Evolutionary relationships in the genus Secale revealed by DArTseq DNA polymorphism

Al-Beyroutiová, Maja; Sabo, Miroslav; Sleziak, Patrik; Dušinský, Roman; Birčák, Erik; Hauptvogel, Pavol; Kilian, Andrzej; Švec, Miroslav

doi:10.1007/s00606-016-1318-2

Cited by 38 publications

(36 citation statements)

References 34 publications

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“…Each marker was homozygous for the reference allele in females and heterozygous in males. This confirms an XX-XY sex determining system in R. clamitans as previously suggested [37]. …”

Section: Resultssupporting

confidence: 91%

“…Compared to other similar approaches, DArTseq™ yields a lower density of markers (10’s of thousands and up to 35,000 loci versus >800,000 loci with a GBS approach) but has substantially higher coverage and results in less missing data [34]. In addition to these advantages of DArTseq™, we chose this platform because it can directly score samples as heterozygous/homozygous at each locus with the lower density approach [34] and due to the ease of optimizing the platform for each species as well as its capacity to produce thousands of short, high quality polymorphic loci using a custom analytical pipeline [35–37]. Four methods of complexity reduction were tested in R. clamitans (data not presented) and double digestions with Pst I- Sph I method was selected.…”

Section: Methodsmentioning

confidence: 99%

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Sex-linked markers in the North American green frog (Rana clamitans) developed using DArTseq provide early insight into sex chromosome evolution

2016

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BackgroundThe extent to which sex reversal is associated with transitions in sex determining systems (XX-XY, ZZ-ZW, etc.) or abnormal sexual differentiation is predominantly unexplored in amphibians. This is in large part because most amphibian taxa have homomorphic sex chromosomes, which has traditionally made it challenging to identify discordance between phenotypic and genetic sex in amphibians, despite all amphibians having a genetic component to sex determination. Recent advances in molecular techniques such as genome complexity reduction and high throughput sequencing present a valuable avenue for furthering our understanding of sex determination in amphibians and other taxa with homomorphic sex chromosomes like many fish and reptiles.ResultsWe use DArTseq as a novel approach to identify sex-linked markers in the North American green frog (Rana clamitans melanota) using lab-reared tadpoles as well as wild-caught adults from seven ponds either in undeveloped, forested habitats or suburban ponds known to be subject to contamination by anthropogenic chemicals. The DArTseq methodology identified 13 sex-linked SNP loci and eight presence-absence loci associated with males, indicating an XX-XY system. Both alleles from a single locus show partial high sequence homology to Dmrt1, a gene linked to sex determination and differentiation throughout Metazoa. Two other loci have sequence similarities to regions of the chimpanzee and human X-chromosome as well as the chicken Z-chromosome. Several loci also show geographic variation in sex-linkage, possibly indicating sex chromosome recombination. While all loci are statistically sex-linked, they show varying degrees of female heterozygosity and male homozygosity, providing further evidence that some markers are on regions of the sex chromosomes undergoing higher rates of recombination and therefore further apart from the putative sex determining locus.ConclusionThe ease of the DArTseq platform provides a useful avenue for future research on sex reversal and sex chromosome evolution in vertebrates, particularly for non-model species with homomorphic or cryptic or nascent sex chromosomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3209-x) contains supplementary material, which is available to authorized users.

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“…Each marker was homozygous for the reference allele in females and heterozygous in males. This confirms an XX-XY sex determining system in R. clamitans as previously suggested [37]. …”

Section: Resultssupporting

confidence: 91%

Section: Methodsmentioning

confidence: 99%

Sex-linked markers in the North American green frog (Rana clamitans) developed using DArTseq provide early insight into sex chromosome evolution

2016

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“…For example, one of the outlier accessions identified is this study is S. sylvestre (B6). Molecular marker-based analyses of genetic diversity indicated this selfpollinating taxon as the most divergent in genus Secale (Bolibok-Bragoszewska et al, 2014;Al-Beyroutiova et al, 2016;Schreiber et al, 2018). Its large proportion of high VAF variants (Figure 4) likely corresponds to homozygosity for alternative alleles, since reference sequences used during variant calling originated from cultivated rye accessions.…”

