Dugan S

References (5)

Title : Hemimetabolous genomes reveal molecular basis of termite eusociality - Harrison_2018_Nat.Ecol.Evol_2_557
Author(s) : Harrison MC , Jongepier E , Robertson HM , Arning N , Bitard-Feildel T , Chao H , Childers CP , Dinh H , Doddapaneni H , Dugan S , Gowin J , Greiner C , Han Y , Hu H , Hughes DST , Huylmans AK , Kemena C , Kremer LPM , Lee SL , Lopez-Ezquerra A , Mallet L , Monroy-Kuhn JM , Moser A , Murali SC , Muzny DM , Otani S , Piulachs MD , Poelchau M , Qu J , Schaub F , Wada-Katsumata A , Worley KC , Xie Q , Ylla G , Poulsen M , Gibbs RA , Schal C , Richards S , Belles X , Korb J , Bornberg-Bauer E
Ref : Nat Ecol Evol , 2 :557 , 2018
Abstract : Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.
ESTHER : Harrison_2018_Nat.Ecol.Evol_2_557
PubMedSearch : Harrison_2018_Nat.Ecol.Evol_2_557
PubMedID: 29403074
Gene_locus related to this paper: blage-a0a2p8y5s3 , blage-a0a2p8yjf8.2 , blage-a0a2p8xjb6

Title : The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species - Papanicolaou_2016_Genome.Biol_17_192
Author(s) : Papanicolaou A , Schetelig MF , Arensburger P , Atkinson PW , Benoit JB , Bourtzis K , Castanera P , Cavanaugh JP , Chao H , Childers C , Curril I , Dinh H , Doddapaneni H , Dolan A , Dugan S , Friedrich M , Gasperi G , Geib S , Georgakilas G , Gibbs RA , Giers SD , Gomulski LM , Gonzalez-Guzman M , Guillem-Amat A , Han Y , Hatzigeorgiou AG , Hernandez-Crespo P , Hughes DS , Jones JW , Karagkouni D , Koskinioti P , Lee SL , Malacrida AR , Manni M , Mathiopoulos K , Meccariello A , Murali SC , Murphy TD , Muzny DM , Oberhofer G , Ortego F , Paraskevopoulou MD , Poelchau M , Qu J , Reczko M , Robertson HM , Rosendale AJ , Rosselot AE , Saccone G , Salvemini M , Savini G , Schreiner P , Scolari F , Siciliano P , Sim SB , Tsiamis G , Urena E , Vlachos IS , Werren JH , Wimmer EA , Worley KC , Zacharopoulou A , Richards S , Handler AM
Ref : Genome Biol , 17 :192 , 2016
Abstract : BACKGROUND: The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control.
RESULTS: The 479 Mb medfly genome is sequenced from adult flies from lines inbred for 20 generations. A high-quality assembly is achieved having a contig N50 of 45.7 kb and scaffold N50 of 4.06 Mb. In-depth curation of more than 1800 messenger RNAs shows specific gene expansions that can be related to invasiveness and host adaptation, including gene families for chemoreception, toxin and insecticide metabolism, cuticle proteins, opsins, and aquaporins. We identify genes relevant to IPM control, including those required to improve SIT.
CONCLUSIONS: The medfly genome sequence provides critical insights into the biology of one of the most serious and widespread agricultural pests. This knowledge should significantly advance the means of controlling the size and invasive potential of medfly populations. Its close relationship to Drosophila, and other insect species important to agriculture and human health, will further comparative functional and structural studies of insect genomes that should broaden our understanding of gene family evolution.
ESTHER : Papanicolaou_2016_Genome.Biol_17_192
PubMedSearch : Papanicolaou_2016_Genome.Biol_17_192
PubMedID: 27659211

Title : Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions - Anstead_2015_Nat.Commun_6_7344
Author(s) : Anstead CA , Korhonen PK , Young ND , Hall RS , Jex AR , Murali SC , Hughes DS , Lee SF , Perry T , Stroehlein AJ , Ansell BR , Breugelmans B , Hofmann A , Qu J , Dugan S , Lee SL , Chao H , Dinh H , Han Y , Doddapaneni HV , Worley KC , Muzny DM , Ioannidis P , Waterhouse RM , Zdobnov EM , James PJ , Bagnall NH , Kotze AC , Gibbs RA , Richards S , Batterham P , Gasser RB
Ref : Nat Commun , 6 :7344 , 2015
Abstract : Lucilia cuprina is a parasitic fly of major economic importance worldwide. Larvae of this fly invade their animal host, feed on tissues and excretions and progressively cause severe skin disease (myiasis). Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina. Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance. These insights have broad implications for designing new methods for the prevention and control of myiasis.
ESTHER : Anstead_2015_Nat.Commun_6_7344
PubMedSearch : Anstead_2015_Nat.Commun_6_7344
PubMedID: 26108605
Gene_locus related to this paper: luccu-a0a0l0bn77 , luccu-a0a0l0clk8 , luccu-a0a0l0bxv5 , luccu-a0a0l0bvt1 , luccu-a0a0l0bw31

