Abstract

The genus Chenopodium, which comprises around 150 species globally, is characterized by its wide geographic distribution and ecological adaptability, particularly in temperate regions. Some species, such as Chenopodium quinoa and Chenopodium pallidicaule, have served as domesticated staple crops in the Andean region of South America for centuries, valued for their robust nutritional profile and adaptability to adverse environmental conditions. In contrast, wild Chenopodium species exhibit broad geographic distributions and diverse niche adaptations, functioning as reservoirs for beneficial traits, including disease resistance and climate hardiness, essential for enhancing domesticated crops through introgression and breeding efforts. However, taxonomic classification within the genus poses challenges due to high phenotypic plasticity and complex evolutionary histories marked by hybridization events. To address these challenges and harness the potential of wild taxa for crop improvement, we present six novel whole-genome assemblies of chenopods which include all eight known Chenopodium subgenomes, A-H. Combining these six assemblies with six previously reported Chenopodium whole-genome assemblies, we present a pangenome analysis of 12 chenopod species and their collective 20 subgenomes. These species encompass a wide range of geographic regions across Eurasia and the Americas, providing genomic resources for comprehensive coverage and characterization of the genus. We annotated a total of 33,457 pan-Chenopodium gene families of which ~65% are dispensable within the genus. Our analysis revealed that structural variations and thus genome evolution has been highly associated with the expansion of several LTR-retrotransposons in specific genome types. An orthogroup gene family phylogeny clarified evolutionary relationships among the genome types, while our chloroplast phylogeny suggested specific polyploidization events. We also introduce a standardized framework for naming and orienting chromosomes across the Chenopodium genus and encourage other Chenopodium researchers to adopt these conventions to foster effective collaborations and advance the quality of interlaboratory studies. The newly assembled Chenopodium genomes, along with our subgenome comparisons, pan-genome, and phylogenetic analyses, provide essential genomic resources for advancing research in the genus. These resources are particularly valuable for enhancing our understanding of the secondary and tertiary gene pools necessary for the future improvement of C. quinoa, ultimately contributing to a more comprehensive understanding of the Chenopodium genus as a whole.

Degree

MS

College and Department

Life Sciences; Plant and Wildlife Sciences

Rights

https://lib.byu.edu/about/copyright/

Date Submitted

2024-06-18

Document Type

Thesis

Handle

http://hdl.lib.byu.edu/1877/etd13734

Keywords

Chenopodium, pangenome, PacBio HiFi, whole genome assembly, subgenome, LTR, genome evolution, ploidy, plant genomics

Language

english

Download

Included in

Life Sciences Commons

Share

COinS