Qu J

References (13)

Title : ABHD7-mediated depalmitoylation of lamin A promotes myoblast differentiation - Shen_2024_Cell.Rep_43_113720
Author(s) : Shen Y , Zheng LL , Fang CY , Xu YY , Wang C , Li JT , Lei MZ , Yin M , Lu HJ , Lei QY , Qu J
Ref : Cell Rep , 43 :113720 , 2024
Abstract : LMNA gene mutation can cause muscular dystrophy, and post-translational modification plays a critical role in regulating its function. Here, we identify that lamin A is palmitoylated at cysteine 522, 588, and 591 residues, which are reversely catalyzed by palmitoyltransferase zinc finger DHHC-type palmitoyltransferase 5 (ZDHHC5) and depalmitoylase alpha/beta hydrolase domain 7 (ABHD7). Furthermore, the metabolite lactate promotes palmitoylation of lamin A by inhibiting the interaction between it and ABHD7. Interestingly, low-level palmitoylation of lamin A promotes, whereas high-level palmitoylation of lamin A inhibits, murine myoblast differentiation. Together, these observations suggest that ABHD7-mediated depalmitoylation of lamin A controls myoblast differentiation.
ESTHER : Shen_2024_Cell.Rep_43_113720
PubMedSearch : Shen_2024_Cell.Rep_43_113720
PubMedID: 38308845
Gene_locus related to this paper: human-EPHX4 , mouse-ephx4

Title : Biodegradation of poly(ethylene terephthalate) through PETase surface-display: From function to structure - Han_2024_J.Hazard.Mater_461_132632
Author(s) : Han W , Zhang J , Chen Q , Xie Y , Zhang M , Qu J , Tan Y , Diao Y , Wang Y , Zhang Y
Ref : J Hazard Mater , 461 :132632 , 2024
Abstract : Polyethylene terephthalate (PET) is one of the most used plastics which has caused some environmental pollution and social problems. Although many newly discovered or modified PET hydrolases have been reported at present, there is still a lack of comparison between their hydrolytic capacities, as well as the need for new biotechnology to apply them for the PET treatment. Here, we systematically studied the surface-display technology for PET hydrolysis using several PET hydrolases. It is found that anchoring protein types had little influence on the surface-display result under T7 promoter, while the PET hydrolase types were more important. By contrast, the newly reported FAST-PETase showed the strongest hydrolysis effect, achieving 71.3% PET hydrolysis in 24 h by pGSA-FAST-PETase. Via model calculation, FAST-PETase indeed exhibited higher temperature tolerance and catalytic capacity. Besides, smaller particle size and lower crystallinity favored the hydrolysis of PET pellets. Through protein structure comparison, we summarized the common characteristics of efficient PET-hydrolyzing enzymes and proposed three main crystal structures of PET enzymes via crystal structural analysis, with ISPETase being the representative and main structure. Surface co-display of FAST-PETase and MHETase can promote the hydrolysis of PET, and the C-terminal of the fusion protein is crucial for PET hydrolysis. The results of our research can be helpful for PET contamination removal as well as other areas involving the application of enzymes. SYNOPSIS: This research can promote the development of better PET hydrolase and its applications in PET pollution treatment via bacteria surface-display.
ESTHER : Han_2024_J.Hazard.Mater_461_132632
PubMedSearch : Han_2024_J.Hazard.Mater_461_132632
PubMedID: 37804764

