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Hybrid genome assembly and annotation of Danionella translucida , a transparent fish with the smallest known vertebrate brain

https://doi.org/10.1101/539692
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jmor.20486openalex-snapshot
Danionella dracula, an escape from the cypriniform Bauplan via developmental truncation?
inferredcites →https://doi.org/10.1007/bf00842977openalex-snapshot
Danionella translucida, a new genus and species of cyprinid fish from Burma, one of the smallest living vertebrates
inferredcites →https://doi.org/10.1038/nature12111openalex-snapshot
The zebrafish reference genome sequence and its relationship to the human genome
inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot
Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/nbt1486openalex-snapshot
Next-generation DNA sequencing
inferredcites →https://doi.org/10.1038/s41587-018-0004-zopenalex-snapshot
Errors in long-read assemblies can critically affect protein prediction
inferredcites →https://doi.org/10.1038/s41592-018-0144-6openalex-snapshot
Transparent Danionella translucida as a genetically tractable vertebrate brain model
inferredcites →https://doi.org/10.1093/bib/bbs017openalex-snapshot
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
inferredcites →https://doi.org/10.1093/bioinformatics/btt310openalex-snapshot
Informed and automated k -mer size selection for genome assembly
inferredcites →https://doi.org/10.1093/bioinformatics/btt476openalex-snapshot
The MaSuRCA genome assembler
inferredcites →https://doi.org/10.1093/bioinformatics/btu031openalex-snapshot
InterProScan 5: genome-scale protein function classification
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/bioinformatics/bty841openalex-snapshot
BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files
inferredcites →https://doi.org/10.1093/gbe/evr090openalex-snapshot
Comparative Analysis of Teleost Genome Sequences Reveals an Ancient Intron Size Expansion in the Zebrafish Lineage
inferredcites →https://doi.org/10.1093/gbe/evy058openalex-snapshot
The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes
inferredcites →https://doi.org/10.1093/gigascience/gix120openalex-snapshot
SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data
inferredcites →https://doi.org/10.1093/gigascience/gix137openalex-snapshot
Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish ( Amphiprion ocellaris ) genome assembly
inferredcites →https://doi.org/10.1093/gigascience/giz026openalex-snapshot
A hybrid de novo assembly of the sea pansy ( Renilla muelleri ) genome
inferredcites →https://doi.org/10.1093/nar/25.5.955openalex-snapshot
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
inferredcites →https://doi.org/10.1093/nar/gkl200openalex-snapshot
AUGUSTUS: ab initio prediction of alternative transcripts
inferredcites →https://doi.org/10.1093/nar/gkw1099openalex-snapshot
UniProt: the universal protein knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkx1098openalex-snapshot
Ensembl 2018
inferredcites →https://doi.org/10.1098/rspb.2009.0141openalex-snapshot
Spectacular morphological novelty in a miniature cyprinid fish, Danionella dracula n. sp.
inferredcites →https://doi.org/10.1101/444026openalex-snapshot
Oxytocin-mediated social preference and socially reinforced reward learning in the miniature fish Danionella cerebrum
inferredcites →https://doi.org/10.1101/gr.6743907openalex-snapshot
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
inferredcites →https://doi.org/10.1186/1471-2105-5-59openalex-snapshot
Gene finding in novel genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1004256openalex-snapshot
DNA Glycosylases Involved in Base Excision Repair May Be Associated with Cancer Risk in BRCA1 and BRCA2 Mutation Carriers
inferredcites →https://doi.org/10.1371/journal.pgen.1004365openalex-snapshot
Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis
inferredcites →https://doi.org/10.1371/journal.pone.0089680openalex-snapshot
A Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures
inferredcites →https://doi.org/10.1371/journal.pone.0112963openalex-snapshot
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
inferredcites →https://doi.org/10.2174/1875036201307010001openalex-snapshot
Comparison of Sequencing Utility Programs

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/dvdy.76openalex-snapshot
Thyroid hormone coordinates developmental trajectories but does not underlie developmental truncation in danionins
inferred← citeshttps://doi.org/10.1101/gr.251314.119openalex-snapshot
The full-length transcriptome of C. elegans using direct RNA sequencing
inferred← citeshttps://doi.org/10.70675/0b3fded9z0768z4976z9f7cz8b7e4a9f1114openalex-snapshot
Phylogenomics and comparative genomics in ant-eating mammals
inferred← citeshttps://doi.org/10.70675/48396303z4bedz424ez9fdbzc8ecba2c0042openalex-snapshot
Divergence of exploratory locomotion and the underlying neuronal circuitry in two closely related vertebrate species
inferred← citeshttps://doi.org/10.7554/elife.63167openalex-snapshot
High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox
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