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1.  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, José | 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. | Ayllón, 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-Calderón, Gloria I. | Grabowski, Jeffrey M. | Jiang, David | Khalil, Sayed M. S. | Kim, Donghun | Kocan, Katherine M. | Koči, 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. | Sánchez-Gracia, Alejandro | Severo, Maiara S. | Silverman, Neal | Šimo, Ladislav | Tojo, Marta | Tornador, Cristian | Van Zee, Janice P. | Vázquez, Jesús | 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 | 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.
Nature Communications  2016;7:10507.
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 ∼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.
Ticks transmit a large number of pathogens that cause human diseases. Here, the authors sequence the genome of the tick Ixodes scapularis and uncover expansion of genes associated with parasitic processes unique to ticks and tick-host interactions.
doi:10.1038/ncomms10507
PMCID: PMC4748124  PMID: 26856261
2.  “Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes” 
Neafsey, Daniel E. | Waterhouse, Robert M. | Abai, Mohammad R. | Aganezov, Sergey S. | Alekseyev, Max A. | Allen, James E. | Amon, James | Arcà, Bruno | Arensburger, Peter | Artemov, Gleb | Assour, Lauren A. | Basseri, Hamidreza | Berlin, Aaron | Birren, Bruce W. | Blandin, Stephanie A. | Brockman, Andrew I. | Burkot, Thomas R. | Burt, Austin | Chan, Clara S. | Chauve, Cedric | Chiu, Joanna C. | Christensen, Mikkel | Costantini, Carlo | Davidson, Victoria L.M. | Deligianni, Elena | Dottorini, Tania | Dritsou, Vicky | Gabriel, Stacey B. | Guelbeogo, Wamdaogo M. | Hall, Andrew B. | Han, Mira V. | Hlaing, Thaung | Hughes, Daniel S.T. | Jenkins, Adam M. | Jiang, Xiaofang | Jungreis, Irwin | Kakani, Evdoxia G. | Kamali, Maryam | Kemppainen, Petri | Kennedy, Ryan C. | Kirmitzoglou, Ioannis K. | Koekemoer, Lizette L. | Laban, Njoroge | Langridge, Nicholas | Lawniczak, Mara K.N. | Lirakis, Manolis | Lobo, Neil F. | Lowy, Ernesto | MacCallum, Robert M. | Mao, Chunhong | Maslen, Gareth | Mbogo, Charles | McCarthy, Jenny | Michel, Kristin | Mitchell, Sara N. | Moore, Wendy | Murphy, Katherine A. | Naumenko, Anastasia N. | Nolan, Tony | Novoa, Eva M. | O'Loughlin, Samantha | Oringanje, Chioma | Oshaghi, Mohammad A. | Pakpour, Nazzy | Papathanos, Philippos A. | Peery, Ashley N. | Povelones, Michael | Prakash, Anil | Price, David P. | Rajaraman, Ashok | Reimer, Lisa J. | Rinker, David C. | Rokas, Antonis | Russell, Tanya L. | Sagnon, N'Fale | Sharakhova, Maria V. | Shea, Terrance | Simão, Felipe A. | Simard, Frederic | Slotman, Michel A. | Somboon, Pradya | Stegniy, Vladimir | Struchiner, Claudio J. | Thomas, Gregg W.C. | Tojo, Marta | Topalis, Pantelis | Tubio, José M.C. | Unger, Maria F. | Vontas, John | Walton, Catherine | Wilding, Craig S. | Willis, Judith H. | Wu, Yi-Chieh | Yan, Guiyun | Zdobnov, Evgeny M. | Zhou, Xiaofan | Catteruccia, Flaminia | Christophides, George K. | Collins, Frank H. | Cornman, Robert S. | Crisanti, Andrea | Donnelly, Martin J. | Emrich, Scott J. | Fontaine, Michael C. | Gelbart, William | Hahn, Matthew W. | Hansen, Immo A. | Howell, Paul I. | Kafatos, Fotis C. | Kellis, Manolis | Lawson, Daniel | Louis, Christos | Luckhart, Shirley | Muskavitch, Marc A.T. | Ribeiro, José M. | Riehle, Michael A. | Sharakhov, Igor V. | Tu, Zhijian | Zwiebel, Laurence J. | Besansky, Nora J.
