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

http://ir.library.oregonstate.edu/concern/articles/8s45qb81v

Supporting information is available online at:  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145031

All raw sequence data are available through NCBI SRA under project number SRP021923. Sequences containing SSRs and designed primers are attached as supplementary material

To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article was published by the Public Library of Science and is in the public domain. The published article can be found at:  http://www.plosone.org/

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  • 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.
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  • Staton, M., Best, T., Khodwekar, S., Owusu, S., Xu, T., Xu, Y., ... & Carlson, J. E. (2015). Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing. PLoS ONE, 10(12), e0145031. doi:10.1371/journal.pone.0145031
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  • description.provenance : Approved for entry into archive by Patricia Black(patricia.black@oregonstate.edu) on 2016-01-22T21:15:54Z (GMT) No. of bitstreams: 2 license_rdf: 1089 bytes, checksum: 0a703d871bf062c5fdc7850b1496693b (MD5) JenningsTaraBotanyPlantPathPreliminaryGenomicCharacterization.pdf: 561862 bytes, checksum: 7fa094b63029c33f2a94afdefe38e91f (MD5)
  • description.provenance : Made available in DSpace on 2016-01-22T21:15:54Z (GMT). No. of bitstreams: 2 license_rdf: 1089 bytes, checksum: 0a703d871bf062c5fdc7850b1496693b (MD5) JenningsTaraBotanyPlantPathPreliminaryGenomicCharacterization.pdf: 561862 bytes, checksum: 7fa094b63029c33f2a94afdefe38e91f (MD5) Previous issue date: 2015-12-23
  • description.provenance : Submitted by Patricia Black (patricia.black@oregonstate.edu) on 2016-01-22T21:14:44Z No. of bitstreams: 2 license_rdf: 1089 bytes, checksum: 0a703d871bf062c5fdc7850b1496693b (MD5) JenningsTaraBotanyPlantPathPreliminaryGenomicCharacterization.pdf: 561862 bytes, checksum: 7fa094b63029c33f2a94afdefe38e91f (MD5)

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