Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

Yeisoo Yu | Oded Cohen | Ilan Paran | Seon-In Yeom | Byung-Dong Kim | Byoung-Cheorl Kang | Eunyoung Seo | Suk-Yoon Kwon | James J. Giovannoni | Ryan W. Kim | Allen Van Deynze | Jocelyn K. C. Rose | Hamid Ashrafi | Jaeyoung Choi | Doil Choi | Junhyung Park | Yeong Deuk Jo | Younhee Shin | Kyongyong Jung | Paul W. Bosland | Young Sam Seo | Yong-Min Kim | C. Shin | Yeisoo Yu | I. Choi | J. Giovannoni | Bong-Woo Lee | W. Kim | D. Choi | R. Kim | H. Ashrafi | Yeon-Ki Kim | J. Rose | Sang-Bong Choi | M. Suh | Saet-Byul Kim | H. Pai | P. Bosland | I. Paran | Hee-Jin Jeong | Jeong Mee Park | Jaeyoung Choi | Kyongyong Jung | Yong-Hwan Lee | Gir-Won Lee | Ki-Tae Kim | Kyeong-Chae Cheong | Sang Jik Lee | Je Min Lee | Sung-Hwan Jo | Suk-Yoon. Kwon | Byung-Dong Kim | Minkyu Park | Seungil Kim | Seon-In Yeom | Y. Choi | Y. Shin | Y. S. Seo | Beom-Soon Choi | Jongsung Lim | I. Yeam | Beom-Seok Park | O. Cohen | T. Hill | W. Kang | Iben Sørensen | Iben Sørensen | Hyung-Taeg Cho | Yong-Hwan Lee | J. H. Huh | A. Deynze | J. Park | JaeYun Lim | Gregory Reeves | Yong-Min Kim | Hyun-ah Lee | Eunyoung Seo | Sang-Keun Oh | Chungyun Bae | Hyeyoung Lee | Shin-Young Kim | Myung-Shin Kim | B. Kang | Y. Jo | Hee-Bum Yang | Jin-Kyung Kwon | June-Sik Kim | S. Lee | S. Noh | Junhyung Park | Hyun A. Kim | H. Kim | Hyung-Taeg Cho | Heeseung Choi | M. Lee | H. Ahn | Hee Kyung Ahn | Chanseok Shin | Sang-Jik Lee | Ki-Tae Kim | Yang Do Choi | Jae Yun Lim | Mi Chung Suh | Saet Buyl Lee | Seungill Kim | Minkyu Park | Hyun-Ah Lee | Kyeongchae Cheong | Gir-Won Lee | Sang Keun Oh | Chungyun Bae | Saet-Byul Kim | Hyeyoung Lee | Shin Young Kim | Myung Shin Kim | Hee Bum Yang | Hee Jin Jeong | Won-Hee Kang | Jin Kyung Kwon | June Hyun Park | Jin Hoe Huh | June Sik Kim | Yeon Ki Kim | Seung Jae Noh | Hyun Jin Kim | Sang Bong Choi | Gregory Reeves | Sung Hwan Jo | Bong Woo Lee | Heeseung Choi | Min Soo Lee | Beom Seok Park | Theresa Hill | Woo Taek Kim | Hyunsook Pai | Inhwa Yeam | Sang Jik Lee | Ik Young Choi | Beom Soon Choi | Jong Sung Lim | Min-Soo Lee | Shinje Kim | Ik-Young Choi | Hyun-Jin Kim | J. Huh | Hye-Young Lee | Jaeyun Lim | Hyun-Ah Lee | Hee-Seung Choi | J. Park | Seungill Kim

[1]  R. Oelmüller,et al.  WRKY transcription factors , 2014, Plant signaling & behavior.

[2]  M. Suh,et al.  Recent advances in cuticular wax biosynthesis and its regulation in Arabidopsis. , 2013, Molecular plant.

[3]  B. Hamberger,et al.  Plant P450s as versatile drivers for evolution of species-specific chemical diversity , 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.

[4]  Wanhui Kim,et al.  Generation and analysis of a complete mutant set for the Arabidopsis FT/TFL1 family shows specific effects on thermo-sensitive flowering regulation , 2013, Journal of experimental botany.