Science (New York, N.Y.)  2014;347(6217):1258522.
Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover, but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.
doi:10.1126/science.1258522
PMCID: PMC4380271  PMID: 25554792
3.  Ensembl Genomes 2016: more genomes, more complexity 
Nucleic Acids Research  2015;44(Database issue):D574-D580.
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces.
doi:10.1093/nar/gkv1209
PMCID: PMC4702859  PMID: 26578574
4.  The fine scale genetic structure of the British population 
Nature  2015;519(7543):309-314.
Summary
Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide SNP data from a carefully chosen geographically diverse sample of 2,039 individuals from the United Kingdom (UK). This reveals a rich and detailed pattern of genetic differentiation with remarkable concordance between genetic clusters and geography. The regional genetic differentiation and differing patterns of shared ancestry with 6,209 individuals from across Europe carry clear signals of historical demographic events. We estimate the genetic contribution to SE England from Anglo-Saxon migrations to be under half, identify the regions not carrying genetic material from these migrations, suggest significant pre-Roman but post-Mesolithic movement into SE England from the Continent, and show that in non-Saxon parts of the UK there exist genetically differentiated subgroups rather than a general “Celtic” population.
doi:10.1038/nature14230
PMCID: PMC4632200  PMID: 25788095
5.  The BioMart community portal: an innovative alternative to large, centralized data repositories 
Smedley, Damian | Haider, Syed | Durinck, Steffen | Pandini, Luca | Provero, Paolo | Allen, James | Arnaiz, Olivier | Awedh, Mohammad Hamza | Baldock, Richard | Barbiera, Giulia | Bardou, Philippe | Beck, Tim | Blake, Andrew | Bonierbale, Merideth | Brookes, Anthony J. | Bucci, Gabriele | Buetti, Iwan | Burge, Sarah | Cabau, Cédric | Carlson, Joseph W. | Chelala, Claude | Chrysostomou, Charalambos | Cittaro, Davide | Collin, Olivier | Cordova, Raul | Cutts, Rosalind J. | Dassi, Erik | Genova, Alex Di | Djari, Anis | Esposito, Anthony | Estrella, Heather | Eyras, Eduardo | Fernandez-Banet, Julio | Forbes, Simon | Free, Robert C. | Fujisawa, Takatomo | Gadaleta, Emanuela | Garcia-Manteiga, Jose M. | Goodstein, David | Gray, Kristian | Guerra-Assunção, José Afonso | Haggarty, Bernard | Han, Dong-Jin | Han, Byung Woo | Harris, Todd | Harshbarger, Jayson | Hastings, Robert K. | Hayes, Richard D. | Hoede, Claire | Hu, Shen | Hu, Zhi-Liang | Hutchins, Lucie | Kan, Zhengyan | Kawaji, Hideya | Keliet, Aminah | Kerhornou, Arnaud | Kim, Sunghoon | Kinsella, Rhoda | Klopp, Christophe | Kong, Lei | Lawson, Daniel | Lazarevic, Dejan | Lee, Ji-Hyun | Letellier, Thomas | Li, Chuan-Yun | Lio, Pietro | Liu, Chu-Jun | Luo, Jie | Maass, Alejandro | Mariette, Jerome | Maurel, Thomas | Merella, Stefania | Mohamed, Azza Mostafa | Moreews, Francois | Nabihoudine, Ibounyamine | Ndegwa, Nelson | Noirot, Céline | Perez-Llamas, Cristian | Primig, Michael | Quattrone, Alessandro | Quesneville, Hadi | Rambaldi, Davide | Reecy, James | Riba, Michela | Rosanoff, Steven | Saddiq, Amna Ali | Salas, Elisa | Sallou, Olivier | Shepherd, Rebecca | Simon, Reinhard | Sperling, Linda | Spooner, William | Staines, Daniel M. | Steinbach, Delphine | Stone, Kevin | Stupka, Elia | Teague, Jon W. | Dayem Ullah, Abu Z. | Wang, Jun | Ware, Doreen | Wong-Erasmus, Marie | Youens-Clark, Ken | Zadissa, Amonida | Zhang, Shi-Jian | Kasprzyk, Arek
Nucleic Acids Research  2015;43(Web Server issue):W589-W598.
