Dinh H

References (6)

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 : The genome of the model beetle and pest Tribolium castaneum - Richards_2008_Nature_452_949
Author(s) : Richards S , Gibbs RA , Weinstock GM , Brown SJ , Denell R , Beeman RW , Gibbs R , Bucher G , Friedrich M , Grimmelikhuijzen CJ , Klingler M , Lorenzen M , Roth S , Schroder R , Tautz D , Zdobnov EM , Muzny D , Attaway T , Bell S , Buhay CJ , Chandrabose MN , Chavez D , Clerk-Blankenburg KP , Cree A , Dao M , Davis C , Chacko J , Dinh H , Dugan-Rocha S , Fowler G , Garner TT , Garnes J , Gnirke A , Hawes A , Hernandez J , Hines S , Holder M , Hume J , Jhangiani SN , Joshi V , Khan ZM , Jackson L , Kovar C , Kowis A , Lee S , Lewis LR , Margolis J , Morgan M , Nazareth LV , Nguyen N , Okwuonu G , Parker D , Ruiz SJ , Santibanez J , Savard J , Scherer SE , Schneider B , Sodergren E , Vattahil S , Villasana D , White CS , Wright R , Park Y , Lord J , Oppert B , Brown S , Wang L , Weinstock G , Liu Y , Worley K , Elsik CG , Reese JT , Elhaik E , Landan G , Graur D , Arensburger P , Atkinson P , Beidler J , Demuth JP , Drury DW , Du YZ , Fujiwara H , Maselli V , Osanai M , Robertson HM , Tu Z , Wang JJ , Wang S , Song H , Zhang L , Werner D , Stanke M , Morgenstern B , Solovyev V , Kosarev P , Brown G , Chen HC , Ermolaeva O , Hlavina W , Kapustin Y , Kiryutin B , Kitts P , Maglott D , Pruitt K , Sapojnikov V , Souvorov A , Mackey AJ , Waterhouse RM , Wyder S , Kriventseva EV , Kadowaki T , Bork P , Aranda M , Bao R , Beermann A , Berns N , Bolognesi R , Bonneton F , Bopp D , Butts T , Chaumot A , Denell RE , Ferrier DE , Gordon CM , Jindra M , Lan Q , Lattorff HM , Laudet V , von Levetsow C , Liu Z , Lutz R , Lynch JA , da Fonseca RN , Posnien N , Reuter R , Schinko JB , Schmitt C , Schoppmeier M , Shippy TD , Simonnet F , Marques-Souza H , Tomoyasu Y , Trauner J , Van der Zee M , Vervoort M , Wittkopp N , Wimmer EA , Yang X , Jones AK , Sattelle DB , Ebert PR , Nelson D , Scott JG , Muthukrishnan S , Kramer KJ , Arakane Y , Zhu Q , Hogenkamp D , Dixit R , Jiang H , Zou Z , Marshall J , Elpidina E , Vinokurov K , Oppert C , Evans J , Lu Z , Zhao P , Sumathipala N , Altincicek B , Vilcinskas A , Williams M , Hultmark D , Hetru C , Hauser F , Cazzamali G , Williamson M , Li B , Tanaka Y , Predel R , Neupert S , Schachtner J , Verleyen P , Raible F , Walden KK , Angeli S , Foret S , Schuetz S , Maleszka R , Miller SC , Grossmann D
Ref : Nature , 452 :949 , 2008
Abstract : Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
ESTHER : Richards_2008_Nature_452_949
PubMedSearch : Richards_2008_Nature_452_949
PubMedID: 18362917
