Future-Proofing Agriculture: De Novo Domestication for Sustainable and Resilient Crops

The worldwide agricultural system confronts a significant challenge represented by the increasing demand for food in the face of a growing global population. This challenge is exacerbated by a reduction in cultivable land and the adverse effects of climate change on crop yield quantity and quality. Breeders actively embrace cutting-edge omics technologies to pursue resilient genotypes in response to these pressing issues. In this global context, new breeding techniques (NBTs) are emerging as the future of agriculture, offering a solution to introduce resilient crops that can ensure food security, particularly against challenging climate events. Indeed, the search for domestication genes as well as the genetic modification of these loci in wild species using genome editing tools are crucial steps in carrying out de novo domestication of wild plants without compromising their genetic background. Current knowledge allows us to take different paths from those taken by early Neolithic farmers, where crop domestication has opposed natural selection. In this process traits and alleles negatively correlated with high resource environment performance are probably eradicated through artificial selection, while others may have been lost randomly due to domestication and genetic bottlenecks. Thus, domestication led to highly productive plants with little genetic diversity, owing to the loss of valuable alleles that had evolved to tolerate biotic and abiotic stresses. Recent technological advances have increased the feasibility of de novo domestication of wild plants as a promising approach for crafting optimal crops while ensuring food security and using a more sustainable, low-input agriculture. Here, we explore what crucial domestication genes are, coupled with the advancement of technologies enabling the precise manipulation of target sequences, pointing out de novo domestication as a promising application for future crop development.

Transcriptomic Analyses Reveal Insights into the Shared Regulatory Network of Phenolic Compounds and Steviol Glycosides in Stevia rebaudiana

Stevia rebaudiana (Bertoni) is a highly valuable crop for the steviol glycoside content in its leaves, which are no-calorie sweeteners hundreds of times more potent than sucrose. The presence of health-promoting phenolic compounds, particularly flavonoids, in the leaf of S. rebaudiana adds further nutritional value to this crop. Although all these secondary metabolites are highly desirable in S. rebaudiana leaves, the genes regulating the biosynthesis of phenolic compounds and the shared gene network between the regulation of biosynthesis of steviol glycosides and phenolic compounds still need to be investigated in this species. To identify putative candidate genes involved in the synergistic regulation of steviol glycosides and phenolic compounds, four genotypes with different contents of these compounds were selected for a pairwise comparison RNA-seq analysis, yielding 1136 differentially expressed genes. Genes that highly correlate with both steviol glycosides and phenolic compound accumulation in the four genotypes of S. rebaudiana were identified using the weighted gene co-expression network analysis. The presence of UDP-glycosyltransferases 76G1, 76H1, 85C1, and 91A1, and several genes associated with the phenylpropanoid pathway, including peroxidase, caffeoyl-CoA O-methyltransferase, and malonyl-coenzyme A:anthocyanin 3-O-glucoside-6″-O-malonyltransferase, along with 21 transcription factors like SCL3, WRK11, and MYB111, implied an extensive and synergistic regulatory network involved in enhancing the production of such compounds in S. rebaudiana leaves. In conclusion, this work identified a variety of putative candidate genes involved in the biosynthesis and regulation of particular steviol glycosides and phenolic compounds that will be useful in gene editing strategies for increasing and steering the production of such compounds in S. rebaudiana as well as in other species.

Discovering the Repeatome of Five Species Belonging to the Asteraceae Family: A Computational Study

Genome divergence by repeat proliferation and/or loss is a process that plays a crucial role in species evolution. Nevertheless, knowledge of the variability related to repeat proliferation among species of the same family is still limited. Considering the importance of the Asteraceae family, here we present a first contribution towards the metarepeatome of five Asteraceae species. A comprehensive picture of the repetitive components of all genomes was obtained by genome skimming with Illumina sequence reads and by analyzing a pool of full-length long terminal repeat retrotransposons (LTR-REs). Genome skimming allowed us to estimate the abundance and variability of repetitive components. The structure of the metagenome of the selected species was composed of 67% repetitive sequences, of which LTR-REs represented the bulk of annotated clusters. The species essentially shared ribosomal DNA sequences, whereas the other classes of repetitive DNA were highly variable among species. The pool of full-length LTR-REs was retrieved from all the species and their age of insertion was established, showing several lineage-specific proliferation peaks over the last 15-million years. Overall, a large variability of repeat abundance at superfamily, lineage, and sublineage levels was observed, indicating that repeats within individual genomes followed different evolutionary and temporal dynamics, and that different events of amplification or loss of these sequences may have occurred after species differentiation.

A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. "Hillquist")

Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession "Hillquist" (R. argutus). "Hillquist" is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The "Hillquist" assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2 Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the "Hillquist" genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.

Genome-wide identification and characterization of exapted transposable elements in the large genome of sunflower (Helianthus annuus L.)