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
doi:10.1093/nar/gkv350
PMCID: PMC4489294  PMID: 25897122
6.  RNA-Rocket: an RNA-Seq analysis resource for infectious disease research 
Bioinformatics  2015;31(9):1496-1498.
Motivation: RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq analysis continue to change, creating a bioinformatics challenge for researchers who wish to exploit these data. Resources that bring together genomic data, analysis tools, educational material and computational infrastructure can minimize the overhead required of life science researchers.
Results: RNA-Rocket is a free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides and a user interface designed to enable both novice and experienced users of RNA-Seq data.
Availability and implementation: RNA-Rocket is available at rnaseq.pathogenportal.org. Source code for this project can be found at github.com/cidvbi/PathogenPortal.
Contact: anwarren@vt.edu
Supplementary information: Supplementary materials are available at Bioinformatics online.
doi:10.1093/bioinformatics/btv002
PMCID: PMC4410666  PMID: 25573919
7.  VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases 
Nucleic Acids Research  2014;43(Database issue):D707-D713.
VectorBase is a National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens. Now in its 11th year, VectorBase currently hosts the genomes of 35 organisms including a number of non-vectors for comparative analysis. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes. Here we describe improvements to our resource and the set of tools available for interrogating and accessing BRC data including the integration of Web Apollo to facilitate community annotation and providing Galaxy to support user-based workflows. VectorBase also actively supports our community through hands-on workshops and online tutorials. All information and data are freely available from our website at https://www.vectorbase.org/.
doi:10.1093/nar/gku1117
PMCID: PMC4383932  PMID: 25510499
8.  The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima 
Chipman, Ariel D. | Ferrier, David E. K. | Brena, Carlo | Qu, Jiaxin | Hughes, Daniel S. T. | Schröder, Reinhard | Torres-Oliva, Montserrat | Znassi, Nadia | Jiang, Huaiyang | Almeida, Francisca C. | Alonso, Claudio R. | Apostolou, Zivkos | Aqrawi, Peshtewani | Arthur, Wallace | Barna, Jennifer C. J. | Blankenburg, Kerstin P. | Brites, Daniela | Capella-Gutiérrez, Salvador | Coyle, Marcus | Dearden, Peter K. | Du Pasquier, Louis | Duncan, Elizabeth J. | Ebert, Dieter | Eibner, Cornelius | Erikson, Galina | Evans, Peter D. | Extavour, Cassandra G. | Francisco, Liezl | Gabaldón, Toni | Gillis, William J. | Goodwin-Horn, Elizabeth A. | Green, Jack E. | Griffiths-Jones, Sam | Grimmelikhuijzen, Cornelis J. P. | Gubbala, Sai | Guigó, Roderic | Han, Yi | Hauser, Frank | Havlak, Paul | Hayden, Luke | Helbing, Sophie | Holder, Michael | Hui, Jerome H. L. | Hunn, Julia P. | Hunnekuhl, Vera S. | Jackson, LaRonda | Javaid, Mehwish | Jhangiani, Shalini N. | Jiggins, Francis M. | Jones, Tamsin E. | Kaiser, Tobias S. | Kalra, Divya | Kenny, Nathan J. | Korchina, Viktoriya | Kovar, Christie L. | Kraus, F. Bernhard | Lapraz, François | Lee, Sandra L. | Lv, Jie | Mandapat, Christigale | Manning, Gerard | Mariotti, Marco | Mata, Robert | Mathew, Tittu | Neumann, Tobias | Newsham, Irene | Ngo, Dinh N. | Ninova, Maria | Okwuonu, Geoffrey | Ongeri, Fiona | Palmer, William J. | Patil, Shobha | Patraquim, Pedro | Pham, Christopher | Pu, Ling-Ling | Putman, Nicholas H. | Rabouille, Catherine | Ramos, Olivia Mendivil | Rhodes, Adelaide C. | Robertson, Helen E. | Robertson, Hugh M. | Ronshaugen, Matthew | Rozas, Julio | Saada, Nehad | Sánchez-Gracia, Alejandro | Scherer, Steven E. | Schurko, Andrew M. | Siggens, Kenneth W. | Simmons, DeNard | Stief, Anna | Stolle, Eckart | Telford, Maximilian J. | Tessmar-Raible, Kristin | Thornton, Rebecca | van der Zee, Maurijn | von Haeseler, Arndt | Williams, James M. | Willis, Judith H. | Wu, Yuanqing | Zou, Xiaoyan | Lawson, Daniel | Muzny, Donna M. | Worley, Kim C. | Gibbs, Richard A. | Akam, Michael | Richards, Stephen
PLoS Biology  2014;12(11):e1002005.
Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.
Author Summary
Arthropods are the most abundant animals on earth. Among them, insects clearly dominate on land, whereas crustaceans hold the title for the most diverse invertebrates in the oceans. Much is known about the biology of these groups, not least because of genomic studies of the fruit fly Drosophila, the water flea Daphnia, and other species used in research. Here we report the first genome sequence from a species belonging to a lineage that has previously received very little attention—the myriapods. Myriapods were among the first arthropods to invade the land over 400 million years ago, and survive today as the herbivorous millipedes and venomous centipedes, one of which—Strigamia maritima—we have sequenced here. We find that the genome of this centipede retains more characteristics of the presumed arthropod ancestor than other sequenced insect genomes. The genome provides access to many aspects of myriapod biology that have not been studied before, suggesting, for example, that they have diversified receptors for smell that are quite different from those used by insects. In addition, it shows specific consequences of the largely subterranean life of this particular species, which seems to have lost the genes for all known light-sensing molecules, even though it still avoids light.
doi:10.1371/journal.pbio.1002005
PMCID: PMC4244043  PMID: 25423365
9.  The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera 
Nature communications  2014;5:4737.
Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n=31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with ortholog-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n=31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.
doi:10.1038/ncomms5737
PMCID: PMC4164777  PMID: 25189940
10.  The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera 
Nature Communications  2014;5:4737.
Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n=31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n=31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.
Butterflies and moths (Lepidoptera) vary in chromosome number. Here, the authors sequence the genome of the Glanville fritillary butterfly, Melitaea cinxia, show it has the ancestral lepidopteran karyotype and provide insight into how chromosomal fusions have shaped karyotype evolution in butterflies and moths.
doi:10.1038/ncomms5737
PMCID: PMC4164777  PMID: 25189940
11.  Genome-Wide Analysis of Cold Adaptation in Indigenous Siberian Populations 
PLoS ONE  2014;9(5):e98076.
Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-)Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels and increased blood pressure that have been attributed to adaptation to the extreme cold climate. In this study we introduce a dataset of 200 individuals from ten indigenous Siberian populations that were genotyped for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. A region on chromosome 11 (chr11:66–69 Mb) contained the largest amount of clustering of significant signals and also the strongest signals in all the different selection tests performed. We present a list of candidate cold adaption genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA) and vascular smooth muscle contraction (PRKG1). By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture.
doi:10.1371/journal.pone.0098076
PMCID: PMC4029955  PMID: 24847810
12.  Apparent Strength Conceals Instability in a Model for the Collapse of Historical States 
PLoS ONE  2014;9(5):e96523.