Title : Aerobic exercise-induced decrease of chemerin improved glucose and lipid metabolism and fatty liver of diabetes mice through key metabolism enzymes and proteins - Lin_2023_Biochim.Biophys.Acta.Mol.Cell.Biol.Lipids__159409
Author(s) : Lin X , Qu J , Yin L , Wang R , Wang X
Ref : Biochimica & Biophysica Acta Molecular & Cellular Biology Lipids , :159409 , 2023
Abstract : Our previous studies have implicated an important role of adipokine chemerin in exercise-induced improvements of glycolipid metabolism and fatty liver in diabetes rat, but the underlying mechanisms remain unknown. This study first used an exogenous chemerin supplement to clarify the roles of decreased chemerin in exercised diabetes mice and possible mechanisms of glucose and lipid metabolism key enzymes and proteins [such as adipose triglyceride lipase (ATGL), lipoprotein lipase (LPL), phosphoenolpyruvate carboxykinase (PEPCK), and glucose transporter 4 (GLUT4)]. In addition, two kinds of adipose-specific chemerin knockout mice were generated to demonstrate the regulation of chemerin on glucose and lipid metabolism enzymes and proteins. We found that in diabetes mice, exercise-induced improvements of glucose and lipid metabolism and fatty liver, and exercise-induced increases of ATGL, LPL, and GLUT4 in liver, gastrocnemius and fat were reversed by exogenous chemerin. Furthermore, in chemerin knockdown mice, chemerin(-/-)adiponectin mice had lower body fat mass, improved blood glucose and lipid, and no fatty liver; while chemerin(-/-)fabp4 mice had hyperlipemia and unchanged body fat mass. Peroxisome proliferator-activated receptor gamma (PPARgamma), ATGL, LPL, GLUT4 and PEPCK in the liver and gastrocnemius had improve changes in chemerin(-/-).adiponectin mice while deteriorated alterations in chemerin(-/-).fabp4 mice, although PPARgamma, ATGL, LPL, and GLUT4 increased in the fat of two kinds of chemerin(-/-) mice. CONCLUSIONS: Decreased chemerin exerts an important role in exercise-induced improvements of glucose and lipid metabolism and fatty liver in diabetes mice, which was likely to be through PPARgamma mediating elevations of ATGL, LPL and GLUT4 in peripheral metabolic organs.
ESTHER : Lin_2023_Biochim.Biophys.Acta.Mol.Cell.Biol.Lipids__159409
PubMedSearch : Lin_2023_Biochim.Biophys.Acta.Mol.Cell.Biol.Lipids__159409
PubMedID: 37871796

Title : Acquisition of T6SS Effector TseL Contributes to the Emerging of Novel Epidemic Strains of Pseudomonas aeruginosa - Ren_2022_Microbiol.Spectr__e0330822
Author(s) : Ren A , Jia M , Liu J , Zhou T , Wu L , Dong T , Cai Z , Qu J , Liu Y , Yang L , Zhang Y
Ref : Microbiol Spectr , :e0330822 , 2022
Abstract : Pseudomonas aeruginosa is an opportunistic pathogen with multiple strategies to interact with other microbes and host cells, gaining fitness in complicated infection sites. The contact-dependent type VI secretion system (T6SS) is one critical secretion apparatus involved in both interbacterial competition and pathogenesis. To date, only limited numbers of T6SS-effectors have been clearly characterized in P. aeruginosa laboratory strains, and the importance of T6SS diversity in the evolution of clinical P. aeruginosa remains unclear. Recently, we characterized a P. aeruginosa clinical strain LYSZa7 from a COVID-19 patient, which adopted complex genetic adaptations toward chronic infections. Bioinformatic analysis has revealed a putative type VI secretion system (T6SS) dependent lipase effector in LYSZa7, which is a homologue of TseL in Vibrio cholerae and is widely distributed in pathogens. We experimentally validated that this TseL homologue belongs to the Tle2, a subfamily of T6SS-lipase effectors; thereby, we name this effector TseL (TseL(PA) in this work). Further, we showed the lipase-dependent bacterial toxicity of TseL(PA), which primarily targets bacterial periplasm. The toxicity of TseL(PA) can be neutralized by two immunity proteins, TsiP1 and TsiP2, which are encoded upstream of tseL. In addition, we proved this TseL(PA) contributes to bacterial pathogenesis by promoting bacterial internalization into host cells. Our study suggests that clinical bacterial strains employ a diversified group of T6SS effectors for interbacterial competition and might contribute to emerging of new epidemic clonal lineages. IMPORTANCE Pseudomonas aeruginosa is one predominant pathogen that causes hospital-acquired infections and is one of the commonest coinfecting bacteria in immunocompromised patients and chronic wounds. This bacterium harbors a diverse accessory genome with a high frequency of gene recombination, rendering its population highly heterogeneous. Numerous Pa lineages coexist in the biofilm, where successful epidemic clonal lineage or strain-specific type commonly acquires genes to increase its fitness over the other organisms. Current studies of Pa genomic diversity commonly focused on antibiotic resistant genes and novel phages, overlooking the contribution of type VI secretion system (T6SS). We characterized a Pa clinical strain LYSZa7 from a COVID-19 patient, which adopted complex genetic adaptations toward chronic infections. We report, in this study, a novel T6SS-lipase effector that is broadly distributed in Pa clinical isolates and other predominant pathogens. The study suggests that hospital transmission may raise the emergence of new epidemic clonal lineages with specified T6SS effectors.
ESTHER : Ren_2022_Microbiol.Spectr__e0330822
PubMedSearch : Ren_2022_Microbiol.Spectr__e0330822
PubMedID: 36546869
Gene_locus related to this paper: pseae-T6SSTseL

