Classic (extensive) orchards in Croatia

Hrvatska ima vrlo povoljne pomoekološke uvjete za uzgoj voćaka. Tradicija uzgoja voćaka duga je više stoljeća, a voćke su se uzgajale na gotovo svim seoskim gospodarstvima, te dijelom i u urbanim sredinama. Intenzivan uzgoj voćaka počeo se značajnije širiti polovinom prošlog stoljeća. Intenzivan uzgoj je u određenoj mjeri potisnuo interes za klasičnim, ali se postojeći voćnjaci visokostablašica uglavnom nisu krčili već su u većoj mjeri bili zapušteni. U novije vrijeme klasični voćnjaci ponovno postaju aktualni. Njihova uloga očituje se u očuvanju genetske raznolikosti, kako voćnih vrsta, tako i biljaka općenito. Posebna vrijednost tih voćnjaka očituje se u očuvanju tipičnog krajobraza ruralnih sredina, te kao osnove sustava organske proizvodnje voća i voćnih prerađevina. U ukupnim površinama voćnjaka u Hrvatskoj, intenzivni (plantažni) voćnjaci zauzimaju 24%, a preostali dio od oko 21.800 ha otpada na klasične voćnjake. U pojedinim županijama udio klasičnih voćnjaka je značajno veći, pa primjerice u Krapinsko-zagorskoj, Karlovačkoj, Varaždinskoj, Primorsko-goranskoj i Ličko-senjskoj županiji klasični voćnjaci visokostablašica zauzimaju više od 95% površina pod voćem. Među voćnim vrstama najviše se na klasičan način uzgajaju trešnje (92,0%), zatim slijede: orah (90,0%), šljiva (89,9%), marelica (87,2%), kruška (75,4%), višnja (73,4%), dok je značajno niži udio breskve i nektarine (53,3%), i najniži jabuke (43,2%).Croatia has very favourable ecological conditions for growing fruit trees. The tradition of growing fruit trees has a long history, and fruit was cultivated at almost all farms, and partly in the urban areas. Intensive cultivation of fruit trees began to expand significantly from the middle of last century. Intensive farming to some extent pushed interest for the classic growing system and the existing classic orchards were generally not managed properly and were largely neglected. In recent years, the classic orchards made again become current. Their role is reflected in the preservation of genetic diversity, both fruit species, and plants in general. The special value of these orchards is reflected in the preservation of the typical landscape of rural areas, as well as the basics of organic production of fruits and fruit products. In respect of the total acreage of orchards in Croatia, intensive (plantation) orchards occupy 24%, and the remaining part of about 21 800 ha are traditional orchards. In some counties, the share of traditional orchards is significantly higher, so for example in Krapinsko-zagorska, Karlovačka, Varaždinska, Primorsko-goranska and Ličko-eenjska, where classic orchards occupy more than 95% of the area under the fruit. Among the fruit species mostly traditionally grown are cherries (92.0%), followed by: nut (90.0%), plums (89.9%), apricots (87.2%), pears (75.4%), cherries (73.4%), while a significantly lower share is that of peaches and nectarines (53.3%), and the lowest are apples (43.2%)

The repetitive DNA landscape in sheep

Repetitive DNA sequences, representing the majority of most mammalian genomes, can be broadly divided into tandemly repeated or satellite sequences (mostly located in the heterochromatin) and transposable elements (TEs) dispersed over the genome. Some repetitive DNA sequences are highly conserved but other sequences show substantial diversification in copy number, sequence and organization between individuals, breeds, and related species. Here, we report the repetitive DNA landscape of sheep (Ovis aries) based on de novo analysis of >6Gbp of sequence from each of five individuals. Major classes of repetitive DNA sequences were identified and quantified by network analysis (using the program RepeatExplorer), frequency analysis of short motifs (K-mers), and alignment to reference genome assemblies. The genomic organization of the major repetitive motifs was characterized by in situ hybridization to chromosomes. The well-known c. 816 bplong centromere-associated satellite SatI represented 4 to 6 % of the genome while SatII (c. 600 bp long) was 1 to 2 % of the genome. Notably, these satellites showed contrasting behaviour at meiotic prophase: Sat I sequences cover a larger area indicating a looser chromatin loop organization. While, Sat II sequences are tightly organized and are attached to the synaptonemal complex (SC) at a more distal position than SatI sequences at the end of SCs of acrocentric chromosomes. The repetitive sequence analysis identified other much less abundant satellite sequences and simple repeats, some with novel genomic distributions. Families of non-LTR retrotransposons including LINEs (L1 and RTE) and derived SINEs represented more than 25 % of the genome. Non-LTR families showed characteristic distributions on chromosomes with some showing greater abundance on metacentric autosomes or on sex chromosomes. Endogenous retrovirus classes grouped into clusters with some families showing centromeric and others more dispersed distributions. Rapidly evolving repetitive sequences allow us to study processes of chromosome or genome evolution and diversification in sheep, and more broadly across the Bovidae

Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids

Structural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x=7, genomes of oats show frequent intergenomic translocations, in contrast to wheats where these translocations are relatively rare. We aimed to show genome structural diversity and genome relationships in tetraploid, hexaploid and octoploid Avena species and amphiploids, establishing patterns of intergenomic translocations across different oat taxa using fluorescence in situ hybridization (FISH) with four well-characterized repetitive DNA sequences: pAs120, AF226603, Ast-R171 and Ast-T116. In A. agadiriana (2n=4x=28), the selected probes hybridized to all chromosomes indicating that this species originated from one (autotetraploid) or closely related ancestors with the same genomes. Hexaploid amphiploids were confirmed as having the genomic composition AACCDD, while octoploid amphiploids showed three different genome compositions: AACCCCDD, AAAACCDD or AABBCCDD. The A, B, C, and D genomes of oats differ significantly in their involvement in non-centromeric, intercalary translocations. There was a predominance of distal intergenomic translocations from the C- into the D-genome chromosomes. Translocations from A- to C-, or D- to C-genome chromosomes were less frequent, proving that at least some of the translocations in oat polyploids are non-reciprocal. Rare translocations from A- to D-, D- to A- and C- to B-genome chromosomes were also visualized. The fundamental research has implications for exploiting genomic biodiversity in oat breeding through introgression from wild species potentially with contrasting chromosomal structures and hence deleterious segmental duplications or large deletions in amphiploid parental lines

Additional file 1: of dsRNA silencing of an R2R3-MYB transcription factor affects flower cell shape in a Dendrobium hybrid

Phylogenetic relationships and subgroup designations in MYB proteins from D. hybrida ( Dh ). Phylogram made using Interspecies Transcription Factor Function Finder (IT3F) At: Arabidopsis thaliana; Os: Oryza sativa, Am: Antirrhinum majus, Gh: Gossypium hirsutum, Fa: Fragaria ananassa, Eg: Eucalyptus gunnii and Le: Lentinula edodes. Black: Arabidopsis; Yellow: monocots; Green: legumes; Red: D. hybrida from this study; Blue: MYB genes with known function; Red dot: gene duplication; Blue dot: Genes in tandem. (ZIP 339 kb

CENH3 morphogenesis reveals dynamic centromere associations during synaptonemal complex formation and the progression through male meiosis in hexaploid wheat.

During meiosis, centromeres in some species undergo a series of associations, but the processes and progression to homologous pairing is still a matter of debate. Here, we aimed to correlate meiotic centromere dynamics and early telomere behaviour to the progression of synapotonemal complex (SC) construction in hexaploid wheat (2n=42) by triple immunolabelling of CENH3 protein marking functional centromeres, and SC proteins ASY1 (unpaired lateral elements) and ZYP1 (central elements in synapsed chromosomes). We show that single or multiple centromere associations formed in meiotic interphase undergo a progressive polarisation (clustering) at the nuclear periphery in early leptotene, leading to formation of the telomere bouquet. Critically, immunolabelling shows the dynamics of these presynaptic centromere associations and a structural reorganisation of the centromeric chromatin coinciding with key events of synapsis initiation from the subtelomeric regions. As short stretches of subtelomeric synapsis emerged at early zygotene, centromere clusters lost their strong polarization, gradually resolving as individual centromeres indicated by more than 21 CENH3 foci associated with unpaired lateral elements. Only following this centromere depolarisation were homologous chromosome arms connected, as observed by the alignment and fusion of interstitial ZYP1 loci elongating at zygotene so synapsis at centromeres is a continuation of the interstitial synapsis. Our results thus reveal that centromere associations are a component of the timing and progression of chromosome synapsis, and the gradual release of the individual centromeres from the clusters correlates with the elongation of interstitial synapsis between the corresponding homologues

Erratum: Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants (vol 120, pg 183, 2017)

There was an error in the history dates. The correct editorial decision date is 17 May 2017. The online issue has been corrected

Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants

Background Polyploidy or whole-genome duplication is now recognized as being present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridization events are found in about half of the world's crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this review, consider genomic aspects of polyploidy.Approaches Discovery of the evolutionary consequences of new, evolutionarily recent and ancient polyploidy requires a range of approaches. Large-scale studies of both single species and whole ecosystems, with hundreds to tens of thousands of individuals, sometimes involving 'garden' or transplant experiments, are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical.Conclusions The success of polyploidy, displacing the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidization events. Strikingly, polyploidization often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting the concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole-genome duplication act as drivers of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution

