Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing
| Autor: | Jeanne Romero-Severson, Teodora Best, Haiying Liang, Scott E. Schlarbaum, Richard Cronn, A. Kathiravetpilla Arumuganathan, Margaret Staton, John E. Carlson, Oliver Gailing, Sudhir Khodwekar, Mark V. Coggeshall, Tara Jennings, Yi Xu, Sandra A. Owusu, Tao Xu |
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| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
DNA
Plant Climate Change lcsh:Medicine Genomics Computational biology Biology Genome DNA sequencing Trees Genomic library lcsh:Science Phylogeny Genetics Whole genome sequencing Multidisciplinary Phylogenetic tree lcsh:R High-Throughput Nucleotide Sequencing food and beverages Sequence Analysis DNA 15. Life on land Genetic marker lcsh:Q Genome Plant Reference genome Microsatellite Repeats Research Article |
| Zdroj: | PLoS ONE, Vol 10, Iss 12, p e0145031 (2015) PLoS ONE |
| ISSN: | 1932-6203 |
| Popis: | Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence. |
| Databáze: | OpenAIRE |
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