Skim-Sequencing Reveals the Likely Origin of the Enigmatic Endangered Sunflower Helianthus schweinitzii

Abstract

Resolving the origin of endangered taxa is an essential component of conservation. This information can be used to guide efforts of bolstering genetic diversity, and also enables species recovery and future evolutionary studies. Here, we used low-coverage whole genome sequencing to clarify the origin of Helianthus schweinitzii, an endangered tetraploid sunflower that is endemic to the Piedmont Plateau in the eastern United States. We surveyed four accessions representing four populations of H. schweinitzii and 38 accessions of six purported parental species. Using de novo approaches, we assembled 87,004 bp of the chloroplast genome and 6770 bp of the nuclear 35S rDNA. Phylogenetic reconstructions based on the chloroplast genome revealed no reciprocal monophyly of taxa. In contrast, nuclear rDNA data strongly supported the currently accepted sections of the genus Helianthus. Information from combined cpDNA and rDNA provided evidence that H. schweinitzii is likely an allo-tetraploid that formed as a result of hybridization between the diploids Helianthus giganteus and Helianthus microcephalus.

Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region

“…Skim sequencing (SkimSeq) is one of the less complex NGS methods, which uses low coverage (1–10X) whole genome sequencing of multiple individuals for high resolution genotyping [ 45 , 46 , 47 , 48 ]. SkimSeq is less laborious with fewer complex steps, is unbiased towards specific alleles, is capable of SNPs detection, which enables informative sampling and validation of the genome [ 49 , 50 , 51 , 52 , 53 ]. This genotyping by sequencing approach is useful in population study with unknown parental genome information to generate detailed diversity analysis and marker-assisted selections [ 45 , 53 ].…”

A Unique Cytoplasmic–Nuclear Interaction in Sunflower (Helianthus annuus L.) Causing Reduced-Vigor Plants and the Genetics of Vigor Restoration

“…Cultivated sunflower ( Helianthus annuus L., 2n = 2× = 34) is one of the few crops native to the United States. The Helianthus genus is well known for its taxonomic complexity, which includes 53 species (14 annual and 39 perennial) and 19 subspecies ( Seiler et al., 2017 ; Anderson et al., 2019 ). The annual species are all diploid (including cultivated sunflower), and the perennial species include 26 diploid, three tetraploid, seven hexaploid, and three mixaploid species.…”