Table_1_The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris.pdf

Cenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in the tropical and subtropical regions of Africa and Asia. In this study, we aimed to investigate the genomic organization and characterize some of the repetitive DNA sequences in this species. Due to the apomictic propagation, various aneuploid genotypes are found, and here, we analyzed a 2n = 4x + 3 = 39 accession. The physical mapping of Ty1-copia and Ty3-gypsy retroelements through fluorescence in situ hybridization with a global assessment of 5-methylcytosine DNA methylation through immunostaining revealed the genome-wide distribution pattern of retroelements and their association with DNA methylation. Approximately one-third of Ty1-copia sites overlapped or spanned centromeric DAPI-positive heterochromatin, while the centromeric regions and arms of some chromosomes were labeled with Ty3-gypsy. Most of the retroelement sites overlapped with 5-methylcytosine signals, except for some Ty3-gypsy on the arms of chromosomes, which did not overlap with anti-5-mC signals. Universal retrotransposon probes did not distinguish genomes of C. ciliaris showing signals in pericentromeric regions of all 39 chromosomes, unlike highly abundant repetitive DNA motifs found in survey genome sequences of C. ciliaris using graph-based clustering. The probes developed from RepeatExplorer clusters gave strong in situ hybridization signals, mostly in pericentromeric regions of about half of the chromosomes, and we suggested that they differentiate the two ancestral genomes in the allotetraploid C. ciliaris, likely having different repeat sequence variants amplified before the genomes came together in the tetraploid.</p

Image_1_The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris.TIF

Cenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in the tropical and subtropical regions of Africa and Asia. In this study, we aimed to investigate the genomic organization and characterize some of the repetitive DNA sequences in this species. Due to the apomictic propagation, various aneuploid genotypes are found, and here, we analyzed a 2n = 4x + 3 = 39 accession. The physical mapping of Ty1-copia and Ty3-gypsy retroelements through fluorescence in situ hybridization with a global assessment of 5-methylcytosine DNA methylation through immunostaining revealed the genome-wide distribution pattern of retroelements and their association with DNA methylation. Approximately one-third of Ty1-copia sites overlapped or spanned centromeric DAPI-positive heterochromatin, while the centromeric regions and arms of some chromosomes were labeled with Ty3-gypsy. Most of the retroelement sites overlapped with 5-methylcytosine signals, except for some Ty3-gypsy on the arms of chromosomes, which did not overlap with anti-5-mC signals. Universal retrotransposon probes did not distinguish genomes of C. ciliaris showing signals in pericentromeric regions of all 39 chromosomes, unlike highly abundant repetitive DNA motifs found in survey genome sequences of C. ciliaris using graph-based clustering. The probes developed from RepeatExplorer clusters gave strong in situ hybridization signals, mostly in pericentromeric regions of about half of the chromosomes, and we suggested that they differentiate the two ancestral genomes in the allotetraploid C. ciliaris, likely having different repeat sequence variants amplified before the genomes came together in the tetraploid.</p

ImmunoFISH: Simultaneous Visualisation of Proteins and DNA Sequences Gives Insight Into Meiotic Processes in Nuclei of Grasses.

ImmunoFISH is a method combining immunolabelling (IL) with fluorescent in situ hybridisation (FISH) to simultaneously detect the nuclear distribution of proteins and specific DNA sequences within chromosomes. This approach is particularly important when analysing meiotic cell division where morphogenesis of individual proteins follows stage-specific changes and is accompanied by a noticeable chromatin dynamism. The method presented here is simple and provides reliable results of high quality signal, low background staining and can be completed within 2 days following preparation. Conventional widefield epifluorescent or laser scanning microscopy can be used for high resolution and three-dimensional analysis. Fixation and preparation techniques were optimised to best preserve nuclear morphology and protein epitopes without the need for any antigen retrieval. Preparation of plant material involved short cross-linking fixation of meiotic tissues with paraformaldehyde (PFA) followed by enzyme digestion and slide-mounting. In order to avoid rapid sample degradation typical of shortly fixed plant materials, and to be able to perform IL later, slides were snap-frozen and stored at -80°C. Ultra-freezing produced a remarkable degree of structural preservation for up to 12 months, whereby sample quality was similar to that of fresh material. Harsh chemicals and sample dehydration were avoided throughout the procedure and permeability was ensured by a 0.1-0.3% detergent treatment. The ImmunoFISH method was developed specifically for studying meiosis in Triticeae, but should also be applicable to other grass and plant species