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

Abstract

BackgroundMilkweeds (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.ResultsA 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.ConclusionsThe 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.

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

“…In numerous angiosperm lineages, a subset of plastid genes, including clpP1 and accD, display accelerated evolutionary rates, but the causes of this recurring phenomenon have remained unclear (Jansen et al 2007;Erixon and Oxelman 2008;Greiner et al 2008b;Guisinger et al 2008Guisinger et al , 2010Guisinger et al , 2011Straub et al 2011;Sloan et al 2012aSloan et al , 2014aBarnard-Kubow et al 2014;Weng et al 2014;Dugas et al 2015;Williams et al 2015;Blazier et al 2016;Zhang et al 2016). We investigated the nuclear genes that contribute to the multisubunit complexes that include ClpP1 and AccD, and incorporated population genetic and structural data to distinguish between relaxed purifying selection and positive selection as drivers of elevated d N /d S values.…”

“…Within angiosperms, most plastid genomes are highly conserved in sequence and structure (Jansen et al 2007;Wicke et al 2011), but multiple independent lineages have experienced accelerated rates of aa substitution in similar subsets of nonphotosynthetic genes (Jansen et al 2007;Erixon and Oxelman 2008;Greiner et al 2008b;Guisinger et al 2008Guisinger et al , 2010Guisinger et al , 2011Straub et al 2011;Sloan et al 2012aSloan et al , 2014aBarnard-Kubow et al 2014;Weng et al 2014;Dugas et al 2015;Williams et al 2015;Zhang et al 2016). Several mechanisms have been hypothesized to explain these repeated accelerations including positive selection, reduced effective population size (N e ), altered DNA repair, changes in gene expression, and pseudogenization following gene transfer to the nucleus (see above citations).…”

Phylogeny and Phylogenetic Nomenclature of the Campanulidae based on an Expanded Sample of Genes and Taxa

“…The target(s), in most cases, are the high-copy elements such as the plastid and mitochondrial genomes, nuclear ribosomal repeats, and additional repetitive elements (Straub et al, 2011(Straub et al, , 2012Steele et al, 2012;Bock et al, 2013;Ripma et al, 2014;Dodsworth et al, 2016;Gardner et al, 2016a). While these markers are easily obtainable because of their high abundance and are capable of being assembled against a growing number of references, the data being used represent only a small fraction of the total data obtained (e.g., plastome data represent only 3% of the data sequenced in Core Goodeniaceae; Gardner et al, 2016a).…”

“…For example, conserved orthologous gene (COS; Fulton et al, 2002), single-copy conserved orthologous gene (COSII; Wu et al, 2006), shared single-copy gene (SSC; Duarte et al, 2010), and/or pentatricopeptide repeat (PPR; Yuan et al, 2009Yuan et al, , 2010 databases have been used to identify phylogenetic markers or regions of those genes for primer development in Oreocarya (Boraginaceae) (Ripma et al, 2014), Asclepias L. (Apocynaceae) (Straub et al, 2011(Straub et al, , 2012, and Penstemon Schmidel (Plantaginaceae) (Blischak et al, 2014). Additionally, genome-skimming data are now being used in conjunction with transcriptome data to develop novel probes for targeting low-copy nuclear genes via Hyb-Seq in taxa such as Asclepias (Apocynaceae) (Weitemier et al, 2014) and Oxalis L. (Oxalidaceae) (Schmickl et al, 2015).…”

“…For instance, one potential use is mining the data sets for candidate low-copy nuclear genes of interest in nonmodel organisms to use in phylogeny reconstruction or downstream evo-devo experiments (Straub et al, 2011(Straub et al, , 2012Blischak et al, 2014;Ripma et al, 2014). The inclusion of nuclear genes in phylogenetic reconstruction often relies on genes with at least two conserved domains from distantly related taxa and the use of degenerate primers (e.g., ADH, GAPDH, CYCLOIDEA [Strand et al, 1997;Hileman, 2003]), which limits the amount of known coding sequence (see Howarth and Donoghue, 2005) and does not include upstream or downstream regulatory elements.…”