[5]  H. Ashrafi,et al.  Identification of QTLs for capsaicinoids, fruit quality, and plant architecture-related traits in an interspecific Capsicum RIL population. , 2013, Genome.

[6]  J. Ohlrogge,et al.  Acyl-Lipid Metabolism , 2013, The arabidopsis book.

[7]  Niranjan Nagarajan,et al.  The draft genome of sweet orange (Citrus sinensis) , 2012, Nature Genetics.

[8]  Mihaela M. Martis,et al.  A physical, genetic and functional sequence assembly of the barley genome , 2012, Nature.

[9]  P. Kersey,et al.  Analysis of the bread wheat genome using whole genome shotgun sequencing , 2012, Nature.

[10]  Saravanaraj N. Ayyampalayam,et al.  The banana (Musa acuminata) genome and the evolution of monocotyledonous plants , 2012, Nature.

[11]  J. Ohlrogge,et al.  A Land-Plant-Specific Glycerol-3-Phosphate Acyltransferase Family in Arabidopsis: Substrate Specificity, sn-2 Preference, and Evolution1[W][OA] , 2012, Plant Physiology.

[12]  G. Hagen,et al.  Getting a grasp on domain III/IV responsible for Auxin Response Factor-IAA protein interactions. , 2012, Plant science : an international journal of experimental plant biology.

[13]  J. Giovannoni,et al.  Uniform ripening Encodes a Golden 2-like Transcription Factor Regulating Tomato Fruit Chloroplast Development , 2012, Science.

[14]  Y. Li-Beisson,et al.  Solving the puzzles of cutin and suberin polymer biosynthesis. , 2012, Current opinion in plant biology.

[15]  Zhangjun Fei,et al.  Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum , 2012, Molecular Genetics and Genomics.

[16]  Daniel W. A. Buchan,et al.  The tomato genome sequence provides insights into fleshy fruit evolution , 2012, Nature.

[17]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[18]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[19]  R. Mattes,et al.  The effects of capsaicin and capsiate on energy balance: critical review and meta-analyses of studies in humans. , 2012, Chemical senses.

[20]  Jeremy D. DeBarry,et al.  MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.

[21]  J. Giovannoni,et al.  Genetics and control of tomato fruit ripening and quality attributes. , 2011, Annual review of genetics.

[22]  J. Abelenda,et al.  Control of flowering and storage organ formation in potato by FLOWERING LOCUS T , 2011, Nature.

[23]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[24]  S. Zhong,et al.  High-throughput illumina strand-specific RNA sequencing library preparation. , 2011, Cold Spring Harbor protocols.

[25]  R. Bino,et al.  Metabolite biodiversity in pepper (Capsicum) fruits of thirty-two diverse accessions: variation in health-related compounds and implications for breeding. , 2011, Phytochemistry.

[26]  Xing Xu,et al.  An Archaeopteryx-like theropod from China and the origin of Avialae , 2011, Nature.

[27]  David M. A. Martin,et al.  Genome sequence and analysis of the tuber crop potato , 2011, Nature.

[28]  M. Lascoux,et al.  Evolution of the PEBP Gene Family in Plants: Functional Diversification in Seed Plant Evolution1[W][OA] , 2011, Plant Physiology.

[29]  S. Kikuchi,et al.  Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. , 2011, Plant & cell physiology.

[30]  Walter Pirovano,et al.  BIOINFORMATICS APPLICATIONS , 2022 .

[31]  F. Beisson,et al.  Cytochrome P450 metabolizing fatty acids in plants: characterization and physiological roles , 2011, The FEBS journal.

[32]  José M. Sempere,et al.  The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 , 2010, Nucleic Acids Res..

[33]  David R. Kelley,et al.  Quake: quality-aware detection and correction of sequencing errors , 2010, Genome Biology.

[34]  Ari Löytynoja,et al.  webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser , 2010, BMC Bioinformatics.

[35]  Roger E Bumgarner,et al.  The genome of the domesticated apple (Malus × domestica Borkh.) , 2010, Nature Genetics.

[36]  Qian Gao,et al.  Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa , 2010, BMC Plant Biology.

[37]  Xingliang Hou,et al.  MOTHER OF FT AND TFL1 Regulates Seed Germination through a Negative Feedback Loop Modulating ABA Signaling in Arabidopsis[C][W] , 2010, Plant Cell.

