The genome of the giant Nomura’s jellyfish sheds light on the early evolution of active predation
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Yun Sung Cho | Jessica A. Weber | M. Kirschner | A. Manica | J. Edwards | J. Bhak | Hak-Min Kim | S. Yum | H. Yim | Amir Karger | V. Luria | S. Jeon | Seung Gu Park | Jessica A Weber | Jung-Hyun Lee | J. Ryu | S. Woo | K. Shin | N. Lee | Youngjune Bhak | Yeonsu Jeon | Oksung Chung | Nayun Lee | Y. Jo | Nayoung Lee | Y. Jeon | Sungwon Jeon
[1] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[2] N. Rawlings,et al. Evolutionary families of metallopeptidases. , 1995, Methods in enzymology.
[3] Nansheng Chen,et al. Genblasta: Enabling Blast to Identify Homologous Gene Sequences , 2022 .
[4] Nicholas H. Putnam,et al. Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization , 2007, Science.
[5] Ioannis Xenarios,et al. The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data. , 2012, Toxicon : official journal of the International Society on Toxinology.
[6] C. Rochette-Egly,et al. The molecular physiology of nuclear retinoic acid receptors. From health to disease. , 2011, Biochimica et biophysica acta.
[7] Pengcheng Li,et al. Jellyfish venomics and venom gland transcriptomics analysis of Stomolophus meleagris to reveal the toxins associated with sting. , 2014, Journal of proteomics.
[8] S. Uye,et al. Combined effects of food supply and temperature on asexual reproduction and somatic growth of polyps of the common jellyfish Aurelia aurita s.l. , 2010 .
[9] Dong Xu,et al. Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes , 2004, BMC Evolutionary Biology.
[10] M. Arai,et al. A Functional Biology of Scyphozoa , 1996, Springer Netherlands.
[11] V. Laudet,et al. Genome-wide in Silico Identification of New Conserved and Functional Retinoic Acid Receptor Response Elements (Direct Repeats Separated by 5 bp)* , 2011, The Journal of Biological Chemistry.
[12] D. Crowe,et al. Characterization of a Retinoic Acid Responsive Element in the Human ets‐1 Promoter , 2000, IUBMB life.
[13] Neil A. Campbell,et al. Biology: Concepts & Connections , 1987 .
[14] W. E. Schwab,et al. The organization and structure of nerve and muscle in the jellyfish Cyanea capillata (coelenterata; scyphozoa) , 1981, Journal of morphology.
[15] Benjamin M. Wheeler,et al. The dynamic genome of Hydra , 2010, Nature.
[16] Sudhir Kumar,et al. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.
[17] A. Antunes,et al. Sea Anemone (Cnidaria, Anthozoa, Actiniaria) Toxins: An Overview , 2012, Marine drugs.
[18] Ning Ma,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[19] Pierre Chambon,et al. The nuclear receptor superfamily: a personal retrospect on the first two decades. , 2005, Molecular endocrinology.
[20] T. Leitz,et al. The role of GLWamides in metamorphosis of Hydractinia echinata , 1998, Development Genes and Evolution.
[21] J. Piatigorsky,et al. Retinoic acid X receptor in the diploblast, Tripedalia cystophora. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[22] B. Schierwater,et al. Isolation of Hox genes from the scyphozoan Cassiopeia xamachana: implications for the early evolution of Hox genes. , 1999, The Journal of experimental zoology.
[23] G. Duester,et al. Mechanisms of retinoic acid signalling and its roles in organ and limb development , 2015, Nature Reviews Molecular Cell Biology.
[24] Esko Ukkonen,et al. Accurate self-correction of errors in long reads using de Bruijn graphs , 2016, Bioinform..
[25] David R. Kelley,et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.
[26] P. Holland,et al. Evolution of homeobox genes , 2013, Wiley interdisciplinary reviews. Developmental biology.
[27] A. Fujiyama,et al. Using the Acropora digitifera genome to understand coral responses to environmental change , 2011, Nature.
[28] T. Nevalainen,et al. Cloning of a novel phospholipase A2 from the cnidarian Adamsia carciniopados. , 2002, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.
[29] L. Llewellyn,et al. Phospholipase A2 in cnidaria. , 2004, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.
[30] B. Schierwater,et al. Axial Patterning and Diversification in the Cnidaria Predate the Hox System , 2006, Current Biology.
