V.; White, Bradley J.; Zhao, Li; Aiden, Erez Lieberman; Mann, Richard S.; Lambrechts, Louis; Powell, Jeffrey R.; Sharakhova, Maria V.; Tu, Zhijian Jake; Robertson, Hugh M.; McBride, Carolyn S.; Hastic, Alex R.; Korlach, Jonas; Neafsey, Daniel E.; Phillippy, Adam M.; Vosshall, Leslie B. (2018-11-22)
    Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector.
  • Thumbnail Image
    Improved reference genome of the arboviral vector Aedes albopictus
    Palatini, Umberto; Masri, Reem A.; Cosme, Luciano V.; Koren, Sergey; Thibaud-Nissen, Françoise; Biedler, James K.; Krsticevic, Flavia; Johnston, J. Spencer; Halbach, Rebecca; Crawford, Jacob E.; Antoshechkin, Igor; Failloux, Anna-Bella; Pischedda, Elisa; Marconcini, Michele; Ghurye, Jay; Rhie, Arang; Sharma, Atashi; Karagodin, Dmitriy A.; Jenrette, Jeremy; Gamez, Stephanie; Miesen, Pascal; Masterson, Patrick; Caccone, Adalgisa; Sharakhova, Maria V.; Tu, Zhijian Jake; Papathanos, Philippos A.; Van Rij, Ronald P.; Akbari, Omar S.; Powell, Jeffrey R.; Phillippy, Adam M.; Bonizzoni, Mariangela (2020-08-26)
    Background The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes. Results We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes. Conclusions The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.