Title : Analysis of the performance of the efficient di-(2-ethylhexyl) phthalate-degrading bacterium Rhodococcus pyridinovorans DNHP-S2 and associated catabolic pathways - Wang_2022_Chemosphere_306_135610
Author(s) : Wang L , Gan D , Gong L , Zhang Y , Wang J , Guan R , Zeng L , Qu J , Dong M
Ref : Chemosphere , 306 :135610 , 2022
Abstract : The widespread use of plastic has led to the global occurrence of phthalate esters (PAEs) pollution. PAEs can be effectively removed from polluted environments by microbe-mediated degradation. Di-(2-ethylhexyl) phthalate (DEHP) has the highest residual concentration in agricultural soil-contaminated areas compared to other PAEs in most of China. The Rhodococcus pyridinovorans DNHP-S2 microbial isolate identified was found to efficiently degrade DEHP. Within a 72 h period, the bacteria were able to degrade 52.47% and 99.75% of 500 mg L(-1) DEHP at 10 degreesC and 35 degreesC, respectively. Dimethyl phthalate (DMP) was first identified as an intermediate metabolite of DEHP, which is different from the previously reported DEHP catabolic pathway. Genomic sequencing of DNHP-S2 identified benzoate 1,2-dioxygenase and catechol 2,3/1,2-dioxygenase as potential mediators of DEHP degradation, consistent with the existence of two downstream metabolic pathways governing DEHP degradation. Three targets DEHP metabolism-related enzymes were found to be DEHP-inducible at the mRNA level, and DNHP-S2 was able to mediate the complete degradation of DEHP at lower temperatures, as confirmed via RT-qPCR. DNHP-S2 was also found to readily break down other PAEs including DMP, di-n-butyl phthalate (DBP), di-n-octyl phthalate (DnOP), and n-butyl benzyl phthalate (BBP). Together, these results thus highlight DNHP-S2 as a bacterial strain with great promise as a tool for the remediation of PAE pollution. In addition to providing new germplasm and genetic resources for use in the context of PAE degradation, these results also offer new insight into the potential mechanisms whereby PAEs undergo catabolic degradation, making them well-suited for use in PAE-contaminated environments.
ESTHER : Wang_2022_Chemosphere_306_135610
PubMedSearch : Wang_2022_Chemosphere_306_135610
PubMedID: 35810862

Title : Old pesticide, new use: Smart and safe enantiomer of isocarbophos in locust control - Kong_2021_Ecotoxicol.Environ.Saf_225_112710
Author(s) : Kong Y , Ji C , Qu J , Chen Y , Wu S , Zhu X , Niu L , Zhao M
Ref : Ecotoxicology & Environmental Safety , 225 :112710 , 2021
Abstract : Locust plagues are still worldwide problems. Selecting active enantiomers from current chiral insecticides is necessary for controlling locusts and mitigating the pesticide pollution in agricultural lands. Herein, two enantiomers of isocarbophos (ICP) were separated and the enantioselectivity in insecticidal activity against the pest Locusta migratoria manilensis (L. migratoria) and mechanisms were investigated. The significant difference of LD(50) between (+)-ICP (0.609 mg/kg bw) and (-)-ICP (79.412 mg/kg bw) demonstrated that (+)-ICP was a more effective enantiomer. The enantioselectivity in insecticidal activity of ICP enantiomers could be attributed to the selective affinity to acetylcholinesterase (AChE). Results of in vivo and in vitro assays suggested that AChE was more sensitive to (+)-ICP. In addition, molecular docking showed that the -CDOKER energies of (+)-ICP and (-)-ICP were 25.6652 and 24.4169, respectively, which suggested a stronger affinity between (+)-ICP and AChE. Significant selectivity also occurred in detoxifying enzymes activities (carboxylesterases (CarEs) and glutathione S-transferases (GSTs)) and related gene expressions. Suppression of detoxifying enzymes activities with (+)-ICP treatment suggested that (-)-ICP may induce the detoxifying enzyme-mediated ICP resistance. A more comprehensive understanding of the enantioselectivity of ICP is necessary for improving regulation and risk assessment of ICP.
ESTHER : Kong_2021_Ecotoxicol.Environ.Saf_225_112710
PubMedSearch : Kong_2021_Ecotoxicol.Environ.Saf_225_112710
PubMedID: 34481357

