Author Report for: Fawcett JANo contact information in database for Fawcett JA
Grbic M, Van Leeuwen T, Clark RM, Rombauts S, Rouze P, Grbic V, Osborne EJ, Dermauw W, Ngoc PC and Van de Peer Y <45 more author(s)> Grbic M, Van Leeuwen T, Clark RM, Rombauts S, Rouze P, Grbic V, Osborne EJ, Dermauw W, Ngoc PC, Ortego F, Hernandez-Crespo P, Diaz I, Martinez M, Navajas M, Sucena E, Magalhaes S, Nagy L, Pace RM, Djuranovic S, Smagghe G, Iga M, Christiaens O, Veenstra JA, Ewer J, Villalobos RM, Hutter JL, Hudson SD, Velez M, Yi SV, Zeng J, Pires-daSilva A, Roch F, Cazaux M, Navarro M, Zhurov V, Acevedo G, Bjelica A, Fawcett JA, Bonnet E, Martens C, Baele G, Wissler L, Sanchez-Rodriguez A, Tirry L, Blais C, Demeestere K, Henz SR, Gregory TR, Mathieu J, Verdon L, Farinelli L, Schmutz J, Lindquist E, Feyereisen R, Van de Peer Y (- 45) Ref: Nature, 479:487, 2011 : PubMed ESTHER: Grbic_2011_Nature_479_487 PubMedSearch: Grbic 2011 Nature 479 487 PubMedID: 22113690 Gene_locus related to this paper: tetur-ACHE Abstract The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant-herbivore interactions, and provides unique opportunities for developing novel plant protection strategies. Title: The Arabidopsis lyrata genome sequence and the basis of rapid genome size change Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J and Guo YL <20 more author(s)> Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL (- 20) Ref: Nat Genet, 43:476, 2011 : PubMed ESTHER: Hu_2011_Nat.Genet_43_476 PubMedSearch: Hu 2011 Nat.Genet 43 476 PubMedID: 21478890 Gene_locus related to this paper: arall-d7kc59, arall-d7kfz1, arall-d7kjk9, arall-d7kk58, arall-d7kuj1, arall-d7kwx5, arall-d7kzq8, arall-d7laf7, arall-D7LAK6, arall-d7ltj2, arall-d7lu11, arall-d7ly06, arall-d7lyn6, arall-d7m1k0, arall-d7m1k1, arall-d7m1k3, arall-d7m1l4, arall-d7m814, arall-d7mbk0, arall-d7mbn8, arall-d7mgs1, arall-d7mi04, arall-d7mld7, arall-d7mpg7, arall-d7mul9, arath-At2g45610, arath-At1g05790, arath-At1g09980, arath-At1g18360, arath-AT1G29120, arath-AT1G73920, arath-AT1G76140, arath-AT2G05260, arath-At2g15230, arath-At2g24280, arath-AT2G42690, arath-At2g47630, arath-AT3G12150, arath-At3g61680, arath-AT3g62590, arath-AT4G00500, arath-AT4G25770, arath-AT4g30610, arath-At5g11650, arath-At5g13640, arath-AT5G19050, arath-AT5G20060, arath-AT5G20520, arath-AT5G27320, arath-At5g42930, arath-At5g47330, arath-CGEP, arath-clh1, arath-clh2, arath-F1N13.220, arath-F2G14.100, arath-F12A4.4, arath-F14O10.2, arath-SCP27, arath-HNL, arath-GID1B, arath-LIP2, arath-At5g17670, arath-pip, arath-PLA11, arath-PLA12, arath-PLA13, arath-PLA15, arath-PLA17, arath-Q8LPF5, arath-Q9FFZ1, arath-Q9FJ29, arath-Q9FKP9, arath-Q9FNF6, arath-q9lhe8, arath-Q9SFF6, arath-q84w08, arath-SCP7, arath-SCP8, arath-SCP26, arath-SCP28, arath-SCP33, arath-SCP40, arath-SCPL34, arath-At4g12230, arath-MES14, arath-T19F11.2, arath-MES10, arath-At5g11790, arath-T26B15.8, arath-ZW18, arall-d7l971, arall-d7lfd3, arall-d7lg04, arall-d7lg05, arall-d7lg06, arall-d7lg07, arall-d7mb17, arall-d7mb18, arall-d7l7v2, arall-d7l7v3, arall-d7lst0, arall-d7lfw9, arall-d7mgs6, arall-d7mur3, arall-d7kjr5, arall-d7l7v1, arall-d7ls88, arall-d7kzg6, arall-d7kcm6, arall-d7krm0, arall-d7kwe4, arall-d7lri7 Abstract We report the 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47 based on 8.3x dideoxy sequence coverage. We predict 32,670 genes in this outcrossing species compared to the 27,025 genes in the selfing species Arabidopsis thaliana. The much smaller 125-Mb genome of A. thaliana, which diverged from A. lyrata 10 million years ago, likely constitutes the derived state for the family. We found evidence for DNA loss from large-scale rearrangements, but most of the difference in genome size can be attributed