Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

Staton, Margaret; Best, Teodora; Khodwekar, Sudhir; Owusu, Sandra A.; Xu, Tao; Xu, Yi; Jennings, Tara; Cronn, Richard; Arumuganathan, Aru K.; Coggeshall, Mark V.; Gailing, Oliver; Liang, Haiying; Romero‐Severson, Jeanne; Schlarbaum, Scott E.; Carlson, John E.

doi:10.1371/journal.pone.0145031

Cited by 29 publications

(34 citation statements)

References 56 publications

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“…Transcriptome sequence data will also provide a rich resource for the identification of Single Nucleotide Polymorphism (SNP) markers. In addition to 14 markers already developed (Owusu et al 2013), we also describe 13 new polymorphic genomic SSRs derived from low coverage genome sequencing (Staton et al 2015). Genetic variation estimates at genomic SSRs were slightly lower but comparable to estimates (He = 0.775, Ho = 0.663, A =11.071) for 14 other genomic SSRs that were characterized in the same sample set (Owusu et al 2013).…”

Section: Discussionmentioning

confidence: 88%

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Development of genic and genomic microsatellites in Gleditsia triacanthos L. (Fabaceae) using Illumina sequencing

et al. 2017

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Abstract. Twenty new polymorphic genic SSRs (EST-SSRs) and 13 genomic SSRs were developed in honeylocust (Gleditsia triacanthos) using Illumina transcriptome and low-coverage genome sequencing. A diversity panel of 40 honeylocust samples covering large parts of the species distribution range was characterized. As expected the level of genetic variation was lower in EST-SSRs than for non-genic genomic SSRs. This is the first report of ESTSSRs for honeylocust. All markers are polymorphic and produce clear single locus amplification products and can be used for genetic diversity and gene flow analyses. The transcriptome sequencing data provide a rich resource for new marker development.

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Section: Discussionmentioning

confidence: 88%

“…For genomic SSR development, Illumina low-coverage genome sequencing was used to generate 14,888,028 paired-end sequences assembled into 13,775,803 contigs in a size range from 93-191 bp (Owusu et al 2013, Staton et al 2015. A total of 4715 primer pairs flanking SSR motifs were identified (Owusu et al 2013).…”

Section: Methodsmentioning

confidence: 99%

Development of genic and genomic microsatellites in Gleditsia triacanthos L. (Fabaceae) using Illumina sequencing

et al. 2017

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“…We present development of a wealth of nuSSR markers for koa and koaia to supplement the shortage of molecular marker data currently available. Past efforts in this arena required use of magnetic beads and the 454 sequencing platform however, following Staton et al (2015), we demonstrate a newer method to improve upon numbers of markers generated. We have described significantly more SSR primer options than those presented in studies of other Acacia spp.…”

Section: Introductionmentioning

confidence: 91%

Development and validation of Acacia koa and A. koaia nuclear SSRs using Illumina sequencing

Lawson

Ebrahimi

2018

Silvae Genetica

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Koa (Acacia koa) and sub-species koaia (A. koaia) are two of more than 1,200 species from the genus Acacia within the Leguminosae (also designated Fabaceae) family. In the past, koa and koaia forests were found throughout the Hawaiian archipelago but populations have dramatically decreased. Comprehensive analyses of simple sequence repeats (SSRs) have not been published previously. Here we use genome sequencing and bioinformatics tools to report development of 100,000+ nuclear SSR (nuSSR) markers for use in koa and koaia genome studies with transcriptome SSR information was included for comparison. Over 10,000 high-value SSRs (40-60 % GC content) were isolated with 3,600+ further validated by ePCR. SSRs generated in this work can assist current efforts to sustainably increase in koa and koaia populations.

