2b-RAD: a simple and flexible method for genome-wide genotyping

Wang, Shi; Meyer, Eli; McKay, John; Matz, Mikhail V.

doi:10.1038/nmeth.2023

Cited by 596 publications

(644 citation statements)

References 21 publications

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“…The quality and integrity of the assembly is demonstrated by the mapping of 94.5% paired-end reads, 99.8% of Sanger-sequenced fosmids and 96.0-99.8% of various transcriptomic datasets generated in this and a previous study 15 (Supplementary Figs 11 and 12; Supplementary Tables 3-6). With the aid of a high-density linkage map (7,489 markers; Supplementary Table 7) constructed by using the 2b-RAD methodology 16 , 1,419 scaffolds (covering ~81% of the assembly) are assigned to the 19 haploid chromosomes ( Fig. 1a; Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

Scallop genome provides insights into evolution of bilaterian karyotype and development

et al. 2017

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Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with many ancestral features. Chromosome-based macrosynteny analysis reveals a striking correspondence between the 19 scallop chromosomes and the 17 presumed ancestral bilaterian linkage groups at a level of conservation previously unseen, suggesting that the scallop may have a karyotype close to that of the bilaterian ancestor. Scallop Hox gene expression follows a new mode of subcluster temporal co-linearity that is possibly ancestral and may provide great potential in supporting diverse bilaterian body plans. Transcriptome analysis of scallop mantle eyes finds unexpected diversity in phototransduction cascades and a potentially ancient Pax2/5/8-dependent pathway for noncephalic eyes. The outstanding preservation of ancestral karyotype and developmental control makes the scallop genome a valuable resource for understanding early bilaterian evolution and biology.

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Section: Resultsmentioning

confidence: 99%

Scallop genome provides insights into evolution of bilaterian karyotype and development

et al. 2017

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“…We used the 2b-RAD method described by Wang et al (2012) to genotype thousands of genome-wide SNPs from nine reference P. flesus individuals, 11 reference demersal flounders, and 21 of the samples collected and analyzed in this study. The nine reference P. flesus individuals were collected at the time of spawning from the Bornholm basin (55 Florin and Höglund (2008) and Momigliano et al (2017a).…”

Section: B-rad Genotypingmentioning

confidence: 99%

Platichthys solemdali sp. nov. (Actinopterygii, Pleuronectiformes): A New Flounder Species From the Baltic Sea

et al. 2018

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The European flounder Platichthys flesus (Linnaeus, 1758) displays two contrasting reproductive behaviors in the Baltic Sea: offshore spawning of pelagic eggs and coastal spawning of demersal eggs, a behavior observed exclusively in the Baltic Sea. Previous studies showed marked differences in behavioral, physiological, and life-history traits of flounders with pelagic and demersal eggs. Furthermore, a recent study demonstrated that flounders with pelagic and demersal eggs represent two reproductively isolated, parapatric species arising from two distinct colonization events from the same ancestral population. Using morphological data we first established that the syntypes on which the original description of P. flesus was based belong to the pelagic-spawning lineage. We then used a combination of morphological and physiological characters as well as genome-wide genetic data to describe flounders with demersal eggs as a new species:Platichthys solemdali sp. nov. The new species can be clearly distinguished from P. flesus based on egg morphology, egg and sperm physiology as well as via population genetic and phylogenetic analyses. While the two species do show some minor morphological differences in the number of anal and dorsal fin rays, no external morphological feature can be used to unambiguously identify individuals to species. Therefore, we developed a simple molecular diagnostic test able to unambiguously distinguish P. solemdali from P. flesus with a single PCR reaction, a tool that should be useful to fishery scientists and managers, as well as to ecologists studying these species.

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“…2b-RAD libraries of two parents and 120 progenies were constructed by using type IIB restriction enzymes, following the protocol developed by Wang et al (2012). In general, library preparation began with the digestion of 100-200 ng genomic DNA in a 15 μl reaction using 4 U BsaXI at 37°C for 3 h. Then, 12 μl of a ligation master mix containing 0.2 μM library-specific adaptors, 1 mM ATP and 800 U T4 DNA ligase was added to the digestion product and incubated at 4°C for 16 h. For the parents, standard BsaXI libraries were constructed with adaptors of fully degenerate cohesive ends, whereas for the progenies, reduced representation libraries were constructed using modified adaptors with 5'-NNG-3' and 5'-NNC-3' overhangs to target a subset of all BsaXI fragments.…”

Section: Library Preparation Sequencing and De Novo Genotypingmentioning

confidence: 99%

High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

et al. 2015

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The sex determination system in crabs is believed to be XY-XX from karyotypy, but centromeres could not be identified in some chromosomes and their morphology is not completely clear. Using quantitative trait locus mapping of the gender phenotype, we revealed a ZW-ZZ sex determination system in Eriocheir sinensis and presented a high-density linkage map covering~98.5% of the genome, with 73 linkage groups corresponding to the haploid chromosome number. All sex-linked markers in the family we used were located on a single linkage group, LG60, and sex linkage was confirmed by genome-wide association studies (GWAS). Forty-six markers detected by GWAS were heterozygous and segregated only in the female parent. The female LG60 was thus the putative W chromosome, with the homologous male LG60 as the Z chromosome. The putative Z and W sex chromosomes were identical in size and carried many homologous loci. Sex ratio (5:1) skewing towards females in induced triploids using unrelated animals also supported a ZW-ZZ system. Transcriptome data were used to search for candidate sex-determining loci, but only one LG60 gene was identified as an ankyrin-2 gene. Double sex-and mab3-related transcription factor 1 (Dmrt1), a Z-linked gene in birds, was located on a putative autosome. With complete genome sequencing and transcriptomic data, more genes on putative sex chromosomes will be characterised, thus leading towards a comprehensive understanding of the sex determination and differentiation mechanisms of E. sinensis, and decapod crustaceans in general.

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2b-RAD: a simple and flexible method for genome-wide genotyping

Cited by 596 publications

References 21 publications

Scallop genome provides insights into evolution of bilaterian karyotype and development

Scallop genome provides insights into evolution of bilaterian karyotype and development

Platichthys solemdali sp. nov. (Actinopterygii, Pleuronectiformes): A New Flounder Species From the Baltic Sea

High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

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