Gene_locus related to this paper: trica-ACHE1 , trica-ACHE2 , trica-d2a0g9 , trica-d2a0h0 , trica-d2a0w9 , trica-d2a0x0 , trica-d2a0x1 , trica-d2a0x3 , trica-d2a0x4.1 , trica-d2a0x4.2 , trica-d2a0x6 , trica-d2a2b8 , trica-d2a2h1 , trica-d2a3c3 , trica-d2a3g9 , trica-d2a5y5 , trica-d2a309 , trica-d2a514 , trica-d2a515 , trica-d2a516 , trica-d2a577 , trica-d2a578 , trica-d6w6x8 , trica-d6w7f9 , trica-d6w7h2 , trica-d6w8e7 , trica-d6w9c0 , trica-d6w855 , trica-d6wac8 , trica-d6wan4 , trica-d6wd50 , trica-d6wd73 , trica-d6wd74 , trica-A0A139WM97 , trica-d6wfu3 , trica-d6wgl2 , trica-d6wj57 , trica-d6wj59 , trica-d6wjs3 , trica-d6wl31 , trica-d6wnv1 , trica-d6wpl0 , trica-d6wqd6 , trica-d6wqr4 , trica-d6ws52 , trica-d6wsm0 , trica-d6wu38 , trica-d6wu39 , trica-d6wu40 , trica-d6wu41 , trica-d6wu44 , trica-d6wvk5 , trica-d6wvz7 , trica-d6wwu9 , trica-d6wwv0 , trica-d6wxz0 , trica-d6wyy1 , trica-d6wyy2 , trica-d6x0z2 , trica-d6x0z5 , trica-d6x0z6 , trica-d6x4b2 , trica-d6x4e8 , trica-d6x4e9 , trica-d6x197 , trica-d7eip7 , trica-d7eld3 , trica-d7us45 , trica-q5wm43 , trica-q5zex9 , trica-d6wie5 , trica-d6w7t0 , trica-d6x4h0 , trica-d6x4h1 , trica-a0a139wae8 , trica-a0a139wc96 , trica-d6x325 , trica-d2a4s2 , trica-d6wvw8

Title : Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032 - Gioia_2007_PLoS.One_2_e928
Author(s) : Gioia J , Yerrapragada S , Qin X , Jiang H , Igboeli OC , Muzny D , Dugan-Rocha S , Ding Y , Hawes A , Liu W , Perez L , Kovar C , Dinh H , Lee S , Nazareth L , Blyth P , Holder M , Buhay C , Tirumalai MR , Liu Y , Dasgupta I , Bokhetache L , Fujita M , Karouia F , Eswara Moorthy P , Siefert J , Uzman A , Buzumbo P , Verma A , Zwiya H , McWilliams BD , Olowu A , Clinkenbeard KD , Newcombe D , Golebiewski L , Petrosino JF , Nicholson WL , Fox GE , Venkateswaran K , Highlander SK , Weinstock GM
Ref : PLoS ONE , 2 :e928 , 2007
Abstract : BACKGROUND: Bacillus spores are notoriously resistant to unfavorable conditions such as UV radiation, gamma-radiation, H2O2, desiccation, chemical disinfection, or starvation. Bacillus pumilus SAFR-032 survives standard decontamination procedures of the Jet Propulsion Lab spacecraft assembly facility, and both spores and vegetative cells of this strain exhibit elevated resistance to UV radiation and H2O2 compared to other Bacillus species. PRINCIPAL FINDINGS: The genome of B. pumilus SAFR-032 was sequenced and annotated. Lists of genes relevant to DNA repair and the oxidative stress response were generated and compared to B. subtilis and B. licheniformis. Differences in conservation of genes, gene order, and protein sequences are highlighted because they potentially explain the extreme resistance phenotype of B. pumilus. The B. pumilus genome includes genes not found in B. subtilis or B. licheniformis and conserved genes with sequence divergence, but paradoxically lacks several genes that function in UV or H2O2 resistance in other Bacillus species. SIGNIFICANCE: This study identifies several candidate genes for further research into UV and H2O2 resistance. These findings will help explain the resistance of B. pumilus and are applicable to understanding sterilization survival strategies of microbes.