[31] S. Tavaré. Some probabilistic and statistical problems in the analysis of DNA sequences , 1986 .
[32] Brad T. Sherman,et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.
[33] C. Alonso. Hox Proteins: Sculpting Body Parts by Activating Localized Cell Death , 2002, Current Biology.
[34] J. Poulain,et al. The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle , 2018, Nature Ecology & Evolution.
[35] Alexander Rich,et al. RNA processing and the evolution of eukaryotes , 1999, Nature Genetics.
[36] J. Jurka,et al. Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.
[37] David R. Kelley,et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.
[38] P. Dollé,et al. Retinoic acid signalling during development , 2012, Development.
[39] T. Fujisawa,et al. Cnidarians and the evolutionary origin of the nervous system , 2009, Development, growth & differentiation.
[40] R. Nusse. An ancient cluster of Wnt paralogues. , 2001, Trends in genetics : TIG.
[41] Ewan Birney,et al. Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.
[42] R. de Rosa,et al. Origins of neurogenesis, a cnidarian view. , 2009, Developmental biology.
[43] R. Greenspan,et al. The genome of the jellyfish Aurelia and the evolution of animal complexity , 2018, Nature Ecology & Evolution.
[44] G. Mastrangelo,et al. Jellyfish Stings and Their Management: A Review , 2013, Marine drugs.
[45] Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.
[46] T. Lotan,et al. The dynamically evolving nematocyst content of an anthozoan, a scyphozoan, and a hydrozoan. , 2015, Molecular biology and evolution.
[47] Yan Zhang,et al. GC3-biased gene domains in mammalian genomes , 2015, Bioinform..
[48] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[49] M. Martindale,et al. Unexpected complexity of the Wnt gene family in a sea anemone , 2005, Nature.
[50] Dongyan Liu,et al. Jellyfish blooms in China: Dominant species, causes and consequences. , 2010, Marine pollution bulletin.
[51] P. Wincker,et al. Are Hox Genes Ancestrally Involved in Axial Patterning? Evidence from the Hydrozoan Clytia hemisphaerica (Cnidaria) , 2009, PloS one.
[52] M. Martindale,et al. Coral comparative genomics reveal expanded Hox cluster in the cnidarian-bilaterian ancestor. , 2012, Integrative and comparative biology.
[53] T. Leitz,et al. Metamorphosis in the Cnidaria , 2002 .
[54] Jeffery P. Demuth,et al. The Evolution of Mammalian Gene Families , 2006, PloS one.
[55] G. Benson,et al. Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.
[56] A. Prange,et al. A novel proteinaceous cytotoxin from the northern Scyphozoa Cyanea capillata (L.) with structural homology to cubozoan haemolysins. , 2011, Toxicon : official journal of the International Society on Toxinology.
[57] V. Hartenstein,et al. Evolutionary origin of rhopalia: insights from cellular‐level analyses of Otx and POU expression patterns in the developing rhopalial nervous system , 2010, Evolution & development.
[58] Patrick R. Leary,et al. The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth , 2014, Biodiversity data journal.
[59] J. Dabiri,et al. Passive energy recapture in jellyfish contributes to propulsive advantage over other metazoans , 2013, Proceedings of the National Academy of Sciences.
[60] P. Bork,et al. The CUB domain. A widespread module in developmentally regulated proteins. , 1993, Journal of molecular biology.
[61] B. Zhu,et al. Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements , 2006, Nature.
[62] J. Finnerty,et al. Origins of Bilateral Symmetry: Hox and Dpp Expression in a Sea Anemone , 2004, Science.
[63] Toni Gabaldón,et al. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..
[64] Colin N. Dewey,et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.
[65] Y. Komiya,et al. Wnt signal transduction pathways , 2008, Organogenesis.
[66] Tatiana V Tatarinova,et al. GC3 biology in corn, rice, sorghum and other grasses , 2010, BMC Genomics.
[67] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[68] T. Mayorova,et al. On some features of embryonic development and metamorphosis of Aurelia aurita (Cnidaria, Scyphozoa) , 2012, Russian Journal of Developmental Biology.
[69] Nansheng Chen,et al. Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences , 2009, Current protocols in bioinformatics.
[70] Alexandros Stamatakis,et al. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..
[71] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[72] Nicolas Servant,et al. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis , 2013, Briefings Bioinform..
[73] Y. Won,et al. Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record. , 2012, Molecular phylogenetics and evolution.
