Repeated Whole-Genome Duplication, Karyotype Reshuffling, and Biased Retention of Stress-Responding Genes in Buckler Mustard

Abstract

Whole-genome duplication (WGD) is usually followed by gene loss and karyotype repatterning. Despite evidence of new adaptive traits associated with WGD, the underpinnings and evolutionary significance of such genome fractionation remain elusive. Here, we use Buckler mustard (Biscutella laevigata) to infer processes that have driven the retention of duplicated genes after recurrent WGDs. In addition to the β- and α-WGD events shared by all Brassicaceae, cytogenetic and transcriptome analyses revealed two younger WGD events that occurred at times of environmental changes in the clade of Buckler mustard (Biscutelleae): a mesopolyploidy event from the late Miocene that was followed by considerable karyotype reshuffling and chromosome number reduction and a neopolyploidy event during the Pleistocene. Although a considerable number of the older duplicates presented signatures of retention under positive selection, the majority of retained duplicates arising from the younger mesopolyploidy WGD event matched predictions of the gene balance hypothesis and showed evidence of strong purifying selection as well as enrichment in gene categories responding to abiotic stressors. Retention of large stretches of chromosomes for both genomic copies supported the hypothesis that cycles of WGD and biased fractionation shaped the genome of this stress-tolerant polypolyloid, promoting the adaptive recruitment of stress-responding genes in the face of environmental challenges.

Figure 1.

Karyotype of Buckler Mustard. Cytomolecular comparative map of B. laevigata subsp varia (2n = 2x = 18) based on chromosome painting analyses. Colors of 48 GBs (A to X) reflect their position on the eight chromosomes AK1 to AK8 in the ACK. The longer and more fluorescent GB duplicates are labeled as #1 and the shorter and less fluorescent copies as #2. Six GBs (G2, H2, I1a, S1, T1, and T2) cannot be localized and are not considered. The size of GBs proportionally corresponds to the size of homoeologous blocks in the Arabidopsis genome, as delimited by A. thaliana BAC clones (Supplemental Table 4).

Figure 2.

Evidence of Selection among Duplicates. Ratio (ω) of nonsynonymous and synonymous substitutions between duplicated transcripts having originated at the α-WGD and the Bl-m-WGD events (colored according to the panel) in Buckler mustard.

Figure 3.

Biased Fractionation following the Bl-m-WGD Event in Buckler Mustard. Fine-scale CCP along GBs A, E, and U is associated with the distribution of retained Bl-m-duplicates in the transcriptome. Transcriptome data are presented on the left of each GB, with the density of transcripts (dens) and of retained duplicates (dupl) as well as evidence of weak (light red) to strong (dark red) purifying selection (sel) along retained duplicates. Using CCP, the longest and most fluorescent GB copy was labeled as #1, and pachytene chromosomes (shown at the bottom) were straightened and displayed alongside the transcriptome data according to differentially painted sub-blocks (Supplemental Data Set 1).

Figure 4.

Overrepresented GO Categories of α-Duplicates and Bl-m-Duplicates Retained under Different Selection Regimes in Buckler Mustard. α-Duplicates (A) and Bl-m-duplicates (B). The strength of selection between duplicates is considered according to ω (i.e., K_a/ K_s ratio): strong purifying selection (ω < 0.6) versus weak selection or neutral divergence (ω between 0.6 and 2) versus strong positive selection (ω > 2). Significantly overrepresented categories are shown by colors according to the panel and corresponding to odd ratios quantifying the enrichment of the particular GO term (i.e., effect size), whereas categories in black are not significant at corrected α = 0.05.