Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments
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Shanshan Liu | Guangyi Fan | Xin Liu | Yaolei Zhang | I. Seim | Haorong Lu | Liping Wang | Z. Shao | Xiang Zeng | Yue Song | Jianwei Chen | Jie Bai | Lingfeng Meng | Xiaoteng Fu | Congyan Wang | Zenghua Shao | Nanxi Liu | Zenghua Shao | Xin Liu | Xin Liu
[1] J. Sun,et al. The Scaly-foot Snail genome and implications for the origins of biomineralised armour , 2020, Nature Communications.
[2] L. Taher,et al. Independent Transposon Exaptation Is a Widespread Mechanism of Redundant Enhancer Evolution in the Mammalian Genome , 2020, Genome biology and evolution.
[3] Jie Huang. BGISEQ-500 Sequencing , 2018, Definitions.
[4] Chong Chen,et al. Red Listing can protect deep-sea biodiversity , 2019, Nature Ecology & Evolution.
[5] M. Tsai,et al. Incorporation of deep-sea and small-sized species provides new insights into gastropods phylogeny. , 2019, Molecular phylogenetics and evolution.
[6] Heng Li,et al. Fast and accurate long-read assembly with wtdbg2 , 2019, Nature Methods.
[7] The UniProt Consortium,et al. UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..
[8] G. Bourque,et al. Ten things you should know about transposable elements , 2018, Genome Biology.
[9] Wei Fan,et al. The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptation , 2018, GigaScience.
[10] A. Wanninger,et al. The evolution of molluscs , 2018, Biological reviews of the Cambridge Philosophical Society.
[11] Nicola Zamboni,et al. The thioredoxin-1 system is essential for fueling DNA synthesis during T-cell metabolic reprogramming and proliferation , 2018, Nature Communications.
[12] Philip E. Steinberg,et al. SCIENTIFIC RATIONALE AND INTERNATIONAL OBLIGATIONS FOR PROTECTION OF ACTIVE HYDROTHERMAL VENT ECOSYSTEMS FROM DEEP-SEA MINING , 2018 .
[13] S. Arnaud-Haondb,et al. Scientific rationale and international obligations for protection of active hydrothermal vent ecosystems from deep-sea mining , 2018 .
[14] Troy J. Kieran,et al. The Novel Evolution of the Sperm Whale Genome , 2017, Genome biology and evolution.
[15] Sudhir Kumar,et al. TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. , 2017, Molecular biology and evolution.
[16] Min Zhao,et al. Whole genome analysis of a schistosomiasis-transmitting freshwater snail , 2017, Nature Communications.
[17] Yanjie Zhang,et al. Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes , 2017, Nature Ecology &Evolution.
[18] S. Koren,et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.
[19] Chong Chen,et al. By more ways than one: Rapid convergence at hydrothermal vents shown by 3D anatomical reconstruction of Gigantopelta (Mollusca: Neomphalina) , 2017, BMC Evolutionary Biology.
[20] B. Degnan,et al. Co-Option and De Novo Gene Evolution Underlie Molluscan Shell Diversity , 2017, Molecular biology and evolution.
[21] C. Laukaitis,et al. The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes , 2016, Genome biology and evolution.
[22] James T. Robinson,et al. Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. , 2016, Cell systems.
[23] Neva C. Durand,et al. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. , 2016, Cell systems.
[24] Daisy E. Pagete. An end-to-end assembly of the Aedes aegypti genome , 2016, 1605.04619.
[25] Jean-Philippe Vert,et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing , 2015, Genome Biology.
[26] J. Copley,et al. The 'scaly-foot gastropod': a new genus and species of hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae) from the Indian Ocean , 2015 .
[27] J. Copley,et al. Low connectivity between ‘scaly-foot gastropod’ (Mollusca: Peltospiridae) populations at hydrothermal vents on the Southwest Indian Ridge and the Central Indian Ridge , 2015, Organisms Diversity & Evolution.
[28] J. Vinther. The origins of molluscs , 2015 .
[29] Neva C. Durand,et al. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.
[30] Zhihai Ma,et al. Widespread contribution of transposable elements to the innovation of gene regulatory networks , 2014, Genome research.
[31] J. Vinther. A molecular palaeobiological perspective on aculiferan evolution , 2014 .
[32] Tetsuya Hayashi,et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads , 2014, Genome research.
[33] Mauricio O. Carneiro,et al. From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.
[34] G. Bourque,et al. The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements , 2013, PLoS genetics.
[35] M. Schilthuizen. Rapid, habitat-related evolution of land snail colour morphs on reclaimed land , 2012, Heredity.
[36] M. Nazıroğlu. Molecular role of catalase on oxidative stress-induced Ca2+ signaling and TRP cation channel activation in nervous system , 2012, Journal of receptor and signal transduction research.
[37] Matthias Mann,et al. In-depth proteomic analysis of a mollusc shell: acid-soluble and acid-insoluble matrix of the limpet Lottia gigantea , 2012, Proteome Science.
[38] A. Marceau. Functions of single-strand DNA-binding proteins in DNA replication, recombination, and repair. , 2012, Methods in molecular biology.
