Chloroplast phylogenomics in Camelina (Brassicaceae) reveals multiple origins of polyploid species and the maternal lineage of C. sativa

Abstract

The genus Camelina (Brassicaceae) comprises 7-8 diploid, tetraploid, and hexaploid species. Of particular agricultural interest is the biofuel crop, C. sativa (gold-of-pleasure or false flax), an allohexaploid domesticated from the widespread weed, C. microcarpa. Recent cytogenetics and genomics work has uncovered the identity of the parental diploid species involved in ancient polyploidization events in Camelina. However, little is known about the maternal subgenome ancestry of contemporary polyploid species. To determine the diploid maternal contributors of polyploid Camelina lineages, we sequenced and assembled 84 Camelina chloroplast genomes for phylogenetic analysis. Divergence time estimation was used to infer the timing of polyploidization events. Chromosome counts were also determined for 82 individuals to assess ploidy and cytotypic variation. Chloroplast genomes showed minimal divergence across the genus, with no observed gene-loss or structural variation. Phylogenetic analyses revealed C. hispida as a maternal diploid parent to the allotetraploid Camelina rumelica, and C. neglecta as the closest extant diploid contributor to the allohexaploids C. microcarpa and C. sativa. The tetraploid C. rumelica appears to have evolved through multiple independent hybridization events. Divergence times for polyploid lineages closely related to C. sativa were all inferred to be very recent, at only ~65 thousand years ago. Chromosome counts confirm that there are two distinct cytotypes within C. microcarpa (2n = 38 and 2n = 40). Based on these findings and other recent research, we propose a model of Camelina subgenome relationships representing our current understanding of the hybridization and polyploidization history of this recently-diverged genus.

Figure 1

Gene map of the Camelina anomala chloroplast genome representative of gene, rRNA, and tRNA composition and orientation across the genus. Functional groups of genes are color-coded according to the key. Genes drawn on the outside of the map are transcribed clockwise and those on the inside are transcribed counterclockwise. The innermost circle represents relative GC content (in dark gray) and AT content (in light gray) of the chloroplast genome.

Figure 2

Maximum-likelihood tree of Camelina inferred using whole chloroplast genomes. Taxon labels are colored according to taxonomy. Numbers on branches correspond to bootstrap supports, values over 50% are shown. Chromosome counts (bolded) are provided to the right of taxa where available. Scale represents evolutionary distance in number of substitutions per site. Asterisks represent previously reported chromosome numbers (see Supplemental Table 1).

Figure 3

Camelineae chronogram inferred using BEAST with coding-gene and whole chloroplast sequence data partitions. Time calibration points include 8.16 Mya for the crown age and 5.97 Mya for Arabidopsis [39, 55]. Blue bars represent the 95% confidence intervals for divergence times.

Figure 4

Proposed parental origins of polyploid Camelina species. Dotted arrows and outlines represent hypothetical events and subgenomes of unclear origin, respectively. Subgenome composition and origins are inferred from data presented herein along with results from previous studies [14, 20].