A chromosome-level genome assembly of chia provides insights into high omega-3 content and coat color variation of its seeds

Comparative genomics points to tandem duplications of SAD gene clusters as drivers of increased α‐linolenic (ω‐3) content in S. hispanica seeds

“…The SCOs alignment placed the S. splendens and S. hispanica with maximum nodal support, confirming their close ancestral relationship (Figure 2a). Their most recent common ancestor was dated to 9.6 MYA which supported previous report by L. Wang et al (2022). The oilseed crops S. indicum and S. hispanica were estimated to have diverged ∼58-59 MYA, similar to the estimated divergence time between E. guttata and S. hispanica (Figure 2a).…”

“…Divergence times between A. thaliana and V. vinifera (115 million years, MYA) and S. indicum and Solanum lycopersicum (82 MYA) were inferred from the TimeTree of Life database (http://timetree.org; Kumar et al, 2017). The divergence time between S. splendens and S. hispanica was retrieved from L. Wang et al (2022). The rates of nucleotide substitution among pairs of paralogs/orthologs were measured using the third codon transversion rates at fourfold degenerative (synonymous) sites (4DTv) to estimate the likelihood of WGD events.…”

“…In addition, a set of studies functionally characterized genes encoding fatty acid desaturases (FADs) against different biotic/abiotic stresses (Xue et al, 2018(Xue et al, , 2023. These studies, together with a genome assembly for S. hispanica (L. Wang et al, 2022), provided new insights, but relatively little is known about the main drivers of high ω-3-PUFA accumulation in S. hispanica seeds.…”

A near complete genome assembly of chia assists in identification of key fatty acid desaturases in developing seeds

“…Telomere repeats were detected at both ends of Chr3 and Chr4, and one end of Chr1, Chr2, Chr5, and Chr6 (Figure 2A). Comparing Shi_PSC_v1 to a recently published chia genome (Wang et al, 2022) revealed multiple Mb-size variations, including three inversions at the peri-telomeric region of Chr1 and the peri-centromeric regions of Chr2 and Chr3 (Supplemental Figure 7A). Further examination indicated that these regions are supported by raw reads in our assembly (Supplemental Figures 7B, C) but are composed of short contigs concatenated together in the 2022 assembly (data not shown).…”

“…Utilizing this highly accurate and complete genome, we annotated transposable elements and protein-coding genes in the chia genome. Compared to a recently published chromosome-level assembly of chia ( Wang et al., 2022 ), our assembly has better contiguity and ~15% more gene models (35,850 vs. 31,069) thanks to the highly accurate CCS reads. Alignment analyses also revealed multiple Mb-size structural variations between two assemblies, demonstrating the importance of multiple high-quality genomes for the same species.…”