Sequencing of Camelina neglecta, a diploid progenitor of the hexaploid oilseed Camelina sativa

Abstract

Summary Camelina neglecta is a diploid species from the genus Camelina, which includes the versatile oilseed Camelina sativa. These species are closely related to Arabidopsis thaliana and the economically important Brassica crop species, making this genus a useful platform to dissect traits of agronomic importance while providing a tool to study the evolution of polyploids. A highly contiguous chromosome‐level genome sequence of C. neglecta with an N50 size of 29.1 Mb was generated utilizing Pacific Biosciences (PacBio, Menlo Park, CA) long‐read sequencing followed by chromosome conformation phasing. Comparison of the genome with that of C. sativa shows remarkable coincidence with subgenome 1 of the hexaploid, with only one major chromosomal rearrangement separating the two. Synonymous substitution rate analysis of the predicted 34 061 genes suggested subgenome 1 of C. sativa directly descended from C. neglecta around 1.2 mya. Higher functional divergence of genes in the hexaploid as evidenced by the greater number of unique orthogroups, and differential composition of resistant gene analogs, might suggest an immediate adaptation strategy after genome merger. The absence of genome bias in gene fractionation among the subgenomes of C. sativa in comparison with C. neglecta, and the complete lack of fractionation of meiosis‐specific genes attests to the neopolyploid status of C. sativa. The assembled genome will provide a tool to further study genome evolution processes in the Camelina genus and potentially allow for the identification and exploitation of novel variation for Camelina crop improvement.

Mapping QTL for vernalization requirement identified adaptive divergence of the candidate gene Flowering Locus C in polyploid Camelina sativa

“…The FLC ortholog in Camelina neglecta , a diploid progenitor of C. sativa , aligns with the winter‐type Csa . FLC.C08 , suggesting this to be the ancestral copy (Chaudhary et al., 2023) (Figure S12) . Csa.FLC.C13 could only be reconstructed from C. alyssum and showed only synonymous sequence variation compared to the reference genome.…”

“…It has previously been shown that C. sativa and its diploid progenitor C. neglecta do not appear to contain an ortholog of a key gene in the A. thaliana flowering pathway, FRIGIDA ( FRI ) (Chaudhary et al., 2023). Thus, the expression of flowering‐related genes was explored to infer whether the well‐defined pathways of A. thaliana (Teotia & Tang, 2015) were in fact good predictors for gene expression in C. sativa (Figure 5; Table S2A).…”

“…Notably, Csa.FLC.C08 in both the spring-type TMP23992 and the reference genotype had a three base-pair deletion in comparison to both winter-types, which was somewhat unexpectedly also reported in another winter-type C. sativa variety, Joelle (Anderson et al, 2018). The FLC ortholog in Camelina neglecta, a diploid progenitor of C. sativa, aligns with the winter-type Csa.FLC.C08, suggesting this to be the ancestral copy (Chaudhary et al, 2023) (Figure S12). Csa.FLC.C13 could only be reconstructed from C. alyssum and showed only synonymous sequence variation compared to the reference genome.…”

“…In conjunction with gene expression analyses, the three orthologs of FLC were identified as the likely candidates contributing to the variation underlying the QTL. Notwithstanding the absence of FRIGIDA (Chaudhary et al, 2023) and FWA, C. sativa was observed to share many of the key genes regulating both flowering time and the vernalization response with A. thaliana (Figure 5), further many of those genes maintained three orthologs in C. sativa and were similarly expressed (Table S2). As presented here, the presence of multiple orthologs can allow various routes for adaptation in the polyploid, thus further studies of flowering time in C. sativa may yet yield insights into the complexities of regulating this fundamental trait in new polyploid species.…”

Mapping QTL for vernalization requirement identified adaptive divergence of the candidate geneFlowering Locus Cin polyploidCamelina sativa

“…It has previously been shown that C. sativa and its diploid progenitor C. neglecta do not appear to contain an ortholog of a key gene in the A. thaliana flowering pathway, FRIGIDA (FRI) (Chaudhary et al, 2022). Thus the expression of flowering-related genes was explored to infer whether the well-defined pathways of A. thaliana (Teotia and Tang, 2015) were in fact good predictors for gene expression in C. sativa (Figure 5; Table S8A).…”