Abstract
Aquatic invasive species are damaging to native ecosystems. Preventing their spread and achieving comprehensive control measures requires an understanding of the genetic structure of an invasive population. Organellar genomes (plastid and mitochondrial) are useful for population level analyses of invasive plant distributions. In this study we generate complete organellar reference genomes using PacBio sequencing, then use these reference sequences for SNP calling of high-throughput, multiplexed, Illumina based organellar sequencing of fresh and historical samples from across the native and invasive range of Nitellopsis obtusa (Desv. in Loisel.) J.Groves, an invasive macroalgae. The data generated by the analytical pipeline we develop indicate introduction to North America from Western Europe. A single nucleotide transversion in the plastid genome separates a group of five samples from Michigan and Wisconsin that either resulted from introductions of two closely related genotypes or a mutation that has arisen in the invasive range. This transversion will serve as a useful tool to understand how Nitellopsis obtusa moves across the landscape. The methods and analyses described here are broadly applicable to invasive and native plant and algae species, and allow efficient genotyping of variable quality samples, including 100-year-old herbarium specimens, to determine population structure and geographic distributions.
Highlights
Aquatic invasive species are damaging to native ecosystems
The Canu assembly of Pacific Biosciences (PacBio) reads from a North American sample resulted in one contig that contained the complete chloroplast genome, and one contig that contained the complete mitochondrial genome
Using the chloroplast genome as a reference, VarScan called 515 Single Nucleotide Polymorphisms (SNPs)/indels; after filtering, 230 SNPs/ indels remained across all individuals from the native and invasive range (Figure S2)
Summary
Aquatic invasive species are damaging to native ecosystems. Preventing their spread and achieving comprehensive control measures requires an understanding of the genetic structure of an invasive population. Organellar genomes (plastid and mitochondrial) are useful for population level analyses of invasive plant distributions. In this study we generate complete organellar reference genomes using PacBio sequencing, use these reference sequences for SNP calling of high-throughput, multiplexed, Illumina based organellar sequencing of fresh and historical samples from across the native and invasive range of Nitellopsis obtusa The data generated by the analytical pipeline we develop indicate introduction
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