Transposable elements (TEs) are an important source of genome variability, playing many roles in the evolution of eukaryotic species. Besides well-known phenomena, TEs may undergo the exaptation process and generate the so-called exapted transposable element genes (ETEs). Here we present a genome-wide survey of ETEs in the large genome of sunflower (Helianthus annuus L.), in which the massive amount of TEs, provides a significant source for exaptation. A library of sunflower TEs was used to build TE-specific Hidden Markov Model profiles, to search for all available sunflower gene products. In doing so, 20 016 putative ETEs were identified and further investigated for the characteristics that distinguish TEs from genes, leading to the validation of 3530 ETEs. The analysis of ETEs transcription patterns under different stress conditions showed a differential regulation triggered by treatments mimicking biotic and abiotic stress; furthermore, the distribution of functional domains of differentially regulated ETEs revealed a relevant presence of domains involved in many aspects of cellular functions. A comparative genomic investigation was performed including species representative of Asterids and appropriate outgroups: the bulk of ETEs that resulted were specific to the sunflower, while few ETEs presented orthologues in the genome of all analyzed species, making the hypothesis of a conserved function. This study highlights the crucial role played by exaptation, actively contributing to species evolution.

Characterisation of LTR-Retrotransposons of Stevia rebaudiana and Their Use for the Analysis of Genetic Variability

Stevia rebaudiana is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The Gypsy retrotransposons were twice as abundant as the Copia ones. A disproportionate abundance of elements belonging to the Chromovirus/Tekay lineage was observed among the Gypsy elements. Only the SIRE and Angela lineages represented significant portions of the genome among the Copia elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage Angela was used to analyse the genetic variability in 25 accessions of S. rebaudiana using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding.

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.

In Silico Genome-Wide Characterisation of the Lipid Transfer Protein Multigenic Family in Sunflower (H. annuus L.)

The sunflower (Helianthus annuus L.) is among the most widely cultivated crops in the world due to the oilseed production. Lipid transfer proteins (LTPs) are low molecular mass proteins encoded by a broad multigenic family in higher plants, showing a vast range of functions; these proteins have not been characterised in sunflower at the genomic level. In this work, we exploited the reliable genome sequence of sunflower to identify and characterise the LTP multigenic family in H. annuus. Overall, 101 sunflower putative LTP genes were identified using a homology search and the HMM algorithm. The selected sequences were characterised through phylogenetic analysis, exon–intron organisation, and protein structural motifs. Sunflower LTPs were subdivided into four clades, reflecting their genomic and structural organisation. This gene family was further investigated by analysing the possible duplication origin of genes, which showed the prevalence of tandem and whole genome duplication events, a result that is in line with polyploidisation events that occurred during sunflower genome evolution. Furthermore, LTP gene expression was evaluated on cDNA libraries constructed on six sunflower tissues (leaf, root, ligule, seed, stamen, and pistil) and from roots treated with stimuli mimicking biotic and abiotic stress. Genes encoding LTPs belonging to three out of four clades responded specifically to external stimuli, especially to abscisic acid, auxin, and the saline environment. Interestingly, genes encoding proteins belonging to one clade were expressed exclusively in sunflower seeds. This work is a first attempt of genome-wide identification and characterisation of the LTP multigenic family in a plant species.

Impact of transposable elements on the evolution of complex living systems and their epigenetic control

Transposable elements (TEs) contribute to genomic innovations, as well as genome instability, across a wide variety of species. Popular designations such as 'selfish DNA' and 'junk DNA,' common in the 1980s, may be either inaccurate or misleading, while a more enlightened view of the TE-host relationship covers a range from parasitism to mutualism. Both plant and animal hosts have evolved epigenetic mechanisms to reduce the impact of TEs, both by directly silencing them and by reducing their ability to transpose in the genome. However, TEs have also been co-opted by both plant and animal genomes to perform a variety of physiological functions, ranging from TE-derived proteins acting directly in normal biological functions to innovations in transcription factor activity and also influencing gene expression. Their presence, in fact, can affect a range of features at genome, phenotype, and population levels. The impact TEs have had on evolution is multifaceted, and many aspects still remain unexplored. In this review, the epigenetic control of TEs is contextualized according to the evolution of complex living systems.

Moderate Salinity Stress Affects Expression of Main Sugar Metabolism and Transport Genes and Soluble Carbohydrate Content in Ripe Fig Fruits (Ficus carica L. cv. Dottato)

Fig trees (Ficus carica L.) are commonly grown in the Mediterranean area, where salinity is an increasing problem in coastal areas. Young, fruiting plants of cv. Dottato were subjected to moderate salt stress (100 mM NaCl added to irrigation water) for 48 days before fruit sampling. To clarify the effect of salinity stress, we investigated changes in the transcription of the main sugar metabolism-related genes involved in the synthesis, accumulation and transport of soluble carbohydrates in ripe fruits by quantitative real-time PCR as well as the content of soluble sugars by quantitative ¹H nuclear magnetic resonance spectroscopy. A general increase in the transcript levels of genes involved in the transport of soluble carbohydrates was observed. Alkaline-neutral and Acid Invertases transcripts, related to the synthesis of glucose and fructose, were up-regulated in ripe fruits of NaCl-stressed plants without a change in the content of D-glucose and D-fructose. The increases in sucrose and D-sorbitol contents were likely the result of the up-regulation of the transcription of Sucrose-Synthase- and Sorbitol-Dehydrogenase-encoding genes.

