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Achieving high-quality ddRAD-like reference catalogs for non-model species: the power of overlapping paired-end reads

https://doi.org/10.1101/2020.04.03.024331

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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/ece3.6483openalex-snapshot

Evaluating the effect of reference genome divergence on the analysis of empirical RADseq datasets

inferredcites →https://doi.org/10.1007/978-0-387-98141-3openalex-snapshot

ggplot2: Elegant Graphics for Data Analysis

inferredcites →https://doi.org/10.1007/978-1-4939-9173-0_14openalex-snapshot

BUSCO: Assessing Genome Assembly and Annotation Completeness

inferredcites →https://doi.org/10.1007/978-3-319-24277-4_9openalex-snapshot

Data Analysis

inferredcites →https://doi.org/10.1007/s00227-018-3366-3openalex-snapshot

Green sea turtle (Chelonia mydas) population history indicates important demographic changes near the mid-Pleistocene transition

inferredcites →https://doi.org/10.1007/s10592-009-9975-0openalex-snapshot

Genetic composition, population structure and phylogeography of the loggerhead sea turtle: colonization hypothesis for the Brazilian rookeries

inferredcites →https://doi.org/10.1017/s002531541700193xopenalex-snapshot

Revisiting the genetic diversity and population structure of the critically endangered leatherback turtles in the South-west Atlantic Ocean: insights for species conservation

inferredcites →https://doi.org/10.1023/a:1018382415005openalex-snapshot

Global phylogeography of the ridley sea turtles (Lepidochelys spp.) as inferred from mitochondrial DNA sequences

inferredcites →https://doi.org/10.1038/ng.2615openalex-snapshot

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

inferredcites →https://doi.org/10.1038/nprot.2017.123openalex-snapshot

Deriving genotypes from RAD-seq short-read data using Stacks

inferredcites →https://doi.org/10.1038/nrg.2015.28openalex-snapshot

Harnessing the power of RADseq for ecological and evolutionary genomics

inferredcites →https://doi.org/10.1038/s41598-018-29325-6openalex-snapshot

Systematic evaluation of error rates and causes in short samples in next-generation sequencing

inferredcites →https://doi.org/10.1038/s41598-020-69613-8openalex-snapshot

Genomic evidence of recent hybridization between sea turtles at Abrolhos Archipelago and its association to low reproductive output

inferredcites →https://doi.org/10.1093/bfgp/elq031openalex-snapshot

RADSeq: next-generation population genetics

inferredcites →https://doi.org/10.1093/bioinformatics/btaa025openalex-snapshot

Identifying and removing haplotypic duplication in primary genome assemblies

inferredcites →https://doi.org/10.1093/bioinformatics/btp163openalex-snapshot

Biopython: freely available Python tools for computational molecular biology and bioinformatics

inferredcites →https://doi.org/10.1093/bioinformatics/btt593openalex-snapshot

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btu393openalex-snapshot

circlize implements and enhances circular visualization in R

inferredcites →https://doi.org/10.1093/bioinformatics/btx330openalex-snapshot

Flexbar 3.0 – SIMD and multicore parallelization

inferredcites →https://doi.org/10.1093/bioinformatics/btz966openalex-snapshot

ipyrad: Interactive assembly and analysis of RADseq datasets

inferredcites →https://doi.org/10.1093/gbe/evz190openalex-snapshot

Sea Turtle Population Genomic Discovery: Global and Locus-Specific Signatures of Polymorphism, Selection, and Adaptive Potential

inferredcites →https://doi.org/10.1093/jhered/esaa024openalex-snapshot

New Genetic Insights About Hybridization and Population Structure of Hawksbill and Loggerhead Turtles From Brazil

inferredcites →https://doi.org/10.1101/gr.223057.117openalex-snapshot

New advances in sequence assembly

inferredcites →https://doi.org/10.1101/pdb.prot5448openalex-snapshot

Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing

inferredcites →https://doi.org/10.1111/1755-0998.12566openalex-snapshot

RAD cap: sequence capture of dual‐digest RAD seq libraries with identifiable duplicates and reduced missing data

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/10.1111/1755-0998.12980openalex-snapshot

A versatile Rapture (RAD‐Capture) platform for genotyping marine turtles

inferredcites →https://doi.org/10.1111/1755-0998.13029openalex-snapshot

An empirical pipeline for choosing the optimal clustering threshold in RADseq studies

inferredcites →https://doi.org/10.1111/1755-0998.13108openalex-snapshot

Accuracy of de novo assembly of DNA sequences from double‐digest libraries varies substantially among software

inferredcites →https://doi.org/10.1111/1755-0998.13144openalex-snapshot

Helping decision making for reliable and cost‐effective 2b‐RAD sequencing and genotyping analyses in non‐model species

inferredcites →https://doi.org/10.1111/2041-210x.12700openalex-snapshot

Bioinformatic processing of RAD‐seq data dramatically impacts downstream population genetic inference

inferredcites →https://doi.org/10.1111/2041-210x.12775openalex-snapshot

Lost in parameter space: a road map for stacks

inferredcites →https://doi.org/10.1111/2041-210x.13038openalex-snapshot

Would an RRS by any other name sound as RAD ?

