Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea
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Title
Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea
Authors
Keywords
Invertebrate genomics, Functional genomics, Hydrostatic pressure, Zebrafish, DNA repair, Phylogenetic analysis, Vertebrates, Sequence alignment
Journal
PLoS Genetics
Volume 17, Issue 5, Pages e1009530
Publisher
Public Library of Science (PLoS)
Online
2021-05-14
DOI
10.1371/journal.pgen.1009530
References
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Note: Only part of the references are listed.- Vision using multiple distinct rod opsins in deep-sea fishes
- (2019) Zuzana Musilova et al. SCIENCE
- Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation
- (2019) Kun Wang et al. Nature Ecology & Evolution
- OUP accepted manuscript
- (2018) BIOINFORMATICS
- ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
- (2018) Chao Zhang et al. BMC BIOINFORMATICS
- De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish
- (2018) Yi Lan et al. BMC GENOMICS
- Organic osmolytes of amphipods from littoral to hadal zones: Increases with depth in trimethylamine N-oxide, scyllo -inositol and other potential pressure counteractants
- (2018) Anna B. Downing et al. DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS
- Life history of abyssal and hadal fishes from otolith growth zones and oxygen isotopic compositions
- (2018) M.E. Gerringer et al. DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS
- Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
- (2018) Lily C. Hughes et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Identification and characterization of a novel nuclear structure containing members of the homologous recombination and DNA damage response pathways
- (2018) Megan L. Sierant et al. Cancer Genetics
- RAD-ical New Insights into RAD51 Regulation
- (2018) Meghan R. Sullivan et al. Genes
- Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation
- (2017) Sergey Koren et al. GENOME RESEARCH
- Rad52 Inverse Strand Exchange Drives RNA-Templated DNA Double-Strand Break Repair
- (2017) Olga M. Mazina et al. MOLECULAR CELL
- Molecular adaptation in the world's deepest-living animal: Insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas
- (2017) Yi Lan et al. MOLECULAR ECOLOGY
- Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
- (2017) Ioanna Kalvari et al. NUCLEIC ACIDS RESEARCH
- Pseudoliparis swirei sp. nov.: A newly-discovered hadal snailfish (Scorpaeniformes: Liparidae) from the Mariana Trench
- (2017) MACKENZIE E. GERRINGER et al. ZOOTAXA
- Uncovering the trimethylamine-producing bacteria of the human gut microbiota
- (2017) Silke Rath et al. Microbiome
- The Sinocyclocheilus cavefish genome provides insights into cave adaptation
- (2016) Junxing Yang et al. BMC BIOLOGY
- Fishes of the hadal zone including new species, in situ observations and depth records of Liparidae
- (2016) Thomas D. Linley et al. DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS
- BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
- (2015) Felipe A. Simão et al. BIOINFORMATICS
- Co-evolution of proteins and solutions: protein adaptation versus cytoprotective micromolecules and their roles in marine organisms
- (2015) P. H. Yancey et al. JOURNAL OF EXPERIMENTAL BIOLOGY
- Tree of Life Reveals Clock-Like Speciation and Diversification
- (2015) S. Blair Hedges et al. MOLECULAR BIOLOGY AND EVOLUTION
- Assembly and diploid architecture of an individual human genome via single-molecule technologies
- (2015) Matthew Pendleton et al. NATURE METHODS
- The Pfam protein families database: towards a more sustainable future
- (2015) Robert D. Finn et al. NUCLEIC ACIDS RESEARCH
- Genome Sequencing of the Perciform Fish Larimichthys crocea Provides Insights into Molecular and Genetic Mechanisms of Stress Adaptation
- (2015) Jingqun Ao et al. PLoS Genetics
- SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information
- (2014) Marten Boetzer et al. BMC BIOINFORMATICS
- Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
- (2014) Rei Kajitani et al. GENOME RESEARCH
- Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
- (2014) Bruce J. Walker et al. PLoS One
- Microscopic insights into the protein-stabilizing effect of trimethylamine N-oxide (TMAO)
- (2014) J. Ma et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Marine fish may be biochemically constrained from inhabiting the deepest ocean depths
- (2014) P. H. Yancey et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Spider genomes provide insight into composition and evolution of venom and silk
- (2014) Kristian W. Sanggaard et al. Nature Communications
- Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes
- (2014) Xinxin You et al. Nature Communications
- Infernal 1.1: 100-fold faster RNA homology searches
- (2013) E. P. Nawrocki et al. BIOINFORMATICS
- MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
- (2013) Koichiro Tamura et al. MOLECULAR BIOLOGY AND EVOLUTION
- The zebrafish reference genome sequence and its relationship to the human genome
- (2013) Kerstin Howe et al. NATURE
- ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments
- (2012) Zhang Zhang et al. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
- Crucial Importance of Water Structure Modification on Trimethylamine N-Oxide Counteracting Effect at High Pressure
- (2012) Rahul Sarma et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
- (2012) Cole Trapnell et al. Nature Protocols
- Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
- (2012) Adam C. English et al. PLoS One
- ProtTest 3: fast selection of best-fit models of protein evolution
- (2011) Diego Darriba et al. BIOINFORMATICS
- FLASH: fast length adjustment of short reads to improve genome assemblies
- (2011) T. Magoc et al. BIOINFORMATICS
- RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
- (2011) Bo Li et al. BMC BIOINFORMATICS
- Five years of FISH-BOL: Brief status report
- (2011) Sven Becker et al. Mitochondrial DNA
- Full-length transcriptome assembly from RNA-Seq data without a reference genome
- (2011) Manfred G Grabherr et al. NATURE BIOTECHNOLOGY
- A Large Aggregation of Liparids at 7703 meters and a Reappraisal of the Abundance and Diversity of Hadal Fish
- (2010) Toyonobu Fujii et al. BIOSCIENCE
- QIIME allows analysis of high-throughput community sequencing data
- (2010) J Gregory Caporaso et al. NATURE METHODS
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
- (2010) Morgan N. Price et al. PLoS One
- TopHat: discovering splice junctions with RNA-Seq
- (2009) Cole Trapnell et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- On the Origin and Evolution of Vertebrate Olfactory Receptor Genes: Comparative Genome Analysis Among 23 Chordate Species
- (2009) Yoshihito Niimura Genome Biology and Evolution
- Comparative sequence analysis of myosin heavy chain proteins from congeneric shallow- and deep-living rattail fish (genus Coryphaenoides)
- (2008) T. Morita JOURNAL OF EXPERIMENTAL BIOLOGY
- jModelTest: Phylogenetic Model Averaging
- (2008) D. Posada MOLECULAR BIOLOGY AND EVOLUTION
- Enzyme Sequence and Its Relationship to Hyperbaric Stability of Artificial and Natural Fish Lactate Dehydrogenases
- (2008) Amanda A. Brindley et al. PLoS One
- Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
- (2008) Brian J Haas et al. GENOME BIOLOGY
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