ORIGIN OF RECOGNITION COMPLEX 3 controls the development of maternal excess endosperm in the Paspalum simplex agamic complex (Poaceae).

Pseudogamous apomixis in Paspalum simplex generates seeds with embryos genetically identical to the mother plant and endosperms deviating from the canonical 2(maternal):1(paternal) parental genome contribution into a maternal excess 4m:1p genome ratio. In P. simplex, the gene homologous to that coding for subunit 3 of the ORIGIN OF RECOGNITION COMPLEX (PsORC3) exists in three isogenic forms: PsORC3a is apomixis specific and constitutively expressed in developing endosperm whereas PsORCb and PsORCc are up-regulated in sexual endosperms and silenced in apomictic ones. This raises the question of how the different arrangement and expression profiles of these three ORC3 isogenes are linked to seed development in interploidy crosses generating maternal excess endosperms. We demonstrate that down-regulation of PsORC3b in sexual tetraploid plants is sufficient to restore seed fertility in interploidy 4n×2n crosses and, in turn, its expression level at the transition from proliferating to endoreduplication endosperm developmental stages dictates the fate of these seeds. Furthermore, we show that only when being maternally inherited can PsORC3c up-regulate PsORC3b. Our findings lay the basis for an innovative route-based on ORC3 manipulation-to introgress the apomictic trait into sexual crops and overcome the fertilization barriers in interploidy crosses.

Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome.

Due to DNA heterozygosity and repeat content, assembly of non-model plant genomes is challenging. Herein, we report a high-quality genome reference of one of the oldest known domesticated species, fig (Ficus carica L.), using Pacific Biosciences single-molecule, real-time sequencing. The fig genome is ~333 Mbp in size, of which 80% has been anchored to 13 chromosomes. Genome-wide analysis of N6 -methyladenine and N4 -methylcytosine revealed high methylation levels in both genes and transposable elements, and a prevalence of methylated over non-methylated genes. Furthermore, the characterization of N6 -methyladenine sites led to the identification of ANHGA, a species-specific motif, which is prevalent for both genes and transposable elements. Finally, exploiting the contiguity of the 13 pseudomolecules, we identified 13 putative centromeric regions. The high-quality reference genome and the characterization of methylation profiles, provides an important resource for both fig breeding and for fundamental research into the relationship between epigenetic changes and phenotype, using fig as a model species.

Interspecific hybridisation and LTR-retrotransposon mobilisation-related structural variation in plants: A case study.

The dynamics of long-terminal-repeat retrotransposons in two poplar species (Populus deltoides and P. nigra) and in an interspecific hybrid, recently synthesized, were investigated by analyzing the genomic abundance and transcription levels of a collection of 828 full-length retroelements identified in the genome sequence of P. trichocarpa, all occurring also in the genomes of P. deltoides and P. nigra. Overall, genomic abundance and transcription levels of many retrotransposons in the hybrid resulted higher or lower than expected by calculating the mean of the parental values. A bioinformatics procedure was established to ascertain the occurrence of the same retrotransposon loci in the three genotypes. The results indicated that retrotransposon abundance variations between the hybrid and the mean value of the parents were due to i) co-segregation of retrotransposon high- or low-abundant haplotypes; ii) new retroelement insertions; iii) retrotransposon loss. Concerning retrotransposon expression, this was generally low, with only 14/828 elements over- or under-expressed in the hybrid than expected by calculating the mean of the parents. It is concluded that interspecific hybridisation between the two poplar species determine quantitative variation and differential expression of some retrotransposons, with possible consequences for the genetic differentiation of the hybrid.

Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.).

BACKGROUND: Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels. RESULTS: After determining the relative genome size of each species, genomic DNA was isolated and subjected to Illumina sequencing. Then, different assembling and clustering approaches allowed exploring the repetitive component of all genomes. On average, repetitive DNA in Helianthus species represented more than 75% of the genome, being composed mostly by long terminal repeat retrotransposons. Also, the prevalence of Gypsy over Copia superfamily was observed and, among lineages, Chromovirus was by far the most represented. Although nearly all the same sublineages are present in all species, we found considerable variability in the abundance of diverse retrotransposon lineages and sublineages, especially between annual and perennial species. CONCLUSIONS: This large variability should indicate that different events of amplification or loss related to these elements occurred following species separation and should have been involved in species differentiation. Our data allowed us inferring on the extent of interspecific repetitive DNA variation related to LTR-RE abundance, investigating the relationship between changes of LTR-RE abundance and the evolution of the genus, and determining the degree of coevolution of different LTR-RE lineages or sublineages between and within species. Moreover, the data suggested that LTR-RE abundance in a species was affected by the annual or perennial habit of that species.

