The role of chromosomal rearrangements in the evolution of Silene latifolia sex chromosomes

Silene latifolia is a model plant for studies of the early steps of sex chromosome evolution. In comparison to mammalian sex chromosomes that evolved 300mya, sex chromosomes of S. latifolia appeared approximately 20mya. Here, we combine results from physical mapping of sex-linked genes using polymerase chain reaction on microdissected arms of the S. latifolia X chromosome, and fluorescence in situ hybridization analysis of a new cytogenetic marker, Silene tandem repeat accumulated on the Y chromosome. The data are interpreted in the light of current genetic linkage maps of the X chromosome and a physical map of the Y chromosome. Our results identify the position of the centromere relative to the mapped genes on the X chromosome. We suggest that the evolution of the S. latifolia Y chromosome has been accompanied by at least one paracentric and one pericentric inversion. These results indicate that large chromosomal rearrangements have played an important role in Y chromosome evolution in S. latifolia and that chromosomal rearrangements are an integral part of sex chromosome evolutio

Dioecious Silene latifolia plants show sexual dimorphism in the vegetative stage

<p>Abstract</p> <p>Background</p> <p>Prior to this study, no differences in gene expression between male and female dioecious plants in the vegetative state had been detected. Among dioecious plants displaying sexual dimorphism, <it>Silene latifolia </it>is one of the most studied species. Although many sexually dimorphic traits have been described in <it>S. latifolia</it>, all of them are quantitative, and they usually become apparent only after the initiation of flowering.</p> <p>Results</p> <p>We present RT-PCR-based evidence that in <it>S. latifolia</it>, sexual dimorphism in gene expression is present long before the initiation of flowering. We describe three ESTs that show sex-specific (two male specific and one female specific) transcription at the rosette stage before the first flowering season.</p> <p>Conclusions</p> <p>To our knowledge, this study provides the first molecular evidence of early pre-flowering sexual dimorphism in angiosperms.</p

Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia

BACKGROUND: Silene latifolia is a dioecious [corrected] plant with well distinguished X and Y chromosomes that is used as a model to study sex determination and sex chromosome evolution in plants. However, efficient utilization of this species has been hampered by the lack of large-scale sequencing resources and detailed analysis of its genome composition, especially with respect to repetitive DNA, which makes up the majority of the genome. METHODOLOGY/PRINCIPAL FINDINGS: We performed low-pass 454 sequencing followed by similarity-based clustering of 454 reads in order to identify and characterize sequences of all major groups of S. latifolia repeats. Illumina sequencing data from male and female genomes were also generated and employed to quantify the genomic proportions of individual repeat families. The majority of identified repeats belonged to LTR-retrotransposons, constituting about 50% of genomic DNA, with Ty3/gypsy elements being more frequent than Ty1/copia. While there were differences between the male and female genome in the abundance of several repeat families, their overall repeat composition was highly similar. Specific localization patterns on sex chromosomes were found for several satellite repeats using in situ hybridization with probes based on k-mer frequency analysis of Illumina sequencing data. CONCLUSIONS/SIGNIFICANCE: This study provides comprehensive information about the sequence composition and abundance of repeats representing over 60% of the S. latifolia genome. The results revealed generally low divergence in repeat composition between the sex chromosomes, which is consistent with their relatively recent origin. In addition, the study generated various data resources that are available for future exploration of the S. latifolia genome

Structure and evolution of Apetala3, a sex-linked gene in Silene latifolia

<p>Abstract</p> <p>Background</p> <p>The evolution of sex chromosomes is often accompanied by gene or chromosome rearrangements. Recently, the gene <it>AP3 </it>was characterized in the dioecious plant species <it>Silene latifolia</it>. It was suggested that this gene had been transferred from an autosome to the Y chromosome.</p> <p>Results</p> <p>In the present study we provide evidence for the existence of an X linked copy of the <it>AP3 </it>gene. We further show that the Y copy is probably located in a chromosomal region where recombination restriction occurred during the first steps of sex chromosome evolution. A comparison of X and Y copies did not reveal any clear signs of degenerative processes in exon regions. Instead, both X and Y copies show evidence for relaxed selection compared to the autosomal orthologues in <it>S. vulgaris </it>and <it>S. conica</it>. We further found that promoter sequences differ significantly. Comparison of the genic region of <it>AP3 </it>between the X and Y alleles and the corresponding autosomal copies in the gynodioecious species <it>S. vulgaris </it>revealed a massive accumulation of retrotransposons within one intron of the Y copy of <it>AP3</it>. Analysis of the genomic distribution of these repetitive elements does not indicate that these elements played an important role in the size increase characteristic of the Y chromosome. However, <it>in silico </it>expression analysis shows biased expression of individual domains of the identified retroelements in male plants.</p> <p>Conclusions</p> <p>We characterized the structure and evolution of <it>AP3</it>, a sex linked gene with copies on the X and Y chromosomes in the dioecious plant <it>S. latifolia</it>. These copies showed complementary expression patterns and relaxed evolution at protein level compared to autosomal orthologues, which suggests subfunctionalization. One intron of the Y-linked allele was invaded by retrotransposons that display sex-specific expression patterns that are similar to the expression pattern of the corresponding allele, which suggests that these transposable elements may have influenced evolution of expression patterns of the Y copy. These data could help researchers decipher the role of transposable elements in degenerative processes during sex chromosome evolution.</p

Sex-chrom, a database on plant sex chromosomes

This work has been supported by the Dirección General de Investigación Científica y Técnica (Spanish Government: CGL2016-75694-P AEI/FEDER, UE; CGL2017-84297-R), by the Generalitat de Catalunya (‘Ajuts a grups de recerca consolidats’ 2017SGR01116’), by the Czech Science Foundation (grants 16-08698S, 18-06147S and 19-03442S) and by CIJA PRESERVATION, SL. SG benefitted from a Ramón y Cajal contract (RYC-2014-16608) from the government of Spain, and SB and NS received Erasmus + grants from the European Union.Introduction Types of plant sex chromosomes, sex determination systems and their diversity Model systems in sex chromosome research Materials and Methods Information sources Data mining Database web environment and construction Results and Discussion Future directions Acknowledgements Author contribution

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

Genome 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.We 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.Our 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

siRNA–Mediated Methylation of Arabidopsis Telomeres

Chromosome termini form a specialized type of heterochromatin that is important for chromosome stability. The recent discovery of telomeric RNA transcripts in yeast and vertebrates raised the question of whether RNA–based mechanisms are involved in the formation of telomeric heterochromatin. In this study, we performed detailed analysis of chromatin structure and RNA transcription at chromosome termini in Arabidopsis. Arabidopsis telomeres display features of intermediate heterochromatin that does not extensively spread to subtelomeric regions which encode transcriptionally active genes. We also found telomeric repeat–containing transcripts arising from telomeres and centromeric loci, a portion of which are processed into small interfering RNAs. These telomeric siRNAs contribute to the maintenance of telomeric chromatin through promoting methylation of asymmetric cytosines in telomeric (CCCTAAA)n repeats. The formation of telomeric siRNAs and methylation of telomeres relies on the RNA–dependent DNA methylation pathway. The loss of telomeric DNA methylation in rdr2 mutants is accompanied by only a modest effect on histone heterochromatic marks, indicating that maintenance of telomeric heterochromatin in Arabidopsis is reinforced by several independent mechanisms. In conclusion, this study provides evidence for an siRNA–directed mechanism of chromatin maintenance at telomeres in Arabidopsis