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Leveraging targeted sequencing for non-model species: a step-by-step guide to obtain a reduced SNP set and a pipeline to automate data processing in the Antarctic Midge, Belgica antarctica

https://doi.org/10.1101/772384
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What this work says

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

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Expression of genes involved in energy mobilization and osmoprotectant synthesis during thermal and dehydration stress in the Antarctic midge, Belgica antarctica
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On the number of segregating sites in genetical models without recombination
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The hitch-hiking effect of a favourable gene
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Applications of next generation sequencing in molecular ecology of non-model organisms
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A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine
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Great ape genetic diversity and population history
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Compact genome of the Antarctic midge is likely an adaptation to an extreme environment
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
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Continuous up-regulation of heat shock proteins in larvae, but not adults, of a polar insect
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Gene expression changes governing extreme dehydration tolerance in an Antarctic insect
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Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution of F ST
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The Sequence Alignment/Map format and SAMtools
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pegas: an R package for population genetics with an integrated–modular approach
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Search and clustering orders of magnitude faster than BLAST
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The variant call format and VCFtools
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Trimmomatic: a flexible trimmer for Illumina sequence data
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Buffy, a Drosophila Bcl‐2 protein, has anti‐apoptotic and cell cycle inhibitory functions
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Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
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Ascertainment Biases in SNP Chips Affect Measures of Population Divergence
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The role of taxonomy in species conservation
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Local ancestry analysis reveals genomic convergence in extremophile fishes
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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1111/1755-0998.12357openalex-snapshot
Genotyping‐in‐Thousands by sequencing (GT‐seq): A cost effective SNP genotyping method based on custom amplicon sequencing
inferredcites →https://doi.org/10.1111/1755-0998.12613openalex-snapshot
Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping‐by‐sequencing data from natural populations
inferredcites →https://doi.org/10.1111/1755-0998.12998openalex-snapshot
The future is now: Amplicon sequencing and sequence capture usher in the conservation genomics era
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Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)
inferredcites →https://doi.org/10.1111/j.1471-8286.2004.00828.xopenalex-snapshot
hierfstat , a package for r to compute and test hierarchical F ‐statistics
inferredcites →https://doi.org/10.1111/j.1755-0998.2010.02846.xopenalex-snapshot
Assessing the power of informative subsets of loci for population assignment: standard methods are upwardly biased
inferredcites →https://doi.org/10.1111/j.1755-0998.2010.02967.xopenalex-snapshot
Next‐generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout
inferredcites →https://doi.org/10.1111/mec.12568openalex-snapshot
Outlier SNP markers reveal fine‐scale genetic structuring across E uropean hake populations ( M erluccius merluccius)
inferredcites →https://doi.org/10.1111/mec.13948openalex-snapshot
Genetics and the conservation of natural populations: allozymes to genomes
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Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations
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Parallel signatures of selection at genomic islands of divergence and the major histocompatibility complex in ecotypes of sockeye salmon across Alaska
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Ecdysone Receptors: From the Ashburner Model to Structural Biology
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Evaluation of approaches for identifying population informative markers from high density SNP Chips
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EggLib: processing, analysis and simulation tools for population genetics and genomics
inferredcites →https://doi.org/10.1186/1471-2164-12-622openalex-snapshot
Comparison of measures of marker informativeness for ancestry and admixture mapping
inferredcites →https://doi.org/10.1186/s12859-014-0356-4openalex-snapshot
ANGSD: Analysis of Next Generation Sequencing Data
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Estimating genomic diversity and population differentiation – an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri
inferredcites →https://doi.org/10.1186/s13059-018-1520-3openalex-snapshot
Conservation of biodiversity in the genomics era
inferredcites →https://doi.org/10.1242/jeb.02714openalex-snapshot
Slow dehydration promotes desiccation and freeze tolerance in the Antarctic midgeBelgica antarctica
inferredcites →https://doi.org/10.1371/journal.pgen.1002504openalex-snapshot
Genomic Tools for Evolution and Conservation in the Chimpanzee: Pan troglodytes ellioti Is a Genetically Distinct Population
inferredcites →https://doi.org/10.1371/journal.pone.0003376openalex-snapshot
Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
inferredcites →https://doi.org/10.1371/journal.pone.0037135openalex-snapshot
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
inferredcites →https://doi.org/10.1371/journal.pone.0079667openalex-snapshot
Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences
inferredcites →https://doi.org/10.1534/genetics.104.117275openalex-snapshot
Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended
inferredcites →https://doi.org/10.1534/genetics.108.092221openalex-snapshot
A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective
inferredcites →https://doi.org/10.2527/jas.2013-6678openalex-snapshot
Selection of SNP from 50K and 777K arrays to predict breed of origin in cattle1
inferredcites →https://doi.org/10.48550/arxiv.1207.3907openalex-snapshot
Haplotype-based variant detection from short-read sequencing
inferredcites →https://doi.org/10.5281/zenodo.1490420openalex-snapshot
PypeAmplicon: Python pipeline for analysis of amplicon data

What points at this work

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

inferred← citeshttps://doi.org/10.1111/1755-0998.13226openalex-snapshot
A GT‐seq panel for walleye ( Sander vitreus ) provides important insights for efficient development and implementation of amplicon panels in non‐model organisms
inferred← citeshttps://doi.org/10.3103/s0095452723030064openalex-snapshot
Bacteria Associated with the Antarctic Endemic Insect Belgica antarctica Jacobs (Diptera Chironomidae)
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