[39] R. Durbin,et al. Inference of human population history from individual whole-genome sequences. , 2011, Nature.
[40] R. Durbin,et al. Inference of Human Population History From Whole Genome Sequence of A Single Individual , 2011, Nature.
[41] C. Marshall,et al. Has the Earth’s sixth mass extinction already arrived? , 2011, Nature.
[42] Martin Kollmar,et al. A novel hybrid gene prediction method employing protein multiple sequence alignments , 2011, Bioinform..
[43] N. Karlsson,et al. Deleted in Malignant Brain Tumors-1 Protein (DMBT1): A Pattern Recognition Receptor with Multiple Binding Sites , 2010, International journal of molecular sciences.
[44] Paramvir S. Dehal,et al. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.
[45] D. Wilkinson,et al. A feedback loop mediated by degradation of an inhibitor is required to initiate neuronal differentiation. , 2010, Genes & development.
[46] Richard Durbin,et al. Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..
[47] Robert B. Hartlage,et al. This PDF file includes: Materials and Methods , 2009 .
[48] A. Warén,et al. Gastropods from Recent Hot Vents and Cold Seeps: Systematics, Diversity and Life Strategies , 2010 .
[49] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[50] Nansheng Chen,et al. Genblasta: Enabling Blast to Identify Homologous Gene Sequences , 2022 .
[51] O. Gascuel,et al. Estimating maximum likelihood phylogenies with PhyML. , 2009, Methods in molecular biology.
[52] A. Mukherjee,et al. The thioredoxin system: a key target in tumour and endothelial cells. , 2008, The British journal of radiology.
[53] C. Biémont. Genome size evolution: Within-species variation in genome size , 2008, Heredity.
[54] Ziheng Yang. PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.
[55] Zhao Xu,et al. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons , 2007, Nucleic Acids Res..
[56] P. Parkhaev. The Cambrian ‘basement’ of gastropod evolution , 2007 .
[57] G. Weinstock,et al. Creating a honey bee consensus gene set , 2007, Genome Biology.
[58] R. Hen,et al. Adaptive changes in serotonin neurons of the raphe nuclei in 5‐HT4 receptor knock‐out mouse , 2006, The European journal of neuroscience.
[59] Nello Cristianini,et al. CAFE: a computational tool for the study of gene family evolution , 2006, Bioinform..
[60] Tao Liu,et al. TreeFam: a curated database of phylogenetic trees of animal gene families , 2005, Nucleic Acids Res..
[61] Ziheng Yang,et al. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. , 2006, Molecular biology and evolution.
[62] J. Jurka,et al. Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.
[63] Paramvir S. Dehal,et al. Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate , 2005, PLoS biology.
[64] T. Wolff. Composition and endemism of the deep-sea hydrothermal vent fauna , 2005 .
[65] S. Goffredi,et al. Novel Forms of Structural Integration between Microbes and a Hydrothermal Vent Gastropod from the Indian Ocean , 2004, Applied and Environmental Microbiology.
[66] R. Durbin,et al. GeneWise and Genomewise. , 2004, Genome research.
[67] H. Kazazian. Mobile Elements: Drivers of Genome Evolution , 2004, Science.
[68] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[69] Nansheng Chen,et al. Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences , 2009, Current protocols in bioinformatics.
[70] Maria Jesus Martin,et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..
[71] B. M. Christensen,et al. Glucosamine:fructose‐6‐phosphate aminotransferase: gene characterization, chitin biosynthesis and peritrophic matrix formation in Aedes aegypti , 2002, Insect molecular biology.
[72] J. François,et al. Involvement of GFA1, which encodes glutamine-fructose-6-phosphate amidotransferase, in the activation of the chitin synthesis pathway in response to cell-wall defects in Saccharomyces cerevisiae. , 2002, European journal of biochemistry.
[73] A. Holmgren,et al. Thioredoxin alters the matrix metalloproteinase/tissue inhibitors of metalloproteinase balance and stimulates human SK-N-SH neuroblastoma cell invasion. , 2001, European journal of biochemistry.
[74] Alex Bateman,et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites , 2001, Nucleic Acids Res..
[75] Cindy Lee Van Dover,et al. The Ecology of Deep-Sea Hydrothermal Vents , 2000 .
[76] Susumu Goto,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..
[77] R. Timpl,et al. Crystal structure of a scavenger receptor cysteine-rich domain sheds light on an ancient superfamily , 1999, Nature Structural Biology.
[78] Hiroyuki Ogata,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..
[79] G. Benson,et al. Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.
[80] P. Csermely,et al. Associate Editor: D. Shugar The 90-kDa Molecular Chaperone Family: Structure, Function, and Clinical Applications. A Comprehensive Review , 1998 .
[81] Ziheng Yang,et al. PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..
[82] V. E. Williams,et al. Regions of allelic hypervariability in the murine Aα immune response gene , 1983, Cell.
[83] David L. Williams,et al. Submarine Thermal Springs on the Gal�pagos Rift , 1979, Science.
[84] Supplemental Information 2: Kyoto Encyclopedia of genes and genomes. , 2022 .