Satellite DNA landscapes after allotetraploidization of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes.

Tony Heitkam,Thomas Schmidt,Charlotte Ost,Susan Liedtke,Ines Walter,Beatrice Weber

doi:10.1111/tpj.14705

Tony Heitkam, Thomas Schmidt + Show 4 more

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https://doi.org/10.1111/tpj.14705

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Abstract

If two related plant species hybridize, their genomes may be combined and duplicated within a single nucleus, thereby forming an allotetraploid. How the emerging plant balances two co-evolved genomes is still a matter of ongoing research. Here, we focus on satellite DNA (satDNA), the fastest turn-over sequence class in eukaryotes, aiming to trace its emergence, amplification, and loss during plant speciation and allopolyploidization. As a model, we used Chenopodium quinoa Willd. (quinoa), an allopolyploid crop with 2n=4x=36 chromosomes. Quinoa originated by hybridization of an unknown female American Chenopodium diploid (AA genome) with an unknown male Old World diploid species (BB genome), dating back 3.3-6.3million years. Applying short read clustering to quinoa (AABB), C.pallidicaule (AA), and C.suecicum (BB) whole genome shotgun sequences, we classified their repetitive fractions, and identified and characterized seven satDNA families, together with the 5S rDNA model repeat. We show unequal satDNA amplification (two families) and exclusive occurrence (four families) in the AA and BB diploids by read mapping as well as Southern, genomic, and fluorescent in situ hybridization. Whereas the satDNA distributions support C. suecicum as possible parental species, we were able to exclude C. pallidicaule as progenitor due to unique repeat profiles.Using quinoa long reads and scaffolds, we detected only limited evidence of intergenomic homogenization of satDNA after allopolyploidization, but were able to exclude dispersal of 5S rRNA genes between subgenomes. Our results exemplify the complex route of tandem repeat evolution through Chenopodium speciation and allopolyploidization, and may provide sequence targets for the identification of quinoa's progenitors.

Highlights

Quinoa (Chenopodium quinoa Willd.) is an allotetraploid crop, domesticated in the SouthAmerican Andes for at least 8000 years (Dillehay et al, 2007)
Having an allotetraploid origin with 2n=4x=36 chromosomes, quinoa was derived from hybridisation of a female American Chenopodium diploid (A genome) with a male Old World diploid (B genome), dating back 3.3 to 6.3 million years (Kolano et al, 2012, Štorchová et al, 2015, Walsh et al, 2015, Jarvis et al, 2017, Maughan et al, 2019)
Combining GISH and FISH, we show that the satellite DNAs target A- and B-specific chromosomes in C. quinoa genomes and reveal a surprisingly low rate of inter-subgenome dispersion

Summary

Introduction

Quinoa (Chenopodium quinoa Willd.) is an allotetraploid crop, domesticated in the SouthAmerican Andes for at least 8000 years (Dillehay et al, 2007). Having an allotetraploid origin with 2n=4x=36 chromosomes, quinoa was derived from hybridisation of a female American Chenopodium diploid (A genome) with a male Old World diploid (B genome), dating back 3.3 to 6.3 million years (Kolano et al, 2012, Štorchová et al, 2015, Walsh et al, 2015, Jarvis et al, 2017, Maughan et al, 2019). For the quinoa genome size of 1.45 to 1.5 Gb (Palomino et al, 2008), additivity of A and B genomes without genome upor downsizing was postulated (Kolano et al, 2016). Three independent quinoa reference genomes have been generated (Yasui et al, 2016, Jarvis et al, 2017, Zou et al, 2017)

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