LTR-retrotransposon dynamics in common fig (Ficus carica L.) genome

BACKGROUND

Long Terminal Repeat retrotransposons (LTR-REs) are repetitive DNA sequences that constitute a large part of the genome. The improvement of sequencing technologies and sequence assembling strategies has achieved genome sequences with much greater reliability than those of the past, especially in relation to repetitive DNA sequences.

RESULTS

In this study, we analysed the genome of Ficus carica L., obtained using third generation sequencing technologies and recently released, to characterise the complete complement of full-length LTR-REs to study their dynamics during fig genome evolution. A total of 1867 full-length elements were identified. Those belonging to the Gypsy superfamily were the most abundant; among these, the Chromovirus/Tekay lineage was the most represented. For the Copia superfamily, Ale was the most abundant lineage. Measuring the estimated insertion time of each element showed that, on average, Ivana and Chromovirus/Tekay were the youngest lineages of Copia and Gypsy superfamilies, respectively. Most elements were inactive in transcription, both constitutively and in leaves of plants exposed to an abiotic stress, except for some elements, mostly belonging to the Copia/Ale lineage. A relationship between the inactivity of an element and inactivity of genes lying in close proximity to it was established.

CONCLUSIONS

The data reported in this study provide one of the first sets of information on the genomic dynamics related to LTR-REs in a plant species with highly reliable genome sequence. Fig LTR-REs are highly heterogeneous in abundance and estimated insertion time, and only a few elements are transcriptionally active. In general, the data suggested a direct relationship between estimated insertion time and abundance of an element and an inverse relationship between insertion time (or abundance) and transcription, at least for Copia LTR-REs.

Structural characterization and duplication modes of pseudogenes in plants

We identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all investigated species except V. vinifera, which showed an unusually high number of retro-pseudogenes in non coding genic regions. By using a pipeline for the classification of sequence duplicates in plant genomes, we compared the relative importance of whole genome, tandem, proximal, transposed and dispersed duplication modes in the pseudo and functional gene complements. Pseudogenes showed higher tendencies than functional genes to genomic dispersion. Dispersed pseudogenes were prevalently fragmented and showed high sequence divergence at flanking regions. On the contrary, those deriving from whole genome duplication were proportionally less than expected based on observations on functional loci and showed higher levels of flanking sequence conservation than dispersed pseudogenes. Pseudogenes deriving from tandem and proximal duplications were in excess compared to functional loci, probably reflecting the high evolutionary rate associated with these duplication modes in plant genomes. These data are compatible with high rates of sequence turnover at neutral sites and double strand break repairs mediated duplication mechanisms.

DNA Modification Patterns within the Transposable Elements of the Fig (Ficus carica L.) Genome

Transposable element activity can be harmful to the host’s genome integrity, but it can also provide selective advantages. One strategy to cope with transposons is epigenetic control through DNA base modifications. We report the non-canonic DNA modification dynamics of fig (Ficus carica L.) by exploiting high-quality genome reference and related N4-methylcytosine (4mC) and N6-methyladenine (6mA) data. Overall, 1.49% of transposon nucleotides showed either 4mC or 6mA modifications: the 4mC/6mA ratio was similar in Class I and Class II transposons, with a prevalence of 4mC, which is comparable to coding genes. Different percentages of 4mC or 6mA were observed among LTR-retrotransposon lineages and sub-lineages. Furthermore, both the Copia and Gypsy retroelements showed higher modification rates in the LTR and coding regions compared with their neighbour regions. Finally, the unconventional methylation of retrotransposons is unrelated to the number of close genes, suggesting that the 4mC and 6mA frequency in LTR-retrotransposons should not be related to transcriptional repression in the adjacency of the element. In conclusion, this study highlighted unconventional DNA modification patterns in fig transposable elements. Further investigations will focus on functional implications, in regards to how modified retroelements affect the expression of neighbouring genes, and whether these epigenetic markers can spread from repeats to genes, shaping the plant phenotype.

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.

A computational genome-wide analysis of long terminal repeats retrotransposon expression in sunflower roots (Helianthus annuus L.)

Long terminal repeats (LTR) retrotransposons have a major role in determining genome size, structure and function, thanks to their ability to transpose. We performed a meta-analysis of LTR-retrotransposon