Section: Discussionmentioning

confidence: 99%

Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

Hawliczek

Bolibok

Tofil

et al. 2020

Preprint

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38Loss of genetic variation negatively impacts breeding efforts and food security. Genebanks house 39 over 7 million accessions representing vast allelic diversity that is a resource for sustainable 40 breeding. Discovery of DNA variations is an important step in the efficient use of these resources. 41While technologies have improved and costs dropped, it remains impractical to consider 42 resequencing millions of accessions. Candidate genes are known for most agronomic traits, 43 providing a list of high priority targets. Heterogeneity in seed stocks means that multiple samples 44 from an accession need to be evaluated to recover available alleles. To address this we developed a 45 pooled amplicon sequencing approach and applied it to the out-crossing cereal rye (Secale cereale). 46Ninety-six plants from an accession were pooled together, and 95 unique accessions evaluated for 47 sequence variation in six target genes involved in seed quality, biotic and abiotic stress resistance, 48 resulting in 74 predicted deleterious variants using multiple algorithms. Rare variants were 49 recovered including those found only in a low percentage of seed. We conclude that this approach 50 provides a rapid and flexible method for evaluating stock heterogeneity, probing allele diversity, 51 and recovering previously hidden variation in large germplasm collections. 52 53

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“…Next generation genotyping was conducted by Diversity Arrays Technology, Canberra, using proprietary DArTseq™ technology (Kilian et al, 2012). DArTSeq has been described in detail in various animal and plant studies (Al-Beyroutiová et al, 2016;Grewe et al, 2015;Melville et al, 2017;Schultz et al, 2018). Briefly, sequences obtained through the DArTseq method involve a restriction enzyme based complexity reduction of the genome and the Illumina Hiseq 2500 (Illumina) ngs platform (Kilian et al, 2012).…”

Section: Next Generation Genotyping Using Dartseq and Blast For Chlmentioning

confidence: 99%

Developing noninvasive methodologies to assess koala population health through detecting Chlamydia from scats

Cristescu

Miller

Schultz

et al. 2019

Molecular Ecology Resources

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Wildlife diseases are a recognized driver of global biodiversity loss, have substantial economic impacts, and are increasingly becoming a threat to human health. Disease surveillance is critical but remains difficult in the wild due to the substantial costs and potential biases associated with most disease detection methods. Noninvasive scat surveys have been proposed as a health monitoring methodology to overcome some of these limitations. Here, we use the known threat of Chlamydia disease to the iconic, yet vulnerable, koala Phascolarctos cinereus to compare three methods for Chlamydia detection in scats: multiplex quantitative PCR, next generation sequencing, and a detection dog specifically trained on scats from Chlamydia‐infected koalas. All three methods demonstrated 100% specificity, while sensitivity was variable. Of particular interest is the variable sensitivity of these diagnostic tests to detect sick individuals (i.e., not only infection as confirmed by Chlamydia‐positive swabs, but with observable clinical signs of the disease); for koalas with urogenital tract disease signs, sensitivity was 78% with quantitative PCR, 50% with next generation genotyping and 100% with the detection dog method. This may be due to molecular methods having to rely on high‐quality DNA whereas the dog most likely detects volatile organic compounds. The most appropriate diagnostic test will vary with disease prevalence and the specific aims of disease surveillance. Acknowledging that detection dogs might not be easily accessible to all, the future development of affordable and portable “artificial noses” to detect diseases from scats in the field might enable cost‐effective, rapid and large‐scale disease surveillance.

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Evolutionary relationships in the genus Secale revealed by DArTseq DNA polymorphism

Cited by 38 publications

References 34 publications

Sex-linked markers in the North American green frog (Rana clamitans) developed using DArTseq provide early insight into sex chromosome evolution

Sex-linked markers in the North American green frog (Rana clamitans) developed using DArTseq provide early insight into sex chromosome evolution

Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

Developing noninvasive methodologies to assess koala population health through detecting Chlamydia from scats

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