[38]  Zinan Wang,et al.  Increased vitamin C content accompanied by an enhanced recycling pathway confers oxidative stress tolerance in Arabidopsis. , 2010, Journal of integrative plant biology.

[39]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[40]  Birgit Kersten,et al.  PlnTFDB: updated content and new features of the plant transcription factor database , 2009, Nucleic Acids Res..

[41]  J. Ohlrogge,et al.  Nanoridges that characterize the surface morphology of flowers require the synthesis of cutin polyester , 2009, Proceedings of the National Academy of Sciences.

[42]  Xiao-Feng Jin,et al.  Genome-wide analysis of the putative AP2/ERF family genes in Vitis vinifera. , 2009 .

[43]  L. Samuels,et al.  Plant cuticles shine: advances in wax biosynthesis and export. , 2009, Current opinion in plant biology.

[44]  Asan,et al.  The genome of the cucumber, Cucumis sativus L. , 2009, Nature Genetics.

[45]  Dawn H. Nagel,et al.  The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.

[46]  J. Vrebalov,et al.  Fleshy Fruit Expansion and Ripening Are Regulated by the Tomato SHATTERPROOF Gene TAGL1[W][OA] , 2009, The Plant Cell Online.

[47]  R. Hawley,et al.  Heterochromatin: A Rapidly Evolving Species Barrier , 2009, PLoS biology.

[48]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[49]  D. Kosma,et al.  Arabidopsis CER8 encodes LONG-CHAIN ACYL-COA SYNTHETASE 1 (LACS1) that has overlapping functions with LACS2 in plant wax and cutin synthesis. , 2009, The Plant journal : for cell and molecular biology.

[50]  L. Mueller,et al.  A Dynamic Interface for Capsaicinoid Systems Biology1[C][W][OA] , 2009, Plant Physiology.

[51]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[52]  P. Morrell,et al.  Genetic diversity and structure in semiwild and domesticated chiles (Capsicum annuum; Solanaceae) from Mexico. , 2009, American journal of botany.

[53]  I. Somssich,et al.  The Role of WRKY Transcription Factors in Plant Immunity[W] , 2009, Plant Physiology.

[54]  Mihaela M. Martis,et al.  The Sorghum bicolor genome and the diversification of grasses , 2009, Nature.

[55]  Y. Eshed,et al.  Co-ordinated regulation of flowering time, plant architecture and growth by FASCICULATE: the pepper orthologue of SELF PRUNING , 2009, Journal of experimental botany.

[56]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[57]  Marta de Torres-Zabala,et al.  Transcriptional regulation by an NAC (NAM-ATAF1,2-CUC2) transcription factor attenuates ABA signalling for efficient basal defence towards Blumeria graminis f. sp. hordei in Arabidopsis. , 2008, The Plant journal : for cell and molecular biology.

[58]  Keithanne Mockaitis,et al.  Auxin receptors and plant development: a new signaling paradigm. , 2008, Annual review of cell and developmental biology.

[59]  Yiguo Hong,et al.  A tomato HD-Zip homeobox protein, LeHB-1, plays an important role in floral organogenesis and ripening , 2008, The Plant journal : for cell and molecular biology.

[60]  Stephen M. Mount,et al.  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) , 2008, Nature.

[61]  J. Long,et al.  TOPLESS Mediates Auxin-Dependent Transcriptional Repression During Arabidopsis Embryogenesis , 2008, Science.

[62]  Daniel F Voytas,et al.  Chromodomains direct integration of retrotransposons to heterochromatin. , 2008, Genome research.

[63]  Mercedes G. López,et al.  Virus-induced silencing of Comt, pAmt and Kas genes results in a reduction of capsaicinoid accumulation in chili pepper fruits , 2008, Planta.

[64]  Jonathan E. Allen,et al.  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.

[65]  H. Matsufuji,et al.  Anti‐oxidant content of different coloured sweet peppers, white, green, yellow, orange and red (Capsicum annuum L.) , 2007 .

[66]  J. Ohlrogge,et al.  Identification of acyltransferases required for cutin biosynthesis and production of cutin with suberin-like monomers , 2007, Proceedings of the National Academy of Sciences.

