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| 1 | Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library显示文摘Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes,however,the utility of this technology for complex plant genomes is unproven.We evaluated the technology for this purpose by sequencing the 3.5-gigabase(Gb)diploid pepper(Capsicum annuum)genome with a single Linked-Read library.Plant genomes,including pepper,are characterized by long,highly similar repetitive sequences.Accordingly,significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus.With a phased assembly approach,we targeted a heterozygous F1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/deletion.The Supernova software generated a highly ordered,more contiguous sequence assembly than all currently available C.annuum reference genomes.Over 83%of the final assembly was anchored and oriented using four publicly available de novo linkage maps.A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly.The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F1 sample that represents pungent and nonpungent peppers,as well as nearly full recovery of the BUSCO2 gene set within each of the two haplotypes.The most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant genomes.This technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction. | Amanda M.Hulse-Kemp Shamoni Maheshwari Kevin Stoffel Theresa A.Hill David Jaffe Stephen R.Williams Neil Weisenfeld Srividya Ramakrishnan Vijay Kumar Preyas Shah Michael C.Schatz Deanna M.Church Allen Van Deynze | 2018 | Horticulture Research2018，5，1： | 4 |
| 2 | Photodynamic therapeutics:basic principles and clinical applications显示文摘 | Allen CM Van Lier JE | 1999 | Drug Discovery Today1999，4，： | 1 |
| 3 | Potent and specific inhibition of the breast cancer resistance protein multidrug transporter in vitro and in mouse intestine by a novel analogue of fumitremorgin C显示文摘 | Allen J D van Loevezijn A Lakhai J M | 2002 | Mol Cancer Ther2002，1，6： | 1 |
| 4 | Topological considerations in isosurface generation显示文摘 | Allen van Gelder Jane wilhelms | 1994 | ACM Trans on Graphics1994，13，4： | 1 |
| 5 | Concordance of the Toxicity of Pharmaceuticals in Humans and in Animals显示文摘 | Harry Olson Graham Betton Denise Robinson Karluss Thomas Alastair Monro Gerald Kolaja Patrick Lilly James Sanders Glenn Sipes William Bracken Michael Dorato Koen Van Deun Peter Smith Bruce Berger Allen Heller | 2000 | Regulatory Toxicology and Pharmacology2000，，1： | 1 |
| 6 | Aeti-vating mTOR mutations in a patient with an extraordinary response on a phaseI trial of everolimus and pazopanib 显示文摘 | Wagle N Grabiner BC Van Allen EM | 2014 | Cancer Discov2014，4，5： | 1 |
| 7 | What do educational mismatches tell us about skill mismatches? a cross-country analysis 显示文摘 | ALLEN J VAN DER VELDEN R | 2007 | European Journal of Education2007，42，1： | 1 |
| 8 | Photodynamic therapeutics: basic principles and clinical applications 显示文摘 | SHARMAN WM ALLEN CM VAN LIER JE | 1999 | Drug Discovery Today1999，4，11： | 1 |
| 9 | Reduction in neural-tube defects after folic acid fortification in Canada显示文摘 | De Wals P Tairou F Van Allen MI | | 0，，： | 1 |
| 10 | Implemen- ting prognostic and predictive biomarkers in CRC clinical trials 显示文摘 | Van Schaeybroeck S Allen WL Turkington RC | 2011 | Nat Rev Clin Oncol2011，8，4： | 1 |
| 11 | Photodynamic therapeutics: basic principles and clinical applications 显示文摘 | Sharman WM Allen CM van Lier JE | 1999 | DDT1999，4，： | 1 |
| 12 | Mixed sclerosing bone dysplasia, small stature, seizure disorder, and mental retardation: a syndromle? 显示文摘 | Jurenka SB Van Allen | 1995 | AmJ MedGenet1995，57，1： | 1 |
| 13 | The major genetic determinants of HIV-1control affect HLA class I peptide presentation显示文摘 | International HIV Controllers Study Pereyra F Jia X McLaren P J Telenti A de Bakker P I Walker B D Ripke S Brumme C J Pulit S L Carrington M Kadie C M Carlson J M Heckerman D Graham R R Plenge R M Deeks S G Gianniny L Crawford G Sullivan J Gonzalez E Davies L Camargo A Moore JM Beattie N Gupta S Crenshaw A Burtt N P Guiducci C Gupta N Gao X Qi Y Yuki Y Piechocka-Trocha A Cutrell E Rosenberg R Moss K L Lemay P O'Leary J Schaefer T Verma P Toth I Block B Baker B Rothchild A Lian J Proudfoot J Alvino D M Vine S Addo M M Allen T M Altfeld M Henn M R Le Gall S Streeck H Haas D W Kuritzkes D R Robbins G K Shafer R W