An explanation for the political processes leading to the sudden collapse of empires and states would be useful for understanding both historical and contemporary political events. We examine political disintegration across eras, cultures and geographical scale to form a simple hypothesis that can be expressed verbally yet formulated mathematically. Factions within a state make choices described by game-theory about whether to accept the political status quo, or to attempt to better their circumstances through costly rebellion. In lieu of precise data we verify our model using sensitivity analysis. We find that a small amount of dissatisfaction is typically harmless to the state, but can trigger sudden collapse when there is a sufficient buildup of political inequality. Contrary to intuition, a state is predicted to be least stable when its leadership is at the height of its political power and thus most able to exert its influence through external warfare, lavish expense or autocratic decree.
doi:10.1371/journal.pone.0096523
PMCID: PMC4014536  PMID: 24810228
13.  Studying Culicoides vectors of BTV in the post-genomic era: Resources, bottlenecks to progress and future directions☆ 
Virus Research  2014;182:43-49.
Highlights
•Culicoides sonorensis is the only colonized species of bluetongue virus vector.•The development of a fully annotated genome for this species is in progress.•Transcriptomic analyses are being employed to investigate functional elements of the genome, particularly genes involved in hematophagy, reproduction, development and vector competence.
Culicoides biting midges (Diptera: Ceratopogonidae) are a major vector group responsible for the biological transmission of a wide variety of globally significant arboviruses, including bluetongue virus (BTV). In this review we examine current biological resources for the study of this genus, with an emphasis on detailing the history of extant colonies and cell lines derived from C. sonorensis, the major vector of BTV in the USA. We then discuss the rapidly developing area of genomic and transcriptomic analyses of biological processes in vectors and introduce the newly formed Culicoides Genomics and Transcriptomics Alliance. Preliminary results from these fields are detailed and finally likely areas of future research are discussed from an entomological perspective describing limitations in our understanding of Culicoides biology that may impede progress in these areas.
doi:10.1016/j.virusres.2013.12.009
PMCID: PMC3979112  PMID: 24355835
Ceratopogonidae; RNA-Seq; Transcriptome; Comparative genomics; Vector; Cell lines
14.  Ensembl Genomes 2013: scaling up access to genome-wide data 
Nucleic Acids Research  2013;42(Database issue):D546-D552.
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.
doi:10.1093/nar/gkt979
PMCID: PMC3965094  PMID: 24163254
15.  Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics 
Arensburger, Peter | Megy, Karine | Waterhouse, Robert M. | Abrudan, Jenica | Amedeo, Paolo | Antelo, Beatriz | Bartholomay, Lyric | Bidwell, Shelby | Caler, Elisabet | Camara, Francisco | Campbell, Corey L. | Campbell, Kathryn S. | Casola, Claudio | Castro, Marta T. | Chandramouliswaran, Ishwar | Chapman, Sinéad B. | Christley, Scott | Costas, Javier | Eisenstadt, Eric | Feshotte, Cedric | Fraser-Liggett, Claire | Guigo, Roderic | Haas, Brian | Hammond, Martin | Hansson, Bill S. | Hemingway, Janet | Hill, Sharon | Howarth, Clint | Ignell, Rickard | Kennedy, Ryan C. | Kodira, Chinnappa D. | Lobo, Neil F. | Mao, Chunhong | Mayhew, George | Michel, Kristin | Mori, Akio | Liu, Nannan | Naveira, Horacio | Nene, Vishvanath | Nguyen, Nam | Pearson, Matthew D. | Pritham, Ellen J. | Puiu, Daniela | Qi, Yumin | Ranson, Hilary | Ribeiro, Jose M. C. | Roberston, Hugh M. | Severson, David W. | Shumway, Martin | Stanke, Mario | Strausberg, Robert | Sun, Cheng | Sutton, Granger | Tu, Zhijian (Jake) | Tubio, Jose Manuel C. | Unger, Maria F. | Vanlandingham, Dana L. | Vilella, Albert J. | White, Owen | White, Jared R. | Wondji, Charles S. | Wortman, Jennifer | Zdobnov, Evgeny M. | Birren, Bruce | Christensen, Bruce M. | Collins, Frank H. | Cornel, Anthony | Dimopoulos, George | Hannick, Linda I. | Higgs, Stephen | Lanzaro, Gregory C. | Lawson, Daniel | Lee, Norman H. | Muskavitch, Marc A. T. | Raikhel, Alexander S. | Atkinson, Peter W.
Science (New York, N.Y.)  2010;330(6000):86-88.
