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Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing
Journal article   Open access   Peer reviewed

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

Shannon C. K. Straub, Mark Fishbein, Tatyana Livshultz, Zachary Foster, Matthew Parks, Kevin Weitemier, Richard C. Cronn and Aaron Liston
BMC genomics, v 12(1), pp 211-211
04 May 2011
DOI: https://doi.org/10.1186/1471-2164-12-211
PMID: 21542930
Featured in Collection :   UN Sustainable Development Goals @ Drexel
url
https://doi.org/10.1186/1471-2164-12-211View
Published, Version of Record (VoR)CC BY V4.0,  Open

Abstract

Biotechnology & Applied Microbiology Genetics & Heredity Life Sciences & Biomedicine Science & Technology
Background: Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. Results: A 0.5x genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29x) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14x). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. Conclusions: The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives. This study represents a first step in the development of a community resource for further study of plant-insect co-evolution, anti-herbivore defense, floral developmental genetics, reproductive biology, chemical evolution, population genetics, and comparative genomics using milkweeds, and A. syriaca in particular, as ecological and evolutionary models.

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Collaboration types
Domestic collaboration
Web of Science research areas
Biotechnology & Applied Microbiology
Genetics & Heredity
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