Chromosome‐scale Salvia hispanica L. (Chia) genome assembly reveals rampant Salvia interspecies introgression

• Published in: The plant genome p. e20494
• Main Authors: Brose, Julia, Hamilton, John P., Schlecht, Nicholas, Zhao, Dongyan, Mejía‐Ponce, Paulina M., Cruz‐Pérez, Arely, Vaillancourt, Brieanne, Wood, Joshua C., Edger, Patrick P., Montes‐Hernandez, Salvador, de Rosas, Guillermo Orozco, Hamberger, Björn, Cibrian‐Jaramillo, Angélica, Buell, C. Robin
• Format: Journal Article
• Language: English
• Published: 27.08.2024
• ISSN: 1940-3372; 1940-3372
• DOI: 10.1002/tpg2.20494

Abstract Salvia hispanica L. (Chia), a member of the Lamiaceae, is an economically important crop in Mesoamerica, with health benefits associated with its seed fatty acid composition. Chia varieties are distinguished based on seed color including mixed white and black (Chia pinta) and black (Chia negra). To facilitate research on Chia and expand on comparative analyses within the Lamiaceae, we generated a chromosome‐scale assembly of a Chia pinta accession and performed comparative genome analyses with a previously published Chia negra genome assembly. The Chia pinta and Chia negra genome sequences were highly similar as shown by a limited number of single nucleotide polymorphisms and extensive shared orthologous gene membership. However, there is an enrichment of terpene synthases in the Chia pinta genome relative to the Chia negra genome. We sequenced and analyzed the genomes of 20 Chia accessions with differing seed color and geographic origin revealing population structure within S. hispanica and interspecific introgressions of Salvia species. As the genus Salvia is polyphyletic, its evolutionary history remains unclear. Using large‐scale synteny analysis within the Lamiaceae and orthologous group membership, we resolved the phylogeny of Salvia species. This study and its collective resources further our understanding of genomic diversity in this food crop and the extent of interspecies hybridizations in Salvia . Core Ideas Genomic diversity exists in Chia associated with genes involved in specialized metabolism. Access to multiple Chia and Salvia species genomes resolved the phylogeny of Salvia. Population structure is present within Chia that reflects geographic origins. Hybridization with Salvia tiliifolia has occurred with domesticated Chia yielding admixed accessions. Plain Language Summary Chia pinta is an economically important crop due to the high fatty acid present in the seeds. There are multiple types of Chia based on the seeds color including mixed white and black (Chia pinta), black (Chia negra), and white (Chia blanca). We sequenced and assembled the genome of Chia pinta along with 20 other accessions to determine population structure. Comparison of the Chia pinta and Chia negra genomes revealed a high degree of similarity but also key differences in terpene synthase composition. We also sequenced 20 other Chia accessions with different seed color and geographic origin to determine a population structure within Chia. The genomic resources generated further our understanding of Chia as a food crop.