Culex quinquefasciatus (the Southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus as well of nematodes that cause lymphatic filariasis. It is one species within the Culex pipiens species complex and enjoys a distribution throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock and humans contributes to its ability to vector pathogens between species. We describe the genomic sequence of C. quinquefasciatus, its repertoire of 18,883 protein-coding genes is 22% larger than Ae. aegypti and 52% larger than An. gambiae with multiple gene family expansions including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.
doi:10.1126/science.1191864
PMCID: PMC3740384  PMID: 20929810
16.  The Evolution of the Anopheles 16 Genomes Project 
G3: Genes|Genomes|Genetics  2013;3(7):1191-1194.
We report the imminent completion of a set of reference genome assemblies for 16 species of Anopheles mosquitoes. In addition to providing a generally useful resource for comparative genomic analyses, these genome sequences will greatly facilitate exploration of the capacity exhibited by some Anopheline mosquito species to serve as vectors for malaria parasites. A community analysis project will commence soon to perform a thorough comparative genomic investigation of these newly sequenced genomes. Completion of this project via the use of short next-generation sequence reads required innovation in both the bioinformatic and laboratory realms, and the resulting knowledge gained could prove useful for genome sequencing projects targeting other unconventional genomes.
doi:10.1534/g3.113.006247
PMCID: PMC3704246  PMID: 23708298
comparative; assembly; vector; malaria; collaboration
17.  Butterfly genome reveals promiscuous exchange of mimicry adaptations among species 
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. | Constant, Richard H. ffrench | Joron, Mathieu | Kronforst, Marcus R. | Mullen, Sean P. | Reed, Robert D. | Scherer, Steven E. | Richards, Stephen | Mallet, James | McMillan, W. Owen | Jiggins, Chris D.
Nature  2012;487(7405):94-98.
The evolutionary importance of hybridization and introgression has long been debated1. We used genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation2-5 . We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,657 predicted genes for Heliconius, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organisation has remained broadly conserved since the Cretaceous, when butterflies split from the silkmoth lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, H. melpomene, H. timareta, and H. elevatus, especially at two genomic regions that control mimicry pattern. Closely related Heliconius species clearly exchange protective colour pattern genes promiscuously, implying a major role for hybridization in adaptive radiation.
doi:10.1038/nature11041
PMCID: PMC3398145  PMID: 22722851
18.  Inference of Population Structure using Dense Haplotype Data 
PLoS Genetics  2012;8(1):e1002453.
The advent of genome-wide dense variation data provides an opportunity to investigate ancestry in unprecedented detail, but presents new statistical challenges. We propose a novel inference framework that aims to efficiently capture information on population structure provided by patterns of haplotype similarity. Each individual in a sample is considered in turn as a recipient, whose chromosomes are reconstructed using chunks of DNA donated by the other individuals. Results of this “chromosome painting” can be summarized as a “coancestry matrix,” which directly reveals key information about ancestral relationships among individuals. If markers are viewed as independent, we show that this matrix almost completely captures the information used by both standard Principal Components Analysis (PCA) and model-based approaches such as STRUCTURE in a unified manner. Furthermore, when markers are in linkage disequilibrium, the matrix combines information across successive markers to increase the ability to discern fine-scale population structure using PCA. In parallel, we have developed an efficient model-based approach to identify discrete populations using this matrix, which offers advantages over PCA in terms of interpretability and over existing clustering algorithms in terms of speed, number of separable populations, and sensitivity to subtle population structure. We analyse Human Genome Diversity Panel data for 938 individuals and 641,000 markers, and we identify 226 populations reflecting differences on continental, regional, local, and family scales. We present multiple lines of evidence that, while many methods capture similar information among strongly differentiated groups, more subtle population structure in human populations is consistently present at a much finer level than currently available geographic labels and is only captured by the haplotype-based approach. The software used for this article, ChromoPainter and fineSTRUCTURE, is available from http://www.paintmychromosomes.com/.
