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An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

https://doi.org/10.1101/060921
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Genome Annotation and Curation Using MAKER and MAKER‐P
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Diet affects the redox system in developing Atlantic cod (Gadus morhua) larvae
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Assembly algorithms for next-generation sequencing data
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Microsatellite mutations in the germline:
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Genome sequencing in microfabricated high-density picolitre reactors
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The sequence and de novo assembly of the giant panda genome
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The genome sequence of Atlantic cod reveals a unique immune system
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The genomic basis of adaptive evolution in threespine sticklebacks
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The bonobo genome compared with the chimpanzee and human genomes
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The oyster genome reveals stress adaptation and complexity of shell formation
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The Norway spruce genome sequence and conifer genome evolution
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The Atlantic salmon genome provides insights into rediploidization
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Full-length transcriptome assembly from RNA-Seq data without a reference genome
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The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits
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The genome of woodland strawberry (Fragaria vesca)
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Intragenic tandem repeats generate functional variability
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Limitations of next-generation genome sequence assembly
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The genome of the miiuy croaker reveals well-developed innate immune and sensory systems
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APDB: a novel measure for benchmarking sequence alignment methods without reference alignments
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CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
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Using native and syntenically mapped cDNA alignments to improve de novo gene finding
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Aggressive assembly of pyrosequencing reads with mates
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The Sequence Alignment/Map format and SAMtools
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BEDTools: a flexible suite of utilities for comparing genomic features
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Efficient construction of an assembly string graph using the FM-index
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Mugsy: fast multiple alignment of closely related whole genomes
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FLASH: fast length adjustment of short reads to improve genome assemblies
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Graph accordance of next-generation sequence assemblies
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CD-HIT: accelerated for clustering the next-generation sequencing data
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Exploring genome characteristics and sequence quality without a reference
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InterProScan 5: genome-scale protein function classification
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Toward better understanding of artifacts in variant calling from high-coverage samples
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
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On genomic repeats and reproducibility
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Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates
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A review of early life history dynamics of Barents Sea cod (Gadus morhua)
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Tandem repeats finder: a program to analyze DNA sequences
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
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Gene identification in novel eukaryotic genomes by self-training algorithm
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Assessing the gene space in draft genomes
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Fine-grained annotation and classification of de novo predicted LTR retrotransposons
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UniProt: a hub for protein information
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The missing indels: an estimate of indel variation in a human genome and analysis of factors that impede detection
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The biological effects of simple tandem repeats: Lessons from the repeat expansion diseases: Table 1.
inferredcites →https://doi.org/10.1101/gr.126599.111openalex-snapshot
Assemblathon 1: A competitive assessment of de novo short read assembly methods
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GAGE: A critical evaluation of genome assemblies and assembly algorithms
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lobSTR: A short tandem repeat profiler for personal genomes
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The landscape of human STR variation
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Tandem repeat variation in human and great ape populations and its impact on gene expression divergence
inferredcites →https://doi.org/10.1101/gr.3722605openalex-snapshot
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
inferredcites →https://doi.org/10.1101/gr.6743907openalex-snapshot
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
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MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations
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A field guide to whole‐genome sequencing, assembly and annotation
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Long‐term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua)
inferredcites →https://doi.org/10.1126/science.1111427openalex-snapshot
Microsatellite Instability Generates Diversity in Brain and Sociobehavioral Traits
inferredcites →https://doi.org/10.1126/science.1170097openalex-snapshot
Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability
inferredcites →https://doi.org/10.1126/science.1250092openalex-snapshot
Ancient hybridizations among the ancestral genomes of bread wheat
inferredcites →https://doi.org/10.1126/science.1251385openalex-snapshot
Comparative genomics reveals insights into avian genome evolution and adaptation
inferredcites →https://doi.org/10.1126/science.1251788openalex-snapshot
A chromosome-based draft sequence of the hexaploid bread wheat ( Triticum aestivum ) genome
inferredcites →https://doi.org/10.1126/science.1253451openalex-snapshot
Whole-genome analyses resolve early branches in the tree of life of modern birds
inferredcites →https://doi.org/10.1139/f04-106openalex-snapshot
Genome-size evolution in fishes
inferredcites →https://doi.org/10.1139/g03-040openalex-snapshot
The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes
inferredcites →https://doi.org/10.1146/annurev-genet-072610-155046openalex-snapshot
Variable Tandem Repeats Accelerate Evolution of Coding and Regulatory Sequences
inferredcites →https://doi.org/10.1159/000084979openalex-snapshot
Repbase Update, a database of eukaryotic repetitive elements
inferredcites →https://doi.org/10.1186/1471-2105-12-1openalex-snapshot
MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity
inferredcites →https://doi.org/10.1186/1471-2105-12-491openalex-snapshot
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
inferredcites →https://doi.org/10.1186/1471-2105-13-238openalex-snapshot
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
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PBHoney: identifying genomic variants via long-read discordance and interrupted mapping
inferredcites →https://doi.org/10.1186/1471-2105-5-59openalex-snapshot
Gene finding in novel genomes
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Evaluation of time profile reconstruction from complex two-color microarray designs
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Differential impact of simultaneous migration on coevolving hosts and parasites.
inferredcites →https://doi.org/10.1186/1471-2164-11-191openalex-snapshot
Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua)
inferredcites →https://doi.org/10.1186/1471-2164-11-277openalex-snapshot
Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach
inferredcites →https://doi.org/10.1186/1471-2164-13-443openalex-snapshot
Maternal 3’UTRs: from egg to onset of zygotic transcription in Atlantic cod
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Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
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Versatile and open software for comparing large genomes
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REAPR: a universal tool for genome assembly evaluation
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The advantages of SMRT sequencing
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An improved genome reference for the African cichlid, Metriaclima zebra
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Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
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Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
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Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons
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Microsatellite Tandem Repeats Are Abundant in Human Promoters and Are Associated with Regulatory Elements
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The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei
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Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
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Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing
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The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

What points at this work

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

inferred← citeshttps://doi.org/10.1016/b978-0-12-801418-9.00003-2openalex-snapshot
An improved version of the Atlantic cod genome and advancements in functional genomics: implications for the future of cod farming
inferred← citeshttps://doi.org/10.1038/srep31235openalex-snapshot
Genomic characterization of the Atlantic cod sex-locus
inferred← citeshttps://doi.org/10.1093/gbe/evw250openalex-snapshot
Successive Losses of Central Immune Genes Characterize the Gadiformes’ Alternate Immunity
inferred← citeshttps://doi.org/10.1101/gr.216465.116openalex-snapshot
HINGE: long-read assembly achieves optimal repeat resolution
inferred← citeshttps://doi.org/10.1111/1755-0998.12623openalex-snapshot
Combining bleach and mild predigestion improves ancient DNA recovery from bones
inferred← citeshttps://doi.org/10.1111/eva.13575openalex-snapshot
Evidence of hybridization between genetically distinct Baltic cod stocks during peak population abundance(s)
inferred← citeshttps://doi.org/10.1126/sciadv.aat8788openalex-snapshot
Codweb: Whole-genome sequencing uncovers extensive reticulations fueling adaptation among Atlantic, Arctic, and Pacific gadids
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