to hundreds of thousands of small deletions, mostly in noncoding DNA and transposons. Analysis of deletions and insertions still segregating in A. thaliana indicates that the process of DNA loss is ongoing, suggesting pervasive selection for a smaller genome. The high-quality reference genome sequence for A. lyrata will be an important resource for functional, evolutionary and ecological studies in the genus Arabidopsis. Title: The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA and Boore JL <60 more author(s)> Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin IT, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL (- 60) Ref: Science, 319:64, 2008 : PubMed ESTHER: Rensing_2008_Science_319_64 PubMedSearch: Rensing 2008 Science 319 64 PubMedID: 18079367 Gene_locus related to this paper: phypa-a9rbi6, phypa-a9rfh1, phypa-a9rg19, phypa-a9rgt9, phypa-a9rhz9, phypa-a9rkj1, phypa-a9rns2, phypa-a9rp52, phypa-a9rq03, phypa-a9ry17, phypa-a9ry72, phypa-a9s5n8, phypa-a9s6w1, phypa-a9s8c7, phypa-a9s299, phypa-a9san7, phypa-a9sc75, phypa-a9se75, phypa-a9sg07, phypa-a9skf7, phypa-a9skr1, phypa-a9skw1, phypa-a9sl58, phypa-a9slp7, phypa-a9smq5, phypa-a9sp13, phypa-a9ssb0, phypa-a9sse1, phypa-a9ssf6, phypa-a9st85, phypa-a9sx74, phypa-a9sy58, phypa-a9syy4, phypa-a9t0n4, phypa-a9t0p4, phypa-a9t1j2, phypa-a9t5h1, phypa-a9t7g6, phypa-a9t8u8, phypa-a9t9c9, phypa-a9t9d9, phypa-a0a7i4d2t7, phypa-a9t498, phypa-a9tbu4, phypa-a9tc36, phypa-a9tds0, phypa-a9te64, phypa-a9tfw2, phypa-a9tin6, phypa-a9tja4, phypa-a9tmp3, phypa-a9tmr4, phypa-a9tql4, phypa-a9tr83, phypa-a9tsl1, phypa-a9tsv6, phypa-a9tu05, phypa-a9tw81, phypa-a9tyr8, phypa-a9u0c9, phypa-a9u0k3, phypa-a9u0p4, phypa-a9u2u7, phypa-a9u3s0, phypa-a9tfm7, phypa-a9tfp6, phypa-a9syg9, phypa-a9tzk2, phypa-a9tvg4, phypa-a9t1y4, phypa-a9tqt6, phypa-a9st18, phypa-a9tix9, phypa-a0a2k1kfe3, phypa-a9sqk3, phypa-a0a2k1ie71, phypa-a0a2k1kg29, phypa-a0a2k1iji3 Abstract We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics. Title: A high quality draft consensus sequence of the genome of a heterozygous grapevine variety Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, FitzGerald LM, Vezzulli S and Viola R <47 more author(s)> Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, FitzGerald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti D, Macalma T, Facci M, Mitchell JT, Perazzolli M, Eldredge G, Gatto P, Oyzerski R, Moretto M, Gutin N, Stefanini M, Chen Y, Segala C, Davenport C, Dematte L, Mraz A, Battilana J, Stormo K, Costa F, Tao Q, Si-Ammour A, Harkins T, Lackey A, Perbost C, Taillon B, Stella A, Solovyev V, Fawcett JA, Sterck L, Vandepoele K, Grando SM, Toppo S, Moser C, Lanchbury J, Bogden R, Skolnick M, Sgaramella V, Bhatnagar SK, Fontana P, Gutin A, Van de Peer Y, Salamini F, Viola R (- 47) Ref: PLoS ONE, 2:e1326, 2007 : PubMed ESTHER: Velasco_2007_PLoS.ONE_2_e1326 PubMedSearch: Velasco 2007 PLoS.ONE 2 e1326 PubMedID: 18094749 Gene_locus related to this paper: vitvi-a5ajc4, vitvi-a5ama3, vitvi-a5ane2, vitvi-a5ayn8, vitvi-a5b3m9, vitvi-a5b5p5, vitvi-a5b6n6, vitvi-a5b6r9, vitvi-a5b7c0, vitvi-a5b7e5, vitvi-a5b8k1, vitvi-a5b8l9, vitvi-a5b8q6, vitvi-a5bft8, vitvi-a5bji4, vitvi-a5bkl0, vitvi-a5blq0, vitvi-a5bm71, vitvi-a5bub9, vitvi-a5c1g2, vitvi-a5c6e7, vitvi-a5c8m8, vitvi-a5c8p7, vitvi-a5c9w6, vitvi-a7pnb4, vitvi-d7t940, vitvi-d7tpk8, vitvi-f6hhx5, vitvi-f6hqf1, vitvi-d7tum4, vitvi-d7stm8, vitvi-a5bej7, vitvi-e0cv10, vitvi-f6gtp7, vitvi-a5bej5 Abstract BACKGROUND: Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented. PRINCIPAL FINDINGS: We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before). CONCLUSIONS: Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape. | |||||||
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