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An evaluation of pool-sequencing transcriptome-based exon capture for population genomics in non-model species

https://doi.org/10.1101/583534
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Evaluation of Gene Structure Prediction Programs
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The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird
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Comparative transcriptomics in three ladybird species supports a role for immunity in invasion biology
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Effective discovery of rare variants by pooled target capture sequencing: A comparative analysis with individually indexed target capture sequencing
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Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment
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Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and identifies remaining conflicting clades (Cichliformes: Cichlidae: Cichlinae)
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Targeted capture and massively parallel sequencing of 12 human exomes
inferredcites →https://doi.org/10.1038/ng.2007.42openalex-snapshot
Genome-wide in situ exon capture for selective resequencing
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Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nrg3803openalex-snapshot
Sequencing pools of individuals — mining genome-wide polymorphism data without big funding
inferredcites →https://doi.org/10.1038/s41431-017-0022-1openalex-snapshot
Exome Pool-Seq in neurodevelopmental disorders
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Patterns of coding variation in the complete exomes of three Neandertals
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GMAP: a genomic mapping and alignment program for mRNA and EST sequences
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FrameDP: sensitive peptide detection on noisy matured sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btq214openalex-snapshot
A statistical method for the detection of variants from next-generation resequencing of DNA pools
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
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Toward better understanding of artifacts in variant calling from high-coverage samples
inferredcites →https://doi.org/10.1093/bioinformatics/btx699openalex-snapshot
Mosdepth: quick coverage calculation for genomes and exomes
inferredcites →https://doi.org/10.1098/rspb.2012.2113openalex-snapshot
Expansion of the antimicrobial peptide repertoire in the invasive ladybirdHarmonia axyridis
inferredcites →https://doi.org/10.1101/gr.129684.111openalex-snapshot
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
inferredcites →https://doi.org/10.1101/gr.194201openalex-snapshot
SSAHA: A Fast Search Method for Large DNA Databases
inferredcites →https://doi.org/10.1111/1755-0998.12222openalex-snapshot
A targeted next‐generation sequencing toolkit for exon‐based cichlid phylogenomics
inferredcites →https://doi.org/10.1111/1755-0998.12449openalex-snapshot
Exon capture phylogenomics: efficacy across scales of divergence
inferredcites →https://doi.org/10.1111/1755-0998.12541openalex-snapshot
An evaluation of transcriptome‐based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)
inferredcites →https://doi.org/10.1111/1755-0998.12905openalex-snapshot
Expressed exome capture sequencing: A method for cost‐effective exome sequencing for all organisms
inferredcites →https://doi.org/10.1111/1755-0998.12924openalex-snapshot
Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species
inferredcites →https://doi.org/10.1111/1755-0998.12986openalex-snapshot
Using transcriptome sequencing and pooled exome capture to study local adaptation in the giga‐genome of Pinus cembra
inferredcites →https://doi.org/10.1111/2041-210x.12988openalex-snapshot
On the universality of target‐enrichment baits for phylogenomic research
inferredcites →https://doi.org/10.1111/bij.12551openalex-snapshot
Phylogenomic analyses of species relationships in the genusSabal(Arecaceae) using targeted sequence capture
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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
inferredcites →https://doi.org/10.1111/mec.12360openalex-snapshot
Estimation of population allele frequencies from next‐generation sequencing data: pool‐versus individual‐based genotyping
inferredcites →https://doi.org/10.1111/mec.12516openalex-snapshot
Unlocking the vault: next‐generation museum population genomics
inferredcites →https://doi.org/10.1111/tpj.12193openalex-snapshot
Whole‐exome targeted sequencing of the uncharacterized pine genome
inferredcites →https://doi.org/10.1126/science.1190371openalex-snapshot
Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude
inferredcites →https://doi.org/10.1186/1471-2164-12-347openalex-snapshot
Exome-wide DNA capture and next generation sequencing in domestic and wild species
inferredcites →https://doi.org/10.1186/1471-2164-13-403openalex-snapshot
Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales
inferredcites →https://doi.org/10.1186/1471-2164-13-618openalex-snapshot
Pre-capture multiplexing improves efficiency and cost-effectiveness of targeted genomic enrichment
inferredcites →https://doi.org/10.1186/1471-2164-13-683openalex-snapshot
Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing
inferredcites →https://doi.org/10.1371/journal.pgen.1000695openalex-snapshot
Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data
inferredcites →https://doi.org/10.1371/journal.pgen.1003815openalex-snapshot
Whole-Exome Sequencing Reveals a Rapid Change in the Frequency of Rare Functional Variants in a Founding Population of Humans
inferredcites →https://doi.org/10.1371/journal.pone.0016163openalex-snapshot
E2F1 Regulates Cellular Growth by mTORC1 Signaling
inferredcites →https://doi.org/10.1371/journal.pone.0026279openalex-snapshot
An Evaluation of Different Target Enrichment Methods in Pooled Sequencing Designs for Complex Disease Association Studies
inferredcites →https://doi.org/10.1371/journal.pone.0070051openalex-snapshot
SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing
inferredcites →https://doi.org/10.1534/g3.115.018564openalex-snapshot
Exome Sequencing: Current and Future Perspectives
inferredcites →https://doi.org/10.1534/genetics.119.302494openalex-snapshot
Comparison of the Full Distribution of Fitness Effects of New Amino Acid Mutations Across Great Apes
inferredcites →https://doi.org/10.18637/jss.v064.i04openalex-snapshot
fitdistrplus : An R Package for Fitting Distributions
inferredcites →https://doi.org/10.2307/2987937openalex-snapshot
Measurement in Medicine: The Analysis of Method Comparison Studies
inferredcites →https://doi.org/10.3389/fpls.2015.00889openalex-snapshot
Insights into molecular and metabolic events associated with fruit response to post-harvest fungal pathogens

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107347openalex-snapshot
Independent evolutionary transitions to pueriparity across multiple timescales in the viviparous genus Salamandra
inferred← citeshttps://doi.org/10.1038/s41576-019-0152-0openalex-snapshot
The potential of genomics for restoring ecosystems and biodiversity
inferred← citeshttps://doi.org/10.24072/pci.genomics.100002openalex-snapshot
Assessing a novel sequencing-based approach for population genomics in non-model species
inferred← citeshttps://doi.org/10.24072/pcjournal.539openalex-snapshot
Unraveling genetic load dynamics during biological invasion: insights from two invasive insect species
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