Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

Etter, Paul D.; Preston, Jessica L.; Bassham, Susan; Cresko, William A.; Johnson, Eric A.

doi:10.1371/journal.pone.0018561

Cited by 192 publications

(219 citation statements)

References 14 publications

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“…RAD‐seq libraries were prepared as described by Etter, Preston, Bassham, Cresko, and Johnson (2011b; see also Etter, Bassham, Hohenlohe, Johnson, & Cresko, 2011a with modifications). All samples were normalized to 25 ng/μl.…”

Section: Methodsmentioning

confidence: 99%

RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

Jeffery

DiBacco

Wyngaarden

et al. 2017

Ecology and Evolution

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Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab (Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia from a northern European source allowed further range expansion, providing a unique opportunity to study the invasion genomics of a species with multiple invasions. Here, we use restriction‐site‐associated DNA sequencing‐derived SNPs to explore fine‐scale genomewide differentiation between these two invasions. We identified 9137 loci from green crab sampled from 11 locations along eastern North America and compared spatial variation to mitochondrial COI sequence variation used previously to characterize these invasions. Overall spatial divergence among invasions was high (pairwise FST ~0.001 to 0.15) and spread across many loci, with a mean FST ~0.052 and 52% of loci examined characterized by FST values >0.05. The majority of the most divergent loci (i.e., outliers, ~1.2%) displayed latitudinal clines in allele frequency highlighting extensive genomic divergence among the invasions. Discriminant analysis of principal components (both neutral and outlier loci) clearly resolved the two invasions spatially and was highly correlated with mitochondrial divergence. Our results reveal extensive cryptic intraspecific genomic diversity associated with differing patterns of colonization success and demonstrates clear utility for genomic approaches to delineating the distribution and colonization success of aquatic invasive species.

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Section: Methodsmentioning

confidence: 99%

RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

Jeffery

DiBacco

Wyngaarden

et al. 2017

Ecology and Evolution

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“…For subsequent analyses, only the first (left) paired-read was used. The DNA fragments created by RAD tag library preparation have a restriction site at one end and are randomly sheared at the other end that results in each instance of a restriction site sequence being sampled many times by the first reads and the genomic DNA sequence in the nearby region being randomly sampled at a lower coverage by the second paired-end reads (Etter et al, 2011), which are therefore less suitable for calling SNPs.…”

Section: Rad Tag Sequencing Rad Data Analysis and Snp Identificationmentioning

confidence: 99%

Assessing patterns of hybridization between North Atlantic eels using diagnostic single-nucleotide polymorphisms

et al. 2014

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The two North Atlantic eel species, the European eel (Anguilla anguilla) and the American eel (Anguilla rostrata), spawn in partial sympatry in the Sargasso Sea, providing ample opportunity to interbreed. In this study, we used a RAD (Restriction site Associated DNA) sequencing approach to identify species-specific diagnostic single-nucleotide polymorphisms (SNPs) and design a low-density array that combined with screening of a diagnostic mitochondrial DNA marker. Eels from Iceland (N ¼ 159) and from the neighboring Faroe Islands (N ¼ 29) were genotyped, along with 94 larvae (49 European and 45 American eel) collected in the Sargasso Sea. Our SNP survey showed that the majority of Icelandic eels are pure European eels but there is also an important contribution of individuals of admixed ancestry (10.7%). Although most of the hybrids were identified as F1 hybrids from European eel female Â American eel male crosses, backcrosses were also detected, including a first-generation backcross (F1 hybrid Â pure European eel) and three individuals identified as second-generation backcrosses originating from American eel Â F1 hybrid backcrosses interbreeding with pure European eels. In comparison, no hybrids were observed in the Faroe Islands, the closest bodies of land to Iceland. It is possible that hybrids show an intermediate migratory behaviour between the two parental species that ultimately brings hybrid larvae to the shores of Iceland, situated roughly halfway between the Sargasso Sea and Europe. Only two hybrids were observed among Sargasso Sea larvae, both backcrosses, but no F1 hybrids, that points to temporal variation in the occurrence of hybridization.

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“…A pilot study to inform the choice of restriction enzyme(s) was therefore carried out in which the DNA of two parents and 20 offspring from the full-sib family was digested using the following four restriction enzymes; two 8-base pair (bp) (Sbfl and SgrAl) and two 6-bp (Pstl and Xmal). Using the methods described by Etter et al (2011) RADseq libraries were prepared for each enzyme using the size range selection of 300 to 700-bp. To get a better coverage of the parents, we used a ratio of five times the amount of parental DNA relative to offspring DNA in order to achieve a 5-fold increase in the number of Illumina reads for the parental samples compared to those for each offspring.…”

Section: Primary Digestion: Selection Of Restriction Enzymementioning

confidence: 99%

QTL analysis and genomic selection using RADseq derived markers in Sitka spruce: the potential utility of within family data

Fuentes-Utrilla

Goswami

Cottrell

et al. 2017

Tree Genetics & Genomes

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Sitka spruce (Picea sitchensis (Bong.) Carr) is the most common commercial plantation species in Britain and a breeding programme based on traditional lines has been in operation since the early 1960s. Rotation lengths of 40-years have led breeders to adopt a process of indirect selection at younger ages based on traits well correlated with final selection, but still the generation interval is unlikely to reduce much below twenty years. Recent successful developments with genomic selection in animal breeding have led tree breeders to consider the application of this technology. In this study a RAD sequence assay was developed as a means of investigating the potential of molecular breeding in a non-model species. DNA was extracted from nearly 500 clonally replicated trees growing in a single full-sibling family at one site in Britain. The technique proved successful in identifying 132 QTLs for 5-year bud-burst and 2 QTLs for 6-year height. In addition, the accuracy of predicting phenotypes by genomic selection was strikingly high at 0.62 and 0.59 respectively. Sensitivity analysis with 200 offspring found only a slight fall in correlation values (0.54 and 0.38) although when the training population reduced to 50 offspring predictive values fell further (0.33 and 0.25). This proved an encouraging first investigation into the potential use of genomic selection in the breeding of Sitka spruce. The authors investigate how problems associated with effective population size and linkage disequilibrium can be avoided and suggest a practical way of incorporating genomic selection into a dynamic breeding programme.

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Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

Cited by 192 publications

References 14 publications

RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

Assessing patterns of hybridization between North Atlantic eels using diagnostic single-nucleotide polymorphisms

QTL analysis and genomic selection using RADseq derived markers in Sitka spruce: the potential utility of within family data

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