Author Summary
The first step in almost every genetic analysis is to establish how sample members are related to each other. High relatedness between individuals can arise if they share a small number of recent ancestors, e.g. if they are distant cousins or a larger number of more distant ones, e.g. if their ancestors come from the same region. The most popular methods for investigating these relationships analyse successive markers independently, simply adding the information they provide. This works well for studies involving hundreds of markers scattered around the genome but is less appropriate now that entire genomes can be sequenced. We describe a “chromosome painting” approach to characterising shared ancestry that takes into account the fact that DNA is transmitted from generation to generation as a linear molecule in chromosomes. We show that the approach increases resolution relative to previous techniques, allowing differences in ancestry profiles among individuals to be resolved at the finest scales yet. We provide mathematical, statistical, and graphical machinery to exploit this new information and to characterize relationships at continental, regional, local, and family scales.
doi:10.1371/journal.pgen.1002453
PMCID: PMC3266881  PMID: 22291602
19.  VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics 
Nucleic Acids Research  2011;40(Database issue):D729-D734.
VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community.
doi:10.1093/nar/gkr1089
PMCID: PMC3245112  PMID: 22135296
20.  Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species 
Nucleic Acids Research  2011;40(Database issue):D91-D97.
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of genomes.
doi:10.1093/nar/gkr895
PMCID: PMC3245118  PMID: 22067447
21.  BioMart Central Portal: an open database network for the biological community 
BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.
Database URL: http://central.biomart.org.
doi:10.1093/database/bar041
PMCID: PMC3263598  PMID: 21930507
22.  Ensembl’s 10th year 
Nucleic Acids Research  2009;38(Database issue):D557-D562.
Ensembl (http://www.ensembl.org) integrates genomic information for a comprehensive set of chordate genomes with a particular focus on resources for human, mouse, rat, zebrafish and other high-value sequenced genomes. We provide complete gene annotations for all supported species in addition to specific resources that target genome variation, function and evolution. Ensembl data is accessible in a variety of formats including via our genome browser, API and BioMart. This year marks the tenth anniversary of Ensembl and in that time the project has grown with advances in genome technology. As of release 56 (September 2009), Ensembl supports 51 species including marmoset, pig, zebra finch, lizard, gorilla and wallaby, which were added in the past year. Major additions and improvements to Ensembl since our previous report include the incorporation of the human GRCh37 assembly, enhanced visualisation and data-mining options for the Ensembl regulatory features and continued development of our software infrastructure.
doi:10.1093/nar/gkp972
PMCID: PMC2808936  PMID: 19906699
23.  VectorBase: a data resource for invertebrate vector genomics 
Nucleic Acids Research  2008;37(Database issue):D583-D587.
VectorBase (http://www.vectorbase.org) is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis. Since our last report VectorBase has initiated a community annotation system, a microarray and gene expression repository and controlled vocabularies for anatomy and insecticide resistance. We have continued to develop both the software infrastructure and tools for interrogating the stored data.
doi:10.1093/nar/gkn857
PMCID: PMC2686483  PMID: 19028744
24.  VectorBase: a home for invertebrate vectors of human pathogens 
Nucleic Acids Research  2006;35(Database issue):D503-D505.
VectorBase () is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for two organisms: Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever.
doi:10.1093/nar/gkl960
PMCID: PMC1751530  PMID: 17145709
25.  WormBase: a comprehensive data resource for Caenorhabditis biology and genomics 
Nucleic Acids Research  2004;33(Database Issue):D383-D389.
WormBase (http://www.wormbase.org), the model organism database for information about Caenorhabditis elegans and related nematodes, continues to expand in breadth and depth. Over the past year, WormBase has added multiple large-scale datasets including SAGE, interactome, 3D protein structure datasets and NCBI KOGs. To accommodate this growth, the International WormBase Consortium has improved the user interface by adding new features to aid in navigation, visualization of large-scale datasets, advanced searching and data mining. Internally, we have restructured the database models to rationalize the representation of genes and to prepare the system to accept the genome sequences of three additional Caenorhabditis species over the coming year.
doi:10.1093/nar/gki066
PMCID: PMC540020  PMID: 15608221

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