The large genome size variation in the Hesperis clade was shaped by the prevalent proliferation of DNA repeats and rarer genome downsizing

Abstract

Background and aims: Most crucifer species (Brassicaceae) have small nuclear genomes (mean 1C-value 617 Mb). The species with the largest genomes occur within the monophyletic Hesperis clade (Mandáková et al., Plant Physiology174: 2062-2071; also known as Clade E or Lineage III). Whereas most chromosome numbers in the clade are 6 or 7, monoploid genome sizes vary 16-fold (256-4264 Mb). To get an insight into genome size evolution in the Hesperis clade (~350 species in ~48 genera), we aimed to identify, quantify and localize in situ the repeats from which these genomes are built. We analysed nuclear repeatomes in seven species, covering the phylogenetic and genome size breadth of the clade, by low-pass whole-genome sequencing.

Methods: Genome size was estimated by flow cytometry. Genomic DNA was sequenced on an Illumina sequencer and DNA repeats were identified and quantified using RepeatExplorer; the most abundant repeats were localized on chromosomes by fluorescence in situ hybridization. To evaluate the feasibility of bacterial artificial chromosome (BAC)-based comparative chromosome painting in Hesperis-clade species, BACs of arabidopsis were used as painting probes.

Key results: Most biennial and perennial species of the Hesperis clade possess unusually large nuclear genomes due to the proliferation of long terminal repeat retrotransposons. The prevalent genome expansion was rarely, but repeatedly, counteracted by purging of transposable elements in ephemeral and annual species.

Conclusions: The most common ancestor of the Hesperis clade has experienced genome upsizing due to transposable element amplification. Further genome size increases, dominating diversification of all Hesperis-clade tribes, contrast with the overall stability of chromosome numbers. In some subclades and species genome downsizing occurred, presumably as an adaptive transition to an annual life cycle. The amplification versus purging of transposable elements and tandem repeats impacted the chromosomal architecture of the Hesperis-clade species.

Keywords: Bunias; Hesperis; Matthiola; Brassicaceae; Genome size evolution; Lineage III; chromosome organization; interstitial telomeric repeats (ITRs); repetitive DNA; retrotransposons; tandem repeats.

Fig. 1.

Bayesian phylogenetic trees of the Hesperis clade with results of ancestral genome size reconstruction. (A) ITS tree. (B) ndhF tree. See Supplementary Data Table 1 for GenBank accession numbers. The reconstructed genome sizes (Mb) are shown at the nodes; posterior probability values are shown in grey. Horizontal bars represent the range of Cx-values for each tribe (C-values are from Table 1 and Kiefer et al., 2014, https://brassibase.cos.uni-heidelberg.de). Species with an analysed repeatome are labelled in red.

Fig. 2.

Relative abundances of repeat families and low/single-copy sequences identified in genomes of the seven Hesperis-clade species analysed.

Fig. 3.

Chromosomal localization of the most abundant tandem repeats and rDNA loci on mitotic metaphase chromosomes in five Hesperis-clade species. Telomeres and ITRs (B) were localized using a FISH probe for the arabidopsis-type telomeric repeat. Chromosomes were counterstained by DAPI (displayed in black and white); FISH signals are shown in colour as indicated. Grey spheroids in the schematic ideograms represent (peri)centromeric regions. EuSy, E. syriacum, ChTe, C. tenella; DoMi, D. micranthus; BuOr, Bu. orientalis; HeSy, H. sylvestris. All scale bars = 10 µm.

Fig. 4.

Chromosomal localization of dispersed repeats on mitotic metaphase chromosomes in seven Hesperis-clade species. (A) E. syriacum (EuSy), (B, C) C. tenella (ChTe), (D) Br. humilis (BrHu), (E, F) M. incana (MaIn) (G, H) D. micranthus (DoMi), (I, J) Bu. orientalis (BuOr), (K, L) H. sylvestris (HeSy) (M, N) Co-localization of tandem repeats (Fig. 3) and Athila retrotransposons in C. tenella (M) and H. sylvestris (N). Arrowheads in (A–C) point to 35S rDNA (NOR) loci. Chromosomes were counterstained by DAPI (displayed in black and white); FISH signals are shown in colour as indicated. Lineage abbreviations: An, Angela; At, Athila; Ch, Chromovirus. Scale bars (complete chromosome spreads) = 10 µm; (insets) = 5 µm (L).