Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species

Abstract

Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine-scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors. We quantified soil properties and light availability of habitats of an allotetraploid Cardamine flexuosa and its diploid progenitors Cardamine amara and Cardamine hirsuta in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA sequencing. We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in C. flexuosa varied spatially and temporally. These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.

Keywords: Cardamine; allopolyploid; homeolog expression; temporal fluctuation; transcriptome; water availability.

Fig. 1

Locations, species compositions, and photographs of representative sites of Cardamine amara, Cardamine hirsuta, and Cardamine flexuosa. (a) Locations of the study areas Irchel (IR), Wehrenbach (WBH), and Küsnacht‐Tobel (KT) in and around Zurich, Switzerland. (b) Locations of sites at IR. (c) Locations of sites at WBH. (d) Locations of sites at KT. (e) The C. hirsuta site. (f) The C. flexuosa site. (g) The C. amara site. In (b–d), different colors of points indicate different species composition: red, C. hirsuta only; orange, C. hirsuta and C. flexuosa; green, C. flexuosa only; blue, C. flexuosa and C. amara; and black, C. amara only. The left and right halves of the circles represent the years 2013 and 2014, respectively, for the sites where the species composition differed between years. In (e–g), an overview (upper panels) and a hemispheric photograph used for light availability analysis (lower panels) are shown with date and site name.

Fig. 2

The results of a principal component analysis of environmental factors from 17 sites of Cardamine amara, Cardamine hirsuta, and Cardamine flexuosa that were subject to the analysis. The relative impacts of different factors are illustrated as vectors. SOSS, sky openness at season start; SOSE, sky openness at season end; IS NO₃ ⁻: incubated soil nitrate; IS NH₄ ⁺: incubated soil ammonium; soil C/N ratio: soil carbon‐to‐nitrogen ratio. The first two principal component (PC) axes accounted for 50% and 19% of total variation, respectively. Different colors of the points indicate different species composition: red, C. hirsuta only; orange, C. hirsuta and C. flexuosa; green, C. flexuosa only; blue, C. flexuosa and C. amara; and black, C. amara only. Blue, green, and red background colors indicate the sites with C. amara, C. flexuosa, and C. hirsuta, respectively. The color of the point is halved for sites with species composition being different between 2013 and 2014. Three sites in the Wehrenbach area are indicated with asterisks.

Fig. 3

The mean ± SD and the range (maximum–minimum) of soil moisture of Cardamine amara, Cardamine hirsuta, and Cardamine flexuosa sites during growing seasons in (a–d) 2013 and (e–h) 2014 measured with a soil moisture sensor at each site (3 ≤ N ≤ 9 per site). (a, e) Mean soil moisture of sites with C. amara. (b, f) Mean soil moisture of sites with C. flexuosa. (c, g) Mean soil moisture of sites with C. hirsuta. In (a–c) and (e–g), the color coding of points corresponds to that in Figs 1, 2, and open and filled arrows indicate the IR5 and KT1 sites, respectively. IR, Irchel; KT, Küsnacht‐Tobel. (d, h) The range of soil moisture on census dates and for the entire growing season (vertical bars on the right) for each species; solid, dotted, and finely dotted lines indicate C. amara, C. flexuosa, and C. hirsuta, respectively. In 2013, C. flexuosa did not occur in the wettest site, KT1, inhabited by C. amara (a, filled arrowhead) but appeared in the driest site, IR5, inhabited by C. hirsuta (b, c, open arrowheads). The opposite was the case in 2014 (e–g).

Fig. 4

The plot of (a) principal component (PC)1 and PC2 and (b) PC2 and PC3 of the result of a principal component analysis of 23 182 homeolog or ortholog expression in Cardamine flexuosa and its diploid progenitor Cardamine amara and Cardamine hirsuta. Points indicate C. flexuosa A (C. amara‐type) subgenome and C. amara (circled in black), whereas triangles indicate C. flexuosa H (C. hirsuta‐type) subgenome and C. hirsuta (circled in red). Different colors in (a) indicate different dates: light brown, 18 April; brown, 2 May; dark brown, 16 May. The colors in (b) correspond to the sites in Fig. 1.

Fig. 5

The numbers and proportional Venn diagrams for the number of genes with homeolog expression ratio change in Cardamine flexuosa. (a, b) A summary of the number of genes with homeolog expression ratio change (a) between sites (IR, Irchel; KT, Küsnacht‐Tobel) and (b) between dates among 23 182 homeologous pairs analyzed. Different sites and dates are indicated with different colors: IR1 in orange, KT2 in green, and KT5 in dark blue; light brown, 18 April; brown, 2 May; dark brown, 16 May. (c) The number of genes overlapping between site‐pairs on each date. (d) The number of genes overlapping between dates for each site‐pair. (e) The number of genes overlapping between date‐pairs on each site. (f) The number of genes overlapping between sites for each date‐pair. In (c–f), the size of circles with less than 190 genes is disproportionally enlarged to make numbers visible.

Fig. 6

Schematic diagram of the Gene Ontology (GO) categories detected at highest proportion for site‐pair by date combination by analysis on genes of Cardamine flexuosa with homeolog expression ratio change using HomeoRoq. Bold lines between sites indicate that the term was significantly enriched between them at each date, and dotted lines indicate no enrichment.