Molecular and cytogenetic analyses in Geranium macrorrhizum L. wild Italian plants.

Geranium macrorrhizum L. is a herbaceous species native to southern Europe and was introduced in central Europe and North America. It is also widely distributed in Italy. In this study, molecular and cytogenetic analyses were carried out on 22 wild plants, collected in central and southern Italy, compared with five cultivated plants, with the main purpose to identify those living near the Marmore waterfalls in central Italy, recently described as the new species Geranium lucarinii. Four barcoding markers (rbcL, matK, trnH-psbA intergenic spacer and internal transcribed spacer region) were sequenced and their variability among the plants was evaluated. Chromosome numbers were determined and 45S rDNA was physically mapped by fluorescence in situ hybridization. Moreover, genomic affinity between wild and cultivated plants was evaluated by genomic in situ hybridization. The results of this study supported that all the plants belong to G. macrorrhizum, including the Marmore population. Barcoding analyses showed a close similarity among the wild plants, and a differentiation, although not significant, between the wild plants on one hand and the cultivated plants on the other. Integrated studies focusing on morphological, genetic and ecological characterization of a larger number of wild populations would allow us to know the extent of the variability within the species.

The Singular Evolution of Olea Genome Structure.

The current view of plant genome evolution proposes that genome size has mainly been determined by polyploidisation and amplification/loss of transposons, with a minor role played by other repeated sequences, such as tandem repeats. In cultivated olive (Olea europaea subsp. europaea var. europaea), available data suggest a singular model of genome evolution, in which a massive expansion of tandem-repeated sequences accompanied changes in nuclear architecture. This peculiar scenario highlights the importance of focusing on Olea genus evolution, to shed light on mechanisms that led to its present genomic structure. Next-generation sequencing technologies, bioinformatics and in situ hybridisation were applied to study the genomic structure of five related Olea taxa, which originated at different times from their last common ancestor. On average, repetitive DNA in the Olea taxa ranged from ~59% to ~73% of the total genome, showing remarkable differences in terms of composition. Among repeats, we identified 11 major families of tandem repeats, with different abundances in the analysed taxa, five of which were novel discoveries. Interestingly, overall tandem repeat abundance was inversely correlated to that of retrotransposons. This trend might imply a competition in the proliferation of these repeat classes. Indeed, O. paniculata, the species closest to the Olea common ancestor, showed very few tandem-repeated sequences, while it was rich in long terminal repeat retrotransposons, suggesting that the amplification of tandem repeats occurred after its divergence from the Olea ancestor. Furthermore, some tandem repeats were physically localised in closely related O. europaea subspecies (i.e., cultivated olive and O. europaea subsp. cuspidata), which showed a significant difference in tandem repeats abundance. For 4 tandem repeats families, a similar number of hybridisation signals were observed in both subspecies, apparently indicating that, after their dissemination throughout the olive genome, these tandem repeats families differentially amplified maintaining the same positions in each genome. Overall, our research identified the temporal dynamics shaping genome structure during Olea speciation, which represented a singular model of genome evolution in higher plants.

Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome.

A sample-sequencing strategy combined with slot-blot hybridization and FISH was used to study the composition of the repetitive component of the sunflower genome. One thousand six hundred thirty-eight sequences for a total of 954,517 bp were analyzed. The fraction of sequences that can be classified as repetitive using computational and hybridization approaches amounts to 62% in total. Almost two thirds remain as yet uncharacterized in nature. Of those characterized, most belong to the gypsy superfamily of LTR-retrotransposons. Unlike in other species, where single families can account for large fractions of the genome, it appears that no transposon family has been amplified to very high levels in sunflower. All other known classes of transposable elements were also found. One family of unknown nature (contig 61) was the most repeated in the sunflower genome. The evolution of the repetitive component in the Helianthus genus and in other Asteraceae was studied by comparative analysis of the hybridization of total genomic DNAs from these species to the sunflower small-insert library and compared to gene-based phylogeny. Very little similarity is observed between Helianthus species and two related Asteraceae species outside of the genus. Most repetitive elements are similar in annual and perennial Helianthus species indicating that sequence amplification largely predates such divergence. Gypsy-like elements are more represented in the annuals than in the perennials, while copia-like elements are similarly represented, attesting a different amplification history of the two superfamilies of LTR-retrotransposons in the Helianthus genus.

Influence of Continuous Spectrum Light on Morphological Traits and Leaf Anatomy of Hazelnut Plantlets.

