Genomic Diversity in Two Related Plant Species with and without Sex Chromosomes - Silene latifolia and S. vulgaris

Abstract

BackgroundGenome size evolution is a complex process influenced by polyploidization, satellite DNA accumulation, and expansion of retroelements. How this process could be affected by different reproductive strategies is still poorly understood.Methodology/Principal FindingsWe analyzed differences in the number and distribution of major repetitive DNA elements in two closely related species, Silene latifolia and S. vulgaris. Both species are diploid and possess the same chromosome number (2n = 24), but differ in their genome size and mode of reproduction. The dioecious S. latifolia (1C = 2.70 pg DNA) possesses sex chromosomes and its genome is 2.5× larger than that of the gynodioecious S. vulgaris (1C = 1.13 pg DNA), which does not possess sex chromosomes. We discovered that the genome of S. latifolia is larger mainly due to the expansion of Ogre retrotransposons. Surprisingly, the centromeric STAR-C and TR1 tandem repeats were found to be more abundant in S. vulgaris, the species with the smaller genome. We further examined the distribution of major repetitive sequences in related species in the Caryophyllaceae family. The results of FISH (fluorescence in situ hybridization) on mitotic chromosomes with the Retand element indicate that large rearrangements occurred during the evolution of the Caryophyllaceae family.Conclusions/SignificanceOur data demonstrate that the evolution of genome size in the genus Silene is accompanied by the expansion of different repetitive elements with specific patterns in the dioecious species possessing the sex chromosomes.

Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome

“…Another interesting feature of Ogre retrotransposons is the presence of relatively well-conserved extra open reading frames (eORFs) of unknown function downstream or upstream of their gag-pol genes (Neumann et al, 2003;Steinbauerov a et al, 2012). In the dioecious plant species S. latifolia, Ogre elements account for c. 13% of the genome and significantly enlarged its size Cegan et al, 2012). Similar levels of Ogre element amplification have also been observed in Vicia panonica (Neumann et al, 2006).…”

“…In the dioecious plant species S. latifolia , Ogre elements account for c . 13% of the genome and significantly enlarged its size (Macas et al ., ; Cegan et al ., ). Similar levels of Ogre element amplification have also been observed in Vicia panonica (Neumann et al ., ).…”

Identification of a Novel Retrotransposon with Sex Chromosome-Specific Distribution in <b><i>Silene latifolia</i></b>

“…Genome size variation in Gossypium is caused by Gorge3 Ty3/gypsy -type retrotransposon [Hawkins et al, 2006] and in hybrid sunflower by specific Ty3/gypsy element [Ungerer et al, 2006]. Vicia pannonica 's genome size expanded due to amplification of the giant gypsy-type retrotransposon Ogre [Neumann et al, 2006], which is also the case in S. latifolia [Cegan et al, 2012]. On the other hand, the widespread occurrence of TEs in the genome may enable removal of large amounts of DNA by unequal intra-strand homologous recombination or illegitimate recombination [Devos et al, 2002;Vitte and Panaud, 2003;Ma et al, 2004].…”

Compensatory mechanisms to climate change in the widely distributed species Silene vulgaris

“…Species in the genus Silene have served as model organisms for answering ecological and evolutionary questions for a long time. They have been used when examining adaptation to extreme soil environments (Bratteler, Lexer, & Widmer, 2006) or researching the evolution of plant sex chromosomes (Cegan et al, 2012;Papadopulos, Chester, Ridout, & Filatov, 2015). Furthermore, S. vulgaris is a very popular study species for examining host-pathogen interactions with male-sterilizing fungi (Microbotryacea) (Hood et al, 2010;McArt, Koch, Irwin, & Adler, 2014).…”