inferredcites →https://doi.org/10.1111/j.1365-294x.2007.03542.xopenalex-snapshot

Population genetics and phylogeography of sea turtles

inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05685.xopenalex-snapshot

Nuclear markers reveal a complex introgression pattern among marine turtle species on the Brazilian coast

inferredcites →https://doi.org/10.1111/jbi.13483openalex-snapshot

The evolutionary history and global phylogeography of the green turtle ( Chelonia mydas )

inferredcites →https://doi.org/10.1111/mec.12350openalex-snapshot

Genotyping‐by‐sequencing in ecological and conservation genomics

inferredcites →https://doi.org/10.1111/mec.12354openalex-snapshot

Stacks: an analysis tool set for population genomics

inferredcites →https://doi.org/10.1111/mec.14077openalex-snapshot

quaddRAD: a new high‐multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage

inferredcites →https://doi.org/10.1111/mec.15165openalex-snapshot

Geography best explains global patterns of genetic diversity and postglacial co‐expansion in marine turtles

inferredcites →https://doi.org/10.1111/mec.15253openalex-snapshot

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

inferredcites →https://doi.org/10.1126/science.1254449openalex-snapshot

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

inferredcites →https://doi.org/10.1146/annurev-ecolsys-110617-062431openalex-snapshot

Using Genomic Data to Infer Historic Population Dynamics of Nonmodel Organisms

inferredcites →https://doi.org/10.1155/2014/675158openalex-snapshot

Defining Loci in Restriction-Based Reduced Representation Genomic Data from Nonmodel Species: Sources of Bias and Diagnostics for Optimal Clustering

inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

inferredcites →https://doi.org/10.1186/gb-2013-14-3-r28openalex-snapshot

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

inferredcites →https://doi.org/10.1186/s13062-018-0208-7openalex-snapshot

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

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.0106713openalex-snapshot

Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol

inferredcites →https://doi.org/10.1371/journal.pone.0179073openalex-snapshot

Optimized double-digest genotyping by sequencing (ddGBS) method with high-density SNP markers and high genotyping accuracy for chickens

inferredcites →https://doi.org/10.1371/journal.pone.0201254openalex-snapshot

A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates

inferredcites →https://doi.org/10.2144/000113809openalex-snapshot

Length and GC-Biases During Sequencing Library Amplification: A Comparison of Various Polymerase-Buffer Systems with Ancient and Modern DNA Sequencing Libraries

inferredcites →https://doi.org/10.3389/fgene.2019.00533openalex-snapshot

Selecting RAD-Seq Data Analysis Parameters for Population Genetics: The More the Better?

inferredcites →https://doi.org/10.3390/genes10010009openalex-snapshot

Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management

inferredcites →https://doi.org/10.7717/peerj.2584openalex-snapshot

VSEARCH: a versatile open source tool for metagenomics

inferredcites →https://doi.org/10.7717/peerj.431openalex-snapshot

dDocent : a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

inferredcites →https://doi.org/10.7717/peerj.7724openalex-snapshot

Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

What points at this work

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

inferred← citeshttps://doi.org/10.1002/age.70096openalex-snapshot

Genetic Diversity and Population Structure of Squalus cf. mitsukurii (Chondrichthyes: Squalidae) Revealed by ddRAD Sequencing

inferred← citeshttps://doi.org/10.1002/ece3.71124openalex-snapshot

Green Turtle Conservation in the Genomic Era—Monitoring an Endangered Mediterranean Population and Its Breeding Habits

inferred← citeshttps://doi.org/10.1017/s0959270925100142openalex-snapshot

Conservation implications of genetic structure in the Critically Endangered Hooded Grebe Podiceps gallardoi

inferred← citeshttps://doi.org/10.1038/s41437-026-00859-0openalex-snapshot

It is hard to be small: Inbreeding depression on male breeding success depends on body size in a threatened songbird

inferred← citeshttps://doi.org/10.1093/molbev/msag082openalex-snapshot

A key regulator of missing-self innate immunity is polymorphic and under diversifying selection

inferred← citeshttps://doi.org/10.1093/ornithology/ukae045openalex-snapshot

Agonistic song rate positively correlates with male breeding success and avian malaria infection in Acrocephalus paludicola (Aquatic Warbler), a promiscuous songbird with female-only parental care

inferred← citeshttps://doi.org/10.1101/2024.04.21.590470openalex-snapshot

It is hard to be small: Inbreeding depression depends on the body size in a threatened songbird

inferred← citeshttps://doi.org/10.1111/1755-0998.13859openalex-snapshot

Scaling‐up RADseq methods for large datasets of non‐invasive samples: Lessons for library construction and data preprocessing

inferred← citeshttps://doi.org/10.1111/jeb.14236openalex-snapshot

Integrating morphological, molecular and cytogenetic data for F2 sea turtle hybrids diagnosis revealed balanced chromosomal sets

inferred← citeshttps://doi.org/10.1111/mec.16113openalex-snapshot

Divergence and hybridization in sea turtles: Inferences from genome data show evidence of ancient gene flow between species

inferred← citeshttps://doi.org/10.1111/mec.16773openalex-snapshot

Evidence of backcross inviability and mitochondrial DNA paternal leakage in sea turtle hybrids

inferred← citeshttps://doi.org/10.3389/fmars.2023.1112842openalex-snapshot

Origins of green turtle fishery bycatch in the central Pacific revealed by mixed genetic markers

inferred← citeshttps://doi.org/10.3390/ijms26188822openalex-snapshot

The Mediterranean Habitat of the Nile Soft-Shelled Turtle (Trionyx triunguis): Genomic and Reproductive Insights into an Endangered Population

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