Light spectra influence growth, development, and quality of plants and seedlings, that is one of the main aspects engaging the interests of private and public researchers and nursery industries. Propagation of hazelnut (Corylus avellana L.), which in the past has been held in low consideration because of the widespread use of rooted suckers directly collected in the field, today is taking on increasing interest due to the strong expansion of hazelnut cultivation. In order to improve the quality of plants and seedlings in greenhouse acclimatization, the effects of light emitting diodes (LED) lights during the ex vitro growth of two hazelnut cultivars (Tonda di Giffoni and Tonda Gentile Romana) were investigated. Plantlets were maintained in a growth chamber and exposed to three different continuous spectrum LED systems as a primary source of illumination and to fluorescent lamps used as control. LEDs differed in the percentage of some wavelength ranges in the spectrum, being AP673L rich in green and red wavelengths, NS1 in blue and green light, G2 in red and far red wavelengths. After a 4-week experimental period, morphometric, biochemical, and histological analyses were carried out. Shoot and leaf growths were influenced by LEDs more than by fluorescent lamps in both cultivars. G2 positively affected biomass increment more than the other LEDs, by inducing not only cell elongation (increase in shoot length, new internodes length, leaf area) but also cell proliferation (increase in new node number). G2 exposure had negative effects on total chlorophyll content but positively affected synthesis of flavonoids in both varieties; therefore, plants grown under this LED showed the lowest nitrogen balance index. Leaf morpho-anatomical analyzed traits (thickness, palisade cell height, number of chloroplasts, number of palisade cells), were influenced especially by G2 and, to a less extent, by NS1 light. Significant differences in some parameters were observed between the two cultivars in response to a same light source. The results obtained underline the importance of light modulation for hazelnut, providing useful information for ex vitro growth of hazelnut plantlets.

High Levels of Variation Within Gene Sequences of Olea europaea L.

Gene sequence variation in cultivated olive (Olea europaea L. subsp. europaea var. europaea), the most important oil tree crop of the Mediterranean basin, has been poorly evaluated up to now. A deep sequence analysis of fragments of four genes, OeACP1, OeACP2, OeLUS and OeSUT1, in 90 cultivars, revealed a wide range of polymorphisms along all recognized allele forms and unexpected allele frequencies and genotype combinations. High linkage values among most polymorphisms were recorded within each gene fragment. The great sequence variability corresponded to a low number of alleles and, surprisingly, to a small fraction of genotype combinations. The distribution, frequency, and combination of the different alleles at each locus is possibly due to natural and human pressures, such as selection, ancestrality, or fitness. Phylogenetic analyses of allele sequences showed distant and complex patterns of relationships among cultivated olives, intermixed with other related forms, highlighting an evolutionary connection between olive cultivars and the O. europaea subspecies cuspidata and cerasiformis. This study demonstrates how a detailed and complete sequence analysis of a few gene portions and a thorough genotyping on a representative set of cultivars can clarify important issues related to sequence polymorphisms, reconstructing the phylogeny of alleles, as well as the genotype combinations. The identification of regions representing blocks of recombination could reveal polymorphisms that represent putatively functional markers. Indeed, specific mutations found on the analyzed OeACP1 and OeACP2 fragments seem to be correlated to the fruit weight.

Characterization of two families of tandem repeated DNA sequences in Potamogeton pectinatus L.

DNA sequences belonging to two families of tandem repeats, PpeRsa1 (362-364 bp in length, 62% A+T residues) and PpeRsa2 (355-359 bp in length, 59% A+T residues), have been isolated from the Potamogeton pectinatus L. genome. The two sequence families do not share significant nucleotide sequence similarity, even if an evolutionary relationship between them could be assumed. The comparison of the cleaving activity of isoschizomeres that are either sensitive or insensitive to methylation of cytosine residues in the target sequence revealed high methylation in both sequence families. The copy number per 1C DNA of PpeRsa1- and PpeRsa2-related sequences is estimated to be 4.92 x 10(4) and 7.96 x 10(4), respectively. Taken together, these sequences account for about 7.5% of the entire genome of P. pectinatus. The chromosomal organization of these sequences was investigated by fluorescent in situ hybridization. PpeRsa1 and PpeRsa2 repeats found related sequences in 52 chromosomes of the P. pectinatus complement (2n = 78). The related sequences were localized around the centromeres and at the chromosome ends in three pairs of chromosomes, while they were found only at the chromosome ends in the remaining pairs. Twenty-six chromosomes did not show any hybridization signal. The hypothesis that the species is a hybrid between a diploid parent and an allotetraploid parent is put forward.