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

Straub SC, Fishbein M, Livshultz T, Foster Z, Parks M, Weitemier K, Cronn RC, Liston A - BMC Genomics (2011)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA. straubs@science.oregonstate.edu

ABSTRACT

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 0.5× 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 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). 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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Repeat types detected among de novo contigs of the Asclepias syriaca nuclear genome. The numbers indicate individual hits in the contig sequences.
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Figure 2: Repeat types detected among de novo contigs of the Asclepias syriaca nuclear genome. The numbers indicate individual hits in the contig sequences.

Mentions: A total of 564 repetitive elements were detected in the A. syriaca de novo contigs (Figure 2). The majority of these repeats were Ty1/copia-like and Ty3/gypsy-like LTR retrotransposons (Figure 2), which are abundant in plants and common across eukaryotes [84-86]. Only the most highly represented repeats in the genome would have high enough coverage at 0.4× total nuclear genome coverage to be assembled, so it is not surprising that the majority of the repeats were Ty1/copia-like and Ty3/gypsy-like retrotransposons. In plant species where retrotransposons have been characterized, it appears to be lineage specific whether Ty1/copia-like or Ty3/gypsy-like retroelements are more abundant in the genome, likely because retrotransposons can proliferate or be lost from genomes over relatively short evolutionary time scales [85,87]. Among other asterids, Ty3/gypsy-like retrotransposons are more prevalent in the sunflower (Helianthus annuus), tomato, and potato genomes, while in carrot (Daucus carota), as in A. syriaca, Ty1/copia-like retrotransposons are more numerous [88-90].


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

Straub SC, Fishbein M, Livshultz T, Foster Z, Parks M, Weitemier K, Cronn RC, Liston A - BMC Genomics (2011)

Repeat types detected among de novo contigs of the Asclepias syriaca nuclear genome. The numbers indicate individual hits in the contig sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3116503&req=5

Figure 2: Repeat types detected among de novo contigs of the Asclepias syriaca nuclear genome. The numbers indicate individual hits in the contig sequences.
Mentions: A total of 564 repetitive elements were detected in the A. syriaca de novo contigs (Figure 2). The majority of these repeats were Ty1/copia-like and Ty3/gypsy-like LTR retrotransposons (Figure 2), which are abundant in plants and common across eukaryotes [84-86]. Only the most highly represented repeats in the genome would have high enough coverage at 0.4× total nuclear genome coverage to be assembled, so it is not surprising that the majority of the repeats were Ty1/copia-like and Ty3/gypsy-like retrotransposons. In plant species where retrotransposons have been characterized, it appears to be lineage specific whether Ty1/copia-like or Ty3/gypsy-like retroelements are more abundant in the genome, likely because retrotransposons can proliferate or be lost from genomes over relatively short evolutionary time scales [85,87]. Among other asterids, Ty3/gypsy-like retrotransposons are more prevalent in the sunflower (Helianthus annuus), tomato, and potato genomes, while in carrot (Daucus carota), as in A. syriaca, Ty1/copia-like retrotransposons are more numerous [88-90].

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA. straubs@science.oregonstate.edu

ABSTRACT

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 0.5× 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 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). 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.

Show MeSH