[74] C. Stoeckert,et al. OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.
[75] L. Pane,et al. Cytotoxic and Cytolytic Cnidarian Venoms. A Review on Health Implications and Possible Therapeutic Applications , 2013, Toxins.
[76] D. Dash,et al. Transcriptome and venom proteome of the box jellyfish Chironex fleckeri , 2015, BMC Genomics.
[77] É. Röttinger,et al. Diversity of Cnidarian Muscles: Function, Anatomy, Development and Regeneration , 2017, Front. Cell Dev. Biol..
[78] C. Rochette-Egly,et al. The Biochemistry of Retinoic Acid Receptors I: Structure, Activation, and Function at the Molecular Level , 2014, Subcellular Biochemistry.
[79] R. Beynon,et al. The astacin family of metalloendopeptidases , 1991, The Journal of biological chemistry.
[80] Pornpimol Charoentong,et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..
[81] Tomislav Domazet-Loso,et al. A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. , 2007, Trends in genetics : TIG.
[82] R. Epstein,et al. A functional significance for codon third bases. , 2000, Gene.
[83] B. Haas,et al. Transcriptome profiling of the dynamic life cycle of the scypohozoan jellyfish Aurelia aurita , 2015, BMC Genomics.
[84] Sean R. Eddy,et al. Hidden Markov model speed heuristic and iterative HMM search procedure , 2010, BMC Bioinformatics.
[85] B. Degnan,et al. Independent evolution of striated muscles in cnidarians and bilaterians , 2012, Nature.
[86] Rajiv C. McCoy,et al. Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements , 2014, bioRxiv.
[87] Xuegong Zhang,et al. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data , 2010, Bioinform..
[88] Joel Dudley,et al. TimeTree: a public knowledge-base of divergence times among organisms , 2006, Bioinform..
[89] Oleg Simakov,et al. Multiple Wnts are involved in Hydra organizer formation and regeneration. , 2009, Developmental biology.
[90] Paramvir S. Dehal,et al. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.
[91] V. Laudet,et al. Evolution of retinoic acid receptors and retinoic acid signaling. , 2014, Sub-cellular biochemistry.
[92] R. Satterlie. Do jellyfish have central nervous systems? , 2011, Journal of Experimental Biology.
[93] H. Ellegren,et al. Determinants of genetic diversity , 2016, Nature Reviews Genetics.
[94] Sudhir Kumar,et al. TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. , 2017, Molecular biology and evolution.
[95] Burkhard Morgenstern,et al. AUGUSTUS: ab initio prediction of alternative transcripts , 2006, Nucleic Acids Res..
[96] J. Woo,et al. A stem-group cnidarian described from the mid-Cambrian of China and its significance for cnidarian evolution , 2011, Nature communications.
[97] Mira V. Han,et al. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. , 2013, Molecular biology and evolution.
[98] Pavel A. Pevzner,et al. De novo identification of repeat families in large genomes , 2005, ISMB.
[99] B. Schierwater,et al. Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models. , 2006, Systematic biology.
[100] Walter Pirovano,et al. BIOINFORMATICS APPLICATIONS , 2022 .
[101] Ulrich C. Klostermeier,et al. Regulation of Polyp-to-Jellyfish Transition in Aurelia aurita , 2014, Current Biology.
[102] Aaron A. Klammer,et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.
[103] T. Nevalainen,et al. Ancient Venom Systems: A Review on Cnidaria Toxins , 2015, Toxins.
[104] J. Poulain,et al. The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle , 2018, Nature Ecology & Evolution.
[105] H. Arnold,et al. Alkali myosin light chains in man are encoded by a multigene family that includes the adult skeletal muscle, the embryonic or atrial, and nonsarcomeric isoforms. , 1988, Gene.
[106] V. Schmid,et al. Evolution of striated muscle: jellyfish and the origin of triploblasty. , 2005, Developmental biology.
[107] Jian Wang,et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.
[108] J. Finnerty,et al. Genomic organization, gene structure, and developmental expression of three clustered otx genes in the sea anemone Nematostella vectensis. , 2007, Journal of experimental zoology. Part B, Molecular and developmental evolution.
[109] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[110] Carl Kingsford,et al. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers , 2011, Bioinform..
[111] Rolf Apweiler,et al. InterProScan - an integration platform for the signature-recognition methods in InterPro , 2001, Bioinform..