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 : Asymmetric Construction of a Multi-Pharmacophore-Containing Dispirotriheterocyclic Scaffold and Identification of a Human Carboxylesterase 1 Inhibitor - Bao_2018_Org.Lett_20_3394
Author(s) : Bao X , Wei S , Qian X , Qu J , Wang B , Zou L , Ge G
Ref : Org Lett , 20 :3394 , 2018
Abstract : A catalytic asymmetric [3 + 2] cyclization of novel 4-isothiocyanato pyrazolones and isatin-derived ketimines was developed, delivering a wide range of intriguing dispirotriheterocyclic products in high yield with excellent diastereoselectivity and enantioselectivity. A chiral sulfoxide derivative of this dispirocyclic product was identified to be a promising hit of the human carboxylesterase 1 inhibitor, and the significant difference of the activity between two enantiomers emphasized the importance of this asymmetric process.
ESTHER : Bao_2018_Org.Lett_20_3394
PubMedSearch : Bao_2018_Org.Lett_20_3394
PubMedID: 29786435

Title : Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species - Pearce_2017_BMC.Biol_15_63
Author(s) : Pearce SL , Clarke DF , East PD , Elfekih S , Gordon KHJ , Jermiin LS , McGaughran A , Oakeshott JG , Papanicolaou A , Perera OP , Rane RV , Richards S , Tay WT , Walsh TK , Anderson A , Anderson CJ , Asgari S , Board PG , Bretschneider A , Campbell PM , Chertemps T , Christeller JT , Coppin CW , Downes SJ , Duan G , Farnsworth CA , Good RT , Han LB , Han YC , Hatje K , Horne I , Huang YP , Hughes DST , Jacquin-Joly E , James W , Jhangiani S , Kollmar M , Kuwar SS , Li S , Liu NY , Maibeche MT , Miller JR , Montagne N , Perry T , Qu J , Song SV , Sutton GG , Vogel H , Walenz BP , Xu W , Zhang HJ , Zou Z , Batterham P , Edwards OR , Feyereisen R , Gibbs RA , Heckel DG , McGrath A , Robin C , Scherer SE , Worley KC , Wu YD
Ref : BMC Biol , 15 :63 , 2017
Abstract : BACKGROUND: Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests. RESULTS: We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100 extra gustatory receptor genes, compared to other lepidopterans with narrower host ranges. The two genomes remain very similar in gene content and order, but H. armigera is more polymorphic overall, and H. zea has lost several detoxification genes, as well as about 50 gustatory receptor genes. It also lacks certain genes and alleles conferring insecticide resistance found in H. armigera. Non-synonymous sites in the expanded gene families above are rapidly diverging, both between paralogues and between orthologues in the two species. Whole genome transcriptomic analyses of H. armigera larvae show widely divergent responses to different host plants, including responses among many of the duplicated detoxification and digestion genes. CONCLUSIONS: The extreme polyphagy of the two heliothines is associated with extensive amplification and neofunctionalisation of genes involved in host finding and use, coupled with versatile transcriptional responses on different hosts. H. armigera's invasion of the Americas in recent years means that hybridisation could generate populations that are both locally adapted and insecticide resistant.
ESTHER : Pearce_2017_BMC.Biol_15_63
PubMedSearch : Pearce_2017_BMC.Biol_15_63
PubMedID: 28756777
Gene_locus related to this paper: helam-a0a2w1bn75 , helam-a0a2w1bp69 , helam-a0a2w1bvf3