Gulick R M Shikuma C M Haubrich R Riddler S Sax P E Daar E S Ribaudo H J Agan B Agarwal S Ahern R L Allen B L Altidor S Altschuler E L Ambardar S Anastos K Anderson B Anderson V Andrady U Antoniskis D Bangsberg D Barbaro D Barrie W Bartczak J Barton S Basden P Basgoz N Bazner S Bellos N C Benson A M Berger J Bernard N F Bernard A M Birch C Bodner S J Bolan R K Boudreaux E T Bradley M Braun J F Brndjar J E Brown S J Brown K Brown S T Burack J Bush LM Cafaro V Campbell O Campbell J Carlson R H Carmichael J K Casey K K Cavacuiti C Celestin G Chambers S T Chez N Chirch L M Cimoch P J Cohen D Cohn LE Conway B Cooper D A Cornelson B Cox D T Cristofano M V Cuchural G Jr Czartoski J L Dahman J M Daly J S Davis B T Davis K Davod S M DeJesus E Dietz C A Dunham E Dunn M E Ellerin T B Eron J J Fangman J J Farel C E Ferlazzo H Fidler S Fleenor-Ford A Frankel R Freedberg K A French N K Fuchs JD Fuller J D Gaberman J Gallant J E Gandhi R T Garcia E Garmon D Gathe J C Jr Gaultier C R Gebre W Gilman F D Gilson I Goepfert P A Gottlieb M S Goulston C Groger R K Gurley T D Haber S Hardwicke R Hardy W D Harrigan P R Hawkins T N Heath S Hecht F M Henry W K Hladek M Hoffman R P Horton J M Hsu R K Huhn G D Hunt P Hupert M J Illeman M L Jaeger H Jellinger R M John M Johnson J A Johnson K L Johnson H Johnson K Joly J Jordan W C Kauffman C A Khanlou H Killian R K Kim A Y Kim D D Kinder C A Kirchner J T Kogelman L Kojic E M Korthuis P T Kurisu W Kwon D S LaMar M Lampiris H Lanzafame M Lederman M M Lee D M Lee J M Lee M J Lee E T Lemoine J Levy J A Llibre J M Liguori M A Little S J Liu A Y Lopez A J Loutfy M R Loy D Mohammed D Y Man A Mansour M K Marconi V C Markowitz M Marques R Martin J N Martin H L Jr Mayer K H McElrath M J McGhee T A McGovern B H McGowan K McIntyre D Mcleod GX Menezes P Mesa G Metroka CE Meyer-Olson D Miller A O Montgomery K Mounzer K C Nagami E H Nagin I Nahass R G Nelson M O Nielsen C Norene D L O'Connor D H Ojikutu B O Okulicz J Oladehin O O Oldfield E C Olender S A Ostrowski M Owen WF Jr Pae E Parsonnet J Pavlatos A M Perlmutter A M Pierce M N Pincus J M Pisani L Price L J Proia L Prokesch R C Pujet H C Ramgopal M Rathod A Rausch M Ravishankar J Rhame F S Richards C S Richman D D Rodes B Rodriguez M Rose R C 3rd Rosenberg E S Rosenthal D Ross P E Rubin D S Rumbaugh E Saenz L Salvaggio M R Sanchez WC Sanjana V M Santiago S Schmidt W Schuitemaker H Sestak P M Shalit P Shay W Shirvani V N Silebi V I Sizemore J M Jr Skolnik P R Sokol-Anderson M Sosman J M Stabile P Stapleton J T Starrett S Stein F Stellbrink H J Sterman FL Stone V E Stone D R Tambussi G Taplitz R A Tedaldi E M Telenti A Theisen W Torres R Tosiello L Tremblay C Tribble M A Trinh P D Tsao A Ueda P Vaccaro A Valadas E Vanig T J Vecino I Vega V M Veikley W Wade B H Walworth C Wanidworanun C Ward D J Warner D A Weber R D Webster D Weis S Wheeler D A White D J Wilkins E Winston A Wlodaver C G van't Wout A Wright D P Yang O O Yurdin D L Zabukovic B W Zachary K C Zeeman B Zhao M | 2010 | Science2010，330，6010： | 1 |
| 14 | Reduction in neural-tube defects after folic acid fortification in Canada显示文摘 | De Wals P Tairou F Van Allen M I | 2007 | N Engl J Med2007，357，： | 1 |
| 15 | An Empirically Based Model of Competitor Intelligence Use显示文摘 | Peyrot M Childs N Van Doren D Allen K | 2002 | Journal of Business Research2002，55，9： | 1 |
| 16 | Astigmatic laser mode converters and transfer of orbital angular momentum显示文摘 | Beijersbergen M Allen L Van der Veen H | 1993 | Optics Communications1993，96，1： | 1 |
| 17 | The basic reproduction number in some discrete-time epidemic models 显示文摘 | ALLEN L J S VAN DEN DRIESSCHE P | 2008 | Journal of Difference Equations and Applications2008，14，5： | 1 |
| 18 | Constriction bands and limb reduction defects in two newborns with fetal ultrasound evidence for vascular disruption 显示文摘 | Van Allen MI Siegel-Bartelt I Dixon I | 1992 | Am J Med Genet1992，44，5： | 1 |
| 19 | Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1infection显示文摘 | Crawford H Prado J G Leslie A HuéS Honeyborne I Reddy S van der Stok M Mncube Z Brander C Rousseau C Mullins J I Kaslow R Goepfert P Allen S Hunter E Mulenga J Kiepiela P Walker B D Goulder P J | 2007 | J Virol2007，81，15： | 1 |
| 20 | Basic principles of celestial navigation显示文摘 | Van Allen J A | 2004 | American Journal of Physics2004，72，11： | 1 |
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