ESTHER : Gioia_2007_PLoS.One_2_e928
PubMedSearch : Gioia_2007_PLoS.One_2_e928
PubMedID: 17895969
Gene_locus related to this paper: bacp2-a8f9m3 , bacp2-a8fa85 , bacp2-a8fgk8 , bacp2-a8fhg9 , bacp2-a8fjc9 , bacpu-AXE , bacpu-b4af62 , bacpu-b4ail3 , bacpu-b4ann4 , bacpu-b4apa9 , bacp2-a8f983 , bacp2-a8fgz0

Title : The DNA sequence of the human X chromosome - Ross_2005_Nature_434_325
Author(s) : Ross MT , Grafham DV , Coffey AJ , Scherer S , McLay K , Muzny D , Platzer M , Howell GR , Burrows C , Bird CP , Frankish A , Lovell FL , Howe KL , Ashurst JL , Fulton RS , Sudbrak R , Wen G , Jones MC , Hurles ME , Andrews TD , Scott CE , Searle S , Ramser J , Whittaker A , Deadman R , Carter NP , Hunt SE , Chen R , Cree A , Gunaratne P , Havlak P , Hodgson A , Metzker ML , Richards S , Scott G , Steffen D , Sodergren E , Wheeler DA , Worley KC , Ainscough R , Ambrose KD , Ansari-Lari MA , Aradhya S , Ashwell RI , Babbage AK , Bagguley CL , Ballabio A , Banerjee R , Barker GE , Barlow KF , Barrett IP , Bates KN , Beare DM , Beasley H , Beasley O , Beck A , Bethel G , Blechschmidt K , Brady N , Bray-Allen S , Bridgeman AM , Brown AJ , Brown MJ , Bonnin D , Bruford EA , Buhay C , Burch P , Burford D , Burgess J , Burrill W , Burton J , Bye JM , Carder C , Carrel L , Chako J , Chapman JC , Chavez D , Chen E , Chen G , Chen Y , Chen Z , Chinault C , Ciccodicola A , Clark SY , Clarke G , Clee CM , Clegg S , Clerc-Blankenburg K , Clifford K , Cobley V , Cole CG , Conquer JS , Corby N , Connor RE , David R , Davies J , Davis C , Davis J , Delgado O , Deshazo D , Dhami P , Ding Y , Dinh H , Dodsworth S , Draper H , Dugan-Rocha S , Dunham A , Dunn M , Durbin KJ , Dutta I , Eades T , Ellwood M , Emery-Cohen A , Errington H , Evans KL , Faulkner L , Francis F , Frankland J , Fraser AE , Galgoczy P , Gilbert J , Gill R , Glockner G , Gregory SG , Gribble S , Griffiths C , Grocock R , Gu Y , Gwilliam R , Hamilton C , Hart EA , Hawes A , Heath PD , Heitmann K , Hennig S , Hernandez J , Hinzmann B , Ho S , Hoffs M , Howden PJ , Huckle EJ , Hume J , Hunt PJ , Hunt AR , Isherwood J , Jacob L , Johnson D , Jones S , de Jong PJ , Joseph SS , Keenan S , Kelly S , Kershaw JK , Khan Z , Kioschis P , Klages S , Knights AJ , Kosiura A , Kovar-Smith C , Laird GK , Langford C , Lawlor S , Leversha M , Lewis L , Liu W , Lloyd C , Lloyd DM , Loulseged H , Loveland JE , Lovell JD , Lozado R , Lu J , Lyne R , Ma J , Maheshwari M , Matthews LH , McDowall J , Mclaren S , McMurray A , Meidl P , Meitinger T , Milne S , Miner G , Mistry SL , Morgan M , Morris S , Muller I , Mullikin JC , Nguyen N , Nordsiek G , Nyakatura G , O'Dell CN , Okwuonu G , Palmer S , Pandian R , Parker D , Parrish J , Pasternak S , Patel D , Pearce AV , Pearson DM , Pelan SE , Perez L , Porter KM , Ramsey Y , Reichwald K , Rhodes S , Ridler KA , Schlessinger D , Schueler MG , Sehra HK , Shaw-Smith C , Shen H , Sheridan EM , Shownkeen R , Skuce CD , Smith ML , Sotheran EC , Steingruber HE , Steward CA , Storey R , Swann RM , Swarbreck D , Tabor PE , Taudien S , Taylor T , Teague B , Thomas K , Thorpe A , Timms K , Tracey A , Trevanion S , Tromans AC , d'Urso M , Verduzco D , Villasana D , Waldron L , Wall M , Wang Q , Warren J , Warry GL , Wei X , West A , Whitehead SL , Whiteley MN , Wilkinson JE , Willey DL , Williams G , Williams L , Williamson A , Williamson H , Wilming L , Woodmansey RL , Wray PW , Yen J , Zhang J , Zhou J , Zoghbi H , Zorilla S , Buck D , Reinhardt R , Poustka A , Rosenthal A , Lehrach H , Meindl A , Minx PJ , Hillier LW , Willard HF , Wilson RK , Waterston RH , Rice CM , Vaudin M , Coulson A , Nelson DL , Weinstock G , Sulston JE , Durbin R , Hubbard T , Gibbs RA , Beck S , Rogers J , Bentley DR
Ref : Nature , 434 :325 , 2005
Abstract : The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.
ESTHER : Ross_2005_Nature_434_325
PubMedSearch : Ross_2005_Nature_434_325
PubMedID: 15772651
Gene_locus related to this paper: human-NLGN3 , human-NLGN4X