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 genomes of two key bumblebee species with primitive eusocial organization - Sadd_2015_Genome.Biol_16_76
Author(s) : Sadd BM , Barribeau SM , Bloch G , de Graaf DC , Dearden P , Elsik CG , Gadau J , Grimmelikhuijzen CJ , Hasselmann M , Lozier JD , Robertson HM , Smagghe G , Stolle E , Van Vaerenbergh M , Waterhouse RM , Bornberg-Bauer E , Klasberg S , Bennett AK , Camara F , Guigo R , Hoff K , Mariotti M , Munoz-Torres M , Murphy T , Santesmasses D , Amdam GV , Beckers M , Beye M , Biewer M , Bitondi MM , Blaxter ML , Bourke AF , Brown MJ , Buechel SD , Cameron R , Cappelle K , Carolan JC , Christiaens O , Ciborowski KL , Clarke DF , Colgan TJ , Collins DH , Cridge AG , Dalmay T , Dreier S , du Plessis L , Duncan E , Erler S , Evans J , Falcon T , Flores K , Freitas FC , Fuchikawa T , Gempe T , Hartfelder K , Hauser F , Helbing S , Humann FC , Irvine F , Jermiin LS , Johnson CE , Johnson RM , Jones AK , Kadowaki T , Kidner JH , Koch V , Kohler A , Kraus FB , Lattorff HM , Leask M , Lockett GA , Mallon EB , Antonio DS , Marxer M , Meeus I , Moritz RF , Nair A , Napflin K , Nissen I , Niu J , Nunes FM , Oakeshott JG , Osborne A , Otte M , Pinheiro DG , Rossie N , Rueppell O , Santos CG , Schmid-Hempel R , Schmitt BD , Schulte C , Simoes ZL , Soares MP , Swevers L , Winnebeck EC , Wolschin F , Yu N , Zdobnov EM , Aqrawi PK , Blankenburg KP , Coyle M , Francisco L , Hernandez AG , Holder M , Hudson ME , Jackson L , Jayaseelan J , Joshi V , Kovar C , Lee SL , Mata R , Mathew T , Newsham IF , Ngo R , Okwuonu G , Pham C , Pu LL , Saada N , Santibanez J , Simmons D , Thornton R , Venkat A , Walden KK , Wu YQ , Debyser G , Devreese B , Asher C , Blommaert J , Chipman AD , Chittka L , Fouks B , Liu J , O'Neill MP , Sumner S , Puiu D , Qu J , Salzberg SL , Scherer SE , Muzny DM , Richards S , Robinson GE , Gibbs RA , Schmid-Hempel P , Worley KC
Ref : Genome Biol , 16 :76 , 2015
Abstract : BACKGROUND: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.
RESULTS: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.
CONCLUSIONS: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.
ESTHER : Sadd_2015_Genome.Biol_16_76
PubMedSearch : Sadd_2015_Genome.Biol_16_76
PubMedID: 25908251

Title : Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology - English_2012_PLoS.One_7_e47768
Author(s) : English AC , Richards S , Han Y , Wang M , Vee V , Qu J , Qin X , Muzny DM , Reid JG , Worley KC , Gibbs RA
Ref : PLoS ONE , 7 :e47768 , 2012
Abstract : Many genomes have been sequenced to high-quality draft status using Sanger capillary electrophoresis and/or newer short-read sequence data and whole genome assembly techniques. However, even the best draft genomes contain gaps and other imperfections due to limitations in the input data and the techniques used to build draft assemblies. Sequencing biases, repetitive genomic features, genomic polymorphism, and other complicating factors all come together to make some regions difficult or impossible to assemble. Traditionally, draft genomes were upgraded to "phase 3 finished" status using time-consuming and expensive Sanger-based manual finishing processes. For more facile assembly and automated finishing of draft genomes, we present here an automated approach to finishing using long-reads from the Pacific Biosciences RS (PacBio) platform. Our algorithm and associated software tool, PBJelly, (publicly available at https://sourceforge.net/projects/pb-jelly/) automates the finishing process using long sequence reads in a reference-guided assembly process. PBJelly also provides "lift-over" co-ordinate tables to easily port existing annotations to the upgraded assembly. Using PBJelly and long PacBio reads, we upgraded the draft genome sequences of a simulated Drosophila melanogaster, the version 2 draft Drosophila pseudoobscura, an assembly of the Assemblathon 2.0 budgerigar dataset, and a preliminary assembly of the Sooty mangabey. With 24x mapped coverage of PacBio long-reads, we addressed 99% of gaps and were able to close 69% and improve 12% of all gaps in D. pseudoobscura. With 4x mapped coverage of PacBio long-reads we saw reads address 63% of gaps in our budgerigar assembly, of which 32% were closed and 63% improved. With 6.8x mapped coverage of mangabey PacBio long-reads we addressed 97% of gaps and closed 66% of addressed gaps and improved 19%. The accuracy of gap closure was validated by comparison to Sanger sequencing on gaps from the original D. pseudoobscura draft assembly and shown to be dependent on initial reference quality.
ESTHER : English_2012_PLoS.One_7_e47768
PubMedSearch : English_2012_PLoS.One_7_e47768
PubMedID: 23185243
Gene_locus related to this paper: drome-GH02439