Title : A catalog of reference genomes from the human microbiome - Nelson_2010_Science_328_994
Author(s) : Nelson KE , Weinstock GM , Highlander SK , Worley KC , Creasy HH , Wortman JR , Rusch DB , Mitreva M , Sodergren E , Chinwalla AT , Feldgarden M , Gevers D , Haas BJ , Madupu R , Ward DV , Birren BW , Gibbs RA , Methe B , Petrosino JF , Strausberg RL , Sutton GG , White OR , Wilson RK , Durkin S , Giglio MG , Gujja S , Howarth C , Kodira CD , Kyrpides N , Mehta T , Muzny DM , Pearson M , Pepin K , Pati A , Qin X , Yandava C , Zeng Q , Zhang L , Berlin AM , Chen L , Hepburn TA , Johnson J , McCorrison J , Miller J , Minx P , Nusbaum C , Russ C , Sykes SM , Tomlinson CM , Young S , Warren WC , Badger J , Crabtree J , Markowitz VM , Orvis J , Cree A , Ferriera S , Fulton LL , Fulton RS , Gillis M , Hemphill LD , Joshi V , Kovar C , Torralba M , Wetterstrand KA , Abouellleil A , Wollam AM , Buhay CJ , Ding Y , Dugan S , Fitzgerald MG , Holder M , Hostetler J , Clifton SW , Allen-Vercoe E , Earl AM , Farmer CN , Liolios K , Surette MG , Xu Q , Pohl C , Wilczek-Boney K , Zhu D
Ref : Science , 328 :994 , 2010
Abstract : The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.
ESTHER : Nelson_2010_Science_328_994
PubMedSearch : Nelson_2010_Science_328_994
PubMedID: 20489017
Gene_locus related to this paper: strp2-q04l35 , strpn-AXE1 , strpn-pepx

Title : Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus - Highlander_2007_BMC.Microbiol_7_99
Author(s) : Highlander SK , Hulten KG , Qin X , Jiang H , Yerrapragada S , Mason EO, Jr. , Shang Y , Williams TM , Fortunov RM , Liu Y , Igboeli O , Petrosino J , Tirumalai M , Uzman A , Fox GE , Cardenas AM , Muzny DM , Hemphill L , Ding Y , Dugan S , Blyth PR , Buhay CJ , Dinh HH , Hawes AC , Holder M , Kovar CL , Lee SL , Liu W , Nazareth LV , Wang Q , Zhou J , Kaplan SL , Weinstock GM
Ref : BMC Microbiol , 7 :99 , 2007
Abstract : BACKGROUND: Community acquired (CA) methicillin-resistant Staphylococcus aureus (MRSA) increasingly causes disease worldwide. USA300 has emerged as the predominant clone causing superficial and invasive infections in children and adults in the USA. Epidemiological studies suggest that USA300 is more virulent than other CA-MRSA. The genetic determinants that render virulence and dominance to USA300 remain unclear. RESULTS: We sequenced the genomes of two pediatric USA300 isolates: one CA-MRSA and one CA-methicillin susceptible (MSSA), isolated at Texas Children's Hospital in Houston. DNA sequencing was performed by Sanger dideoxy whole genome shotgun (WGS) and 454 Life Sciences pyrosequencing strategies. The sequence of the USA300 MRSA strain was rigorously annotated. In USA300-MRSA 2658 chromosomal open reading frames were predicted and 3.1 and 27 kilobase (kb) plasmids were identified. USA300-MSSA contained a 20 kb plasmid with some homology to the 27 kb plasmid found in USA300-MRSA. Two regions found in US300-MRSA were absent in USA300-MSSA. One of these carried the arginine deiminase operon that appears to have been acquired from S. epidermidis. The USA300 sequence was aligned with other sequenced S. aureus genomes and regions unique to USA300 MRSA were identified. CONCLUSION: USA300-MRSA is highly similar to other MRSA strains based on whole genome alignments and gene content, indicating that the differences in pathogenesis are due to subtle changes rather than to large-scale acquisition of virulence factor genes. The USA300 Houston isolate differs from another sequenced USA300 strain isolate, derived from a patient in San Francisco, in plasmid content and a number of sequence polymorphisms. Such differences will provide new insights into the evolution of pathogens.
ESTHER : Highlander_2007_BMC.Microbiol_7_99
PubMedSearch : Highlander_2007_BMC.Microbiol_7_99
PubMedID: 17986343
Gene_locus related to this paper: staa3-q2fkj0 , staau-LIP , staau-lipas , staau-MW0741 , staau-MW2456 , staau-q6gfm6 , staau-SA0011 , staau-SA0569 , staau-SA0572 , staau-SA0897 , staau-SA1143 , staau-SA2240 , staau-SA2306 , staau-SA2367 , staau-SA2422 , staau-SAV0321 , staau-SAV0446 , staau-SAV0457 , staau-SAV0655 , staau-SAV1014 , staau-SAV1765 , staau-SAV1793 , staau-SAV2188 , staau-SAV2350 , staau-SAV2594