YABBY transcription factor family in the octoploid Fragaria × ananassa and five diploid Fragaria species.

YABBY genes encode specific TFs of seed plants involved in development and formation of leaves, flowers, and fruit. In the present work, genome-wide and expression analyses of the YABBY gene family were performed in six species of the Fragaria genus: Fragaria × ananassa, F. daltoniana, F. nilgerrensis, F. pentaphylla, F. viridis, and F. vesca. The chromosomal location, synteny pattern, gene structure, and phylogenetic analyses were carried out. By combining RNA-seq data and RT-qPCR analysis we explored specific expression of YABBYs in F. × ananassa and F. vesca. We also analysed the promoter regions of FaYABBYs and performed MeJA application to F. × ananassa fruit to observe effects on gene expression. We identified and characterized 25 YABBY genes in F. × ananassa and six in each of the other five species, which belong to FIL/YAB3 (YABBY1), YAB2 (YABBY2), YAB5 (YABBY5), CRC, and INO clades previously described. Division of the YABBY1 clade into YABBY1.1 and YABBY1.2 subclades is reported. We observed differential expression according to tissue, where some FaYABBYs are expressed mainly in leaves and flowers and to a minor extent during fruit development of F. × ananassa. Specifically, the FaINO genes contain jasmonate-responsive cis-acting elements in their promoters which may be functional since FaINOs are upregulated in F. × ananassa fruit under MeJA treatment. This study suggests that YABBY TFs play an important role in the development- and environment-associated responses of the Fragaria genus.

Plastidic isoprenoid biosynthesis in tomato: physiological and molecular analysis in genotypes resistant and sensitive to drought stress.

Isoprenoid compounds synthesised in the plastids are involved in plant response to water deficit. The functionality of the biosynthetic pathway of these compounds under drought stress has been analysed at the physiological and molecular levels in two related species of tomato (Solanum chilense and Solanum lycopersicum) that differ in their tolerance to abiotic challenge. Expression analysis of the genes encoding enzymes of these pathways (DXS, IPI, GGPPS, PSY1, NCED and HPT1) in plants at different RWC values shows significant differences for only GGPPS and HPT1, with higher expression in the tolerant S. chilense. Chlorophyll, carotenoids, α-tocopherol and ABA content was also determined in both species under different drought conditions. In agreement with HPT1 transcriptional activity, higher α-tocopherol content was observed in S. chilense than in S. lycopersicum, which correlates with a lower degree of lipoperoxidation in the former species. These results suggest that, in addition to lower stomatal conductance, α-tocopherol biosynthesis is part of the adaptation mechanisms of S. chilense to adverse environmental conditions.

Highly heterogeneous families of Ty1/copia retrotransposons in the Lycopersicon chilense genome.

We have used the degenerated oligonucleotide primers-PCR (DOP-PCR) technique to determine the presence of Ty1/copia-related retrotransposons in the wild species of tomato, Lycopersicon chilense. Using degenerated oligonucleotides corresponding to highly conserved domains in the Ty1/copia retrotransposons, fragments of roughly 300 bp were obtained by PCR amplification. These were cloned in a plasmid vector and the nucleotide sequence determined for 20 clones, 19 of which showed sequence homology to retrotransposon-related sequences. Comparison of the deduced amino-acid sequence of these clones with those reported for other retrotransposons has allowed their classification into four distinct families: TLC1-TLC4. The level of amino-acid sequence similarity between these elements extends from 66.7% (between TLC1 and TLC2) to 42.6% (between TLC2 and TLC3). Altogether, the four families comprise about 0.17% of the L. chilense genome. RT-PCR analysis shows that the four TLC families are transcriptionally active, suggesting a mechanism for the generation of the observed diversity between the L. chilense retrotransposons.

Dissociation of protamine-DNA complexes by Xenopus nucleoplasmin and minichromosome assembly in vitro.

Nucleoplasmin, an acidic thermostable protein abundant in the nucleus of Xenopus laevis oocytes, has been found to dissociate complexes of pUC19 DNA and protein phi 1, an intermediate protamine present in ripe sperm from the mollusc Mytilus edulis. Cruder preparations of nucleoplasmin, such as the amphibian oocyte S150 extract and its thermostable fraction, also dissociate the heterologous DNA-phi 1 complexes and, in addition, promote the assembly of plasmid DNA into a minichromosome displaying regular nucleosomal periodicity, as revealed by micrococcal nuclease digestion. In contrast, purified nucleoplasmin complemented with rat hepatocyte core histone octamers in the presence of DNA topoisomerase I, although capable of inducing nucleoprotein formation onto the complexed DNA, fails to position nucleosomes at the native spacings seen in chromatin in vivo. These data favour the existence of a general mechanism to bring about, in a concerted manner, removal of sperm-specific nuclear proteins and reconstitution of somatic chromatin following fertilization.

Coexistence of two chromatin structures in sperm nuclei of the bivalve mollusc Protothaca thaca.

The chromatin of the spermatozoa from the bivalve mollusc Protothaca thaca, has a peculiar composition in which coexist core histones with sperm-specific proteins H1 and Pt1, the latter being a protein exhibiting features intermediate between histones and protamines. In this paper, we report an analysis of chromatin organization using micrococcal nuclease digestion, salt fractionation of soluble chromatin derived from nuclease digestion and crosslinking experiments. The results obtained indicate that it is possible to obtain two types of chromatin, one which is soluble, more accessible to micrococcal nuclease action and which does not contain Pt1, and another insoluble type, more resistant to micrococcal nuclease and enriched in protein Pt1. The crosslinking experiments show that the protein Pt1 interacts with itself and with core histones but not with sperm-specific H1. These results have led us to propose a special structural arrangement for this chromatin. Based in the data reported here we propose the coexistence in the genome of P. thaca of two interspersed chromatin domains, one nucleosomal and the other nonnucleosomal containing protein Pt1.

Cloning and characterization of a highly conserved satellite DNA from the mollusc Mytilus edulis.

Sperm DNA of the common mussel, Mytilus edulis, has been found to contain a highly repeated sequence identifiable upon restriction with the endonuclease ApaI. The repetitive nucleotide (nt) sequence amounts to 0.63% of the mollusc genome with an estimated copy number of 5.4 x 10(4) copies per haploid complement. The monomer unit with a 173-bp repeat length has been cloned. Progressive DNA digestions with ApaI yield ladder-like banding patterns on agarose gels, indicating that the repeated elements are tandemly arranged in the genome and therefore represent a sequence of satellite DNA. The degree of internal redundancy of the reiterated sequence is deemed negligible, since nt sequence analysis of a random set of cloned monomers has detected the presence of only a few direct repeats while inverted repeated motifs or any other internal substructures appear absent. The homologies found among cloned monomers are strikingly high, averaging 95%. The results suggest that the exceptional sequence homogeneity of this satellite DNA may be attributed either to some homogenizing mechanism or to evolutionary conserved trends.