A footprint of desiccation tolerance in the genome of Xerophyta viscosa

[1]  S. Shabala.  Plant Stress Physiology , 2017 .

[2]  P. Dörmann,et al.  ABI5 Is a Regulator of Seed Maturation and Longevity in Legumes , 2016, Plant Cell.

[3]  H. Hilhorst,et al.  Key genes involved in desiccation tolerance and dormancy across life forms. , 2016, Plant science : an international journal of experimental plant biology.

[4]  Y. Fujita,et al.  Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties , 2016, DNA research : an international journal for rapid publication of reports on genes and genomes.

[5]  M. Schatz,et al.  Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.

[6]  D. Bartels,et al.  Surviving metabolic arrest: photosynthesis during desiccation and rehydration in resurrection plants , 2016, Annals of the New York Academy of Sciences.

[7]  Robert D. Finn,et al.  The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..

[8]  Xiuren Zhang,et al.  Trehalose Accumulation Triggers Autophagy during Plant Desiccation , 2015, PLoS genetics.

[9]  Haibao Tang,et al.  Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum , 2015, Nature.

[10]  S. Kelly,et al.  OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy , 2015, Genome Biology.

[11]  S. Mundree,et al.  A molecular physiological review of vegetative desiccation tolerance in the resurrection plant Xerophyta viscosa (Baker) , 2015, Planta.

[12]  Xinhua Yang,et al.  The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration , 2015, Proceedings of the National Academy of Sciences.

[13]  Kazuo Shinozaki,et al.  Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants , 2015, Front. Plant Sci..

[14]  E. Mauceli,et al.  Genome-wide Association Study Identifies Shared Risk Loci Common to Two Malignancies in Golden Retrievers , 2015, PLoS genetics.

[15]  Katharina J. Hoff,et al.  BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS , 2016, Bioinform..

[16]  Huaiyu Mi,et al.  The InterPro protein families database: the classification resource after 15 years , 2014, Nucleic Acids Res..

[17]  Christina A. Cuomo,et al.  Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.

[18]  Robert D. Finn,et al.  Rfam 12.0: updates to the RNA families database , 2014, Nucleic Acids Res..

[19]  B. Langmead,et al.  Lighter: fast and memory-efficient sequencing error correction without counting , 2014, Genome Biology.

[20]  Chengxi Ye,et al.  DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies , 2014, Scientific Reports.

[21]  P. Šmarda,et al.  Ecological and evolutionary significance of genomic GC content diversity in monocots , 2014, Proceedings of the National Academy of Sciences.

[22]  L. Farinelli,et al.  Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef) , 2014, BMC Genomics.

[23]  Walter Pirovano,et al.  SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information , 2014, BMC Bioinformatics.

[24]  D. Gaff,et al.  Drying without senescence in resurrection plants , 2014, Front. Plant Sci..

[25]  D. Bartels,et al.  Desiccation tolerance in resurrection plants: new insights from transcriptome, proteome and metabolome analysis , 2013, Front. Plant Sci..

[26]  H. Rogniaux,et al.  LEA polypeptide profiling of recalcitrant and orthodox legume seeds reveals ABI3-regulated LEA protein abundance linked to desiccation tolerance , 2013, Journal of experimental botany.

[27]  Sean R. Eddy,et al.  Infernal 1.1: 100-fold faster RNA homology searches , 2013, Bioinform..

[28]  Sandra Pelletier,et al.  A Regulatory Network-Based Approach Dissects Late Maturation Processes Related to the Acquisition of Desiccation Tolerance and Longevity of Medicago truncatula Seeds1[C][W][OPEN] , 2013, Plant Physiology.

[29]  Marco Thines,et al.  The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine , 2013, eLife.

[30]  M. Oliver,et al.  The evolution of desiccation tolerance in angiosperm plants: a rare yet common phenomenon. , 2013, Functional plant biology : FPB.

[31]  R. Gibbs,et al.  Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology , 2012, PloS one.

[32]  Hongwei Guo,et al.  Gene network analysis and functional studies of senescence-associated genes reveal novel regulators of Arabidopsis leaf senescence. , 2012, Journal of integrative plant biology.

[33]  Gabor T. Marth,et al.  Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.

[34]  J. Keilwagen,et al.  Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon , 2012, Nucleic acids research.

[35]  Mihai Pop,et al.  Exploiting sparseness in de novo genome assembly , 2012, BMC Bioinformatics.

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

[37]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

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

[39]  E. P. Fontes,et al.  The Binding Protein BiP Attenuates Stress-Induced Cell Death in Soybean via Modulation of the N-Rich Protein-Mediated Signaling Pathway1[C][W][OA] , 2011, Plant Physiology.

[40]  Robert D. Finn,et al.  HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..