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“…To plot the syntenic regions, cM distances on the genetic maps of green ash were converted to base pairs using an averaged cM/bp value, based on the total linkage length in cM of the map and the estimated total genome size of green ash (i.e. 961Mb) (Staton et al, 2015).…”

Section: Comparative Analysis With Genetic Maps Of Two Asterid and Twmentioning

confidence: 99%

“…In this study, a total of 5,712 high quality single nucleotide polymorphisms (SNPs) were discovered using a minimum allele frequency of 1% across the entire genome through genotyping-by-sequencing. We also screened hundreds of genomic-and EST-based microsatellite markers (SSRs) from previous de novo assemblies (Staton et al 2015;Lane et al 2016). A first genetic linkage map of green ash was constructed from 91 individuals in a full-sib family, combining 2,719 SNP and 84 SSR segregating markers among the parental maps.…”

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The first genetic linkage map forFraxinus pennsylvanicaand syntenic relationships with four related species

Koch

Coggeshall

et al. 2018

Preprint

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Green ash (Fraxinus pennsylvanica) is an outcrossing, diploid (2n=46) hardwood tree species, native to North America. Native ash species in North America are being threatened by the rapid invasion of emerald ash borer (EAB, Agrilus planipennis) from Asia. Green ash, the most widely distributed ash species, is severely affected by EAB infestation, yet few resources for genetic studies and improvement of green ash are available. In this study, a total of 5,712 high quality single nucleotide polymorphisms (SNPs) were discovered using a minimum allele frequency of 1% across the entire genome through genotyping-by-sequencing. We also screened hundreds of genomic-and EST-based microsatellite markers (SSRs) from previous de novo assemblies (Staton et al. 2015;Lane et al. 2016). A first genetic linkage map of green ash was constructed from 91 individuals in a full-sib family, combining 2,719 SNP and 84 SSR segregating markers among the parental maps. The consensus SNP and SSR map contains a total of 1,201 markers in 23 linkage groups spanning 2008.87cM, at an average inter-marker distance of 1.67 cM with a minimum logarithm of odds (LOD) of 6 and maximum recombination fraction of 0.40. Comparisons of the organization the green ash map with the genomes of asterid species coffee and tomato, and genomes of the rosid species poplar and peach, showed areas of conserved gene order, with overall synteny strongest with coffee. KeywordsGreen ash, linkage map, single nucleotide polymorphism (SNP), simple sequence repeats (SSRs), Genotyping-by-Sequencing (GBS), syntenyThe genetic and molecular mechanisms underlying diverse biological traits in green ash are unknown. Genetic linkage maps are powerful tools for genomics and genetics research. With a large number of DNA markers, fine mapping of quantitative trait loci (QTL) can support marker-assisted selection for breeding programs. Candidate genes can also be positioned within the quantitative trait locus (QTL) regions identified by association studies. Combined with transcriptome studies, differentially expressed genes can be mapped and localized so that genes related to specific traits of interest can be characterized. In addition, linkage maps can also be used to conduct comparative analyses with other species to detect genomic synteny and to improve and correct chromosome-scale genome assemblies. Linkage maps have been reported in many non-model species (Tian et al. 2015;Moumouni et al. 2015;Raman et al. 2014), but the resolution of genetic maps depends on the number of markers segregating in the mapping population.Recently, the innovation of NGS methods for genetic marker discovery combined with reduced costs has facilitated the genotyping of thousands of SNPs across hundreds of samples. New methods, such as reduced-representation libraries (RRLs) (Van Tassell et al. 2008), restriction-site associated sequencing (RAD-seq) (Davey and Blaxter 2010) and genotyping-bysequencing (GBS) (Elshire et al. 2011), utilize restriction enzyme digestion of target genomes to reduce the complex...

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Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

Cited by 29 publications

References 56 publications

Development of genic and genomic microsatellites in Gleditsia triacanthos L. (Fabaceae) using Illumina sequencing

Development of genic and genomic microsatellites in Gleditsia triacanthos L. (Fabaceae) using Illumina sequencing

Development and validation of Acacia koa and A. koaia nuclear SSRs using Illumina sequencing

The first genetic linkage map forFraxinus pennsylvanicaand syntenic relationships with four related species

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