[67]  Gerben van Ooijen,et al.  Structure and function of resistance proteins in solanaceous plants. , 2007, Annual review of phytopathology.

[68]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[69]  A. Fernie,et al.  A Reevaluation of the Key Factors That Influence Tomato Fruit Softening and Integrity1[W][OA] , 2007, Plant Physiology.

[70]  Lars Arvestad,et al.  Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms. , 2007, Journal of experimental zoology. Part B, Molecular and developmental evolution.

[71]  Zongli Hu,et al.  Cloning and characterization of the EIN2-homology gene LeEIN2 from tomato , 2007, DNA sequence : the journal of DNA sequencing and mapping.

[72]  B. Roe,et al.  Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes , 2006, Proceedings of the National Academy of Sciences.

[73]  Graham J King,et al.  A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening , 2006, Nature Genetics.

[74]  Kazuo Shinozaki,et al.  Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. , 2006, Annual review of plant biology.

[75]  Y. Eshed,et al.  The tomato FT ortholog triggers systemic signals that regulate growth and flowering and substitute for diverse environmental stimuli. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[76]  S. Tanksley,et al.  Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome , 2006, Genetics.

[77]  Sören Lehmann,et al.  Capsaicin, a component of red peppers, inhibits the growth of androgen-independent, p53 mutant prostate cancer cells. , 2006, Cancer research.

[78]  S. Trenkamp,et al.  Genetic and biochemical evidence for involvement of HOTHEAD in the biosynthesis of long-chain alpha-,omega-dicarboxylic fatty acids and formation of extracellular matrix. , 2006, Planta.

[79]  J. Ohlrogge,et al.  Cuticular Lipid Composition, Surface Structure, and Gene Expression in Arabidopsis Stem Epidermis1[W] , 2005, Plant Physiology.

[80]  Y. Elkind,et al.  Characterization of physiological and biochemical factors associated with postharvest water loss in ripe pepper fruit during storage , 2005 .

[81]  D. Choi,et al.  Expression of a novel NAC domain-containing transcription factor (CaNAC1) is preferentially associated with incompatible interactions between chili pepper and pathogens , 2005, Planta.

[82]  Kede Liu,et al.  The Pun1 gene for pungency in pepper encodes a putative acyltransferase. , 2005, The Plant journal : for cell and molecular biology.

[83]  Jianwen Fang,et al.  Tracker: continuous HMMER and BLAST searching , 2005, Bioinform..

[84]  M. Westerterp-Plantenga,et al.  Sensory and gastrointestinal satiety effects of capsaicin on food intake , 2005, International Journal of Obesity.

[85]  Steven Salzberg,et al.  TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders , 2004, Bioinform..

[86]  Kazuo Shinozaki,et al.  A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stress-signaling pathway. , 2004, The Plant journal : for cell and molecular biology.

[87]  J. Concato,et al.  Treatment options in knee osteoarthritis: the patient's perspective. , 2004, Archives of internal medicine.

[88]  F. Tomás-Barberán,et al.  Characterization and quantitation of antioxidant constituents of sweet pepper (Capsicum annuum L.). , 2004, Journal of agricultural and food chemistry.

[89]  R. Durbin,et al.  GeneWise and Genomewise. , 2004, Genome research.

[90]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[91]  Keisuke Ito,et al.  Induction of Apoptosis in Leukemic Cells by Homovanillic Acid Derivative, Capsaicin, through Oxidative Stress , 2004, Cancer Research.

[92]  M. C. Heath.  Hypersensitive response-related death , 2000, Plant Molecular Biology.

[93]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[94]  M. Westerterp-Plantenga,et al.  Effect of capsaicin on substrate oxidation and weight maintenance after modest body-weight loss in human subjects , 2003, British Journal of Nutrition.

[95]  R. Michelmore,et al.  Genome-Wide Analysis of NBS-LRR–Encoding Genes in Arabidopsis Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.009308. , 2003, The Plant Cell Online.

[96]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[97]  E. Birney,et al.  Apollo: a sequence annotation editor , 2002, Genome Biology.

[98]  Y. Surh.  More than spice: capsaicin in hot chili peppers makes tumor cells commit suicide. , 2002, Journal of the National Cancer Institute.

[99]  Cédric Feschotte,et al.  Plant transposable elements: where genetics meets genomics , 2002, Nature Reviews Genetics.