[41]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[42]  J. Ryals,et al.  A Sister Group Contrast Using Untargeted Global Metabolomic Analysis Delineates the Biochemical Regulation Underlying Desiccation Tolerance in Sporobolus stapfianus[C][W][OA] , 2011, Plant Cell.

[43]  Miklós Csuös,et al.  Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood , 2010, Bioinform..

[44]  M. C. S. Rodriguez,et al.  Transcriptomes of the desiccation-tolerant resurrection plant Craterostigma plantagineum. , 2010, The Plant journal : for cell and molecular biology.

[45]  R. Quatrano,et al.  Role of ABA and ABI3 in Desiccation Tolerance , 2010, Science.

[46]  Yuling Bai,et al.  High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6. , 2008, The Plant journal : for cell and molecular biology.

[47]  F. Salamini,et al.  Retrotransposons and siRNA have a role in the evolution of desiccation tolerance leading to resurrection of the plant Craterostigma plantagineum. , 2008, The New phytologist.

[48]  S. Dongen,et al.  Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data , 2007, PLoS Comput. Biol..

[49]  M. Wise,et al.  The continuing conundrum of the LEA proteins , 2007, Naturwissenschaften.

[50]  P. Alpert.  Constraints of tolerance: why are desiccation-tolerant organisms so small or rare? , 2006, Journal of Experimental Biology.

[51]  B. Mishler,et al.  Desiccation Tolerance in Bryophytes: A Reflection of the Primitive Strategy for Plant Survival in Dehydrating Habitats?1 , 2005, Integrative and comparative biology.

[52]  D. Field,et al.  Orphans as taxonomically restricted and ecologically important genes. , 2005, Microbiology.

[53]  Burkhard Morgenstern,et al.  AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints , 2005, Nucleic Acids Res..

[54]  Ian Korf,et al.  Gene finding in novel genomes , 2004, BMC Bioinformatics.

[55]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[56]  B. Mishler,et al.  The evolution of vegetative desiccation tolerance in land plants , 2000, Plant Ecology.

[57]  A. Benko-Iseppon,et al.  Cytogenetics and cytotaxonomy ofVelloziaceae , 1997, Plant Systematics and Evolution.

[58]  A. Kermode.  Approaches to elucidate the basis of desiccation-tolerance in seeds , 1997, Seed Science Research.

[59]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[60]  T. Wilkins,et al.  A modified hot borate method significantly enhances the yield of high-quality RNA from cotton (Gossypium hirsutum L.). , 1994, Analytical biochemistry.

[61]  H. Lichtenthaler,et al.  Resynthesis of Thylakoids and Functional Chloroplasts in the Desiccated Leaves of the Poikilochlorophyllous Plant Xerophyta scabrida upon Rehydration , 1993 .

[62]  J. Bewley.  Physiological Aspects of Desiccation Tolerance , 1979 .

[63]  D. Gaff,et al.  Desiccation-Tolerant Flowering Plants in Southern Africa , 1971, Science.

[64]  B. Mueller‐Roeber,et al.  University of Groningen Molecular mechanisms of desiccation tolerance in the resurrection glacial relic , 2017 .

[65]  A. Dai.  Increasing drought under global warming in observations and models , 2013 .

[66]  Russ B. Altman,et al.  Genome Analysis , 2011, Bioinform..

[67]  D. Bartels,et al.  Plant Desiccation Tolerance , 2011 .

[68]  S. Porembski.  Evolution, Diversity, and Habitats of Poikilohydrous Vascular Plants , 2011 .

[69]  J. Bajić.  Exploring the longevity of dry Craterostigma wilmsii (homoiochlorophyllous) and Xerophyta humilis (poikolichlorophyllous) under simulated field conditions , 2006 .

[70]  Kimberly Van Auken,et al.  WormBase: a multi-species resource for nematode biology and genomics , 2004, Nucleic Acids Res..

[71]  Z. Csintalan,et al.  Ecophysiological responses of homoiochlorophyllous and poikilochlorophyllous desiccation tolerant plants: a comparison and an ecological perspective , 2004, Plant Growth Regulation.

[72]  B Marshall,et al.  Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource , 2004, Nucleic Acids Res..

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

[74]  K. Ingemar Jönsson,et al.  A model on the evolution of cryptobiosis , 2003 .

[75]  A. Rychter,et al.  Plant tolerance to abiotic stresses in agriculture : role of genetic engineering , 2000 .

[76]  S. Mundree,et al.  Some Physiological and Molecular Insights into the Mechanisms of Desiccation Tolerance in the Resurrection Plant Xerophyta viscosa Baker , 2000 .

[77]  H. Lichtenthaler,et al.  Reconstitution of photosynthesis upon rehydration in the desiccated leaves of the poikilochlorophyllous shrub Xerophyta scabrida at elevated CO2 , 1996 .

[78]  C. Cassa,et al.  Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations , 2011, Bioinform..