[100]  J. Vrebalov,et al.  A MADS-Box Gene Necessary for Fruit Ripening at the Tomato Ripening-Inhibitor (Rin) Locus , 2002, Science.

[101]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[102]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[103]  G. Hagen,et al.  Auxin Response Factors , 2001, Journal of Plant Growth Regulation.

[104]  Rolf Apweiler,et al.  InterProScan - an integration platform for the signature-recognition methods in InterPro , 2001, Bioinform..

[105]  J. Giovannoni,et al.  MOLECULAR BIOLOGY OF FRUIT MATURATION AND RIPENING. , 2001, Annual review of plant physiology and plant molecular biology.

[106]  H. Klee,et al.  Members of the tomato LeEIL (EIN3-like) gene family are functionally redundant and regulate ethylene responses throughout plant development. , 2001, The Plant journal : for cell and molecular biology.

[107]  Wen Huang,et al.  The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant , 2001, Nucleic Acids Res..

[108]  N. Chua,et al.  Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. , 2000, Genes & development.

[109]  D. Zamir,et al.  An alternative pathway to beta -carotene formation in plant chromoplasts discovered by map-based cloning of beta and old-gold color mutations in tomato. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[110]  H J Klee,et al.  The tomato ethylene receptors NR and LeETR4 are negative regulators of ethylene response and exhibit functional compensation within a multigene family. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[111]  B. Staskawicz,et al.  Expression of the Bs2 pepper gene confers resistance to bacterial spot disease in tomato. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[112]  P. Huijser,et al.  Characterization of the FIDDLEHEAD Gene of Arabidopsis Reveals a Link between Adhesion Response and Cell Differentiation in the Epidermis , 1999, Plant Cell.

[113]  B C Meyers,et al.  Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. , 1999, The Plant journal : for cell and molecular biology.

[114]  Phillip SanMiguel,et al.  The paleontology of intergene retrotransposons of maize , 1998, Nature Genetics.

[115]  M. Ganal,et al.  The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. , 1998, Development.

[116]  J Schultz,et al.  SMART, a simple modular architecture research tool: identification of signaling domains. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[117]  D. Julius,et al.  The capsaicin receptor: a heat-activated ion channel in the pain pathway , 1997, Nature.

[118]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[119]  Gapped BLAST and PSI-BLAST: A new , 1997 .

[120]  Cornelius S. Barry,et al.  Differential expression of the 1-aminocyclopropane-1-carboxylate oxidase gene family of tomato. , 1996, The Plant journal : for cell and molecular biology.

[121]  Hsiao-Ching Yen,et al.  An Ethylene-Inducible Component of Signal Transduction Encoded by Never-ripe , 1995, Science.

[122]  M. Kuntz,et al.  Metabolism of cyclic carotenoids: a model for the alteration of this biosynthetic pathway in Capsicum annuum chromoplasts. , 1995, The Plant journal : for cell and molecular biology.

[123]  M. Van Montagu,et al.  Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. , 1994, The Plant cell.

[124]  J. Deli,et al.  Carotenoid composition of yellow pepper during ripening: isolation of beta-cryptoxanthin 5,6-epoxide , 1991 .

[125]  A. Lupas,et al.  Predicting coiled coils from protein sequences , 1991, Science.

[126]  B. Ames,et al.  Ascorbate is an outstanding antioxidant in human blood plasma. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[127]  L. Mejia,et al.  Carotenoid Content and Vitamin A Activity of Some Common Cultivars of Mexican Peppers (Caps&m annuum) as Determined by HPLC , 1988 .

[128]  F. Guengerich.  Cytochromes P-450. , 1988, Comparative biochemistry and physiology. C, Comparative pharmacology and toxicology.

[129]  K. Iwai,et al.  Intracellular localization of capsaicin and its analogues in Capsicum fruit II. The vacuole as the intracellular accumulation site of capsaicinoid in the protoplast of Capsicum fruit , 1980 .

[130]  E. Leete,et al.  Biosynthesis of capsaicin and dihydrocapsaicin in Capsicum frutescens. , 1968, Journal of the American Chemical Society.

[131]  D. J. Bennett,et al.  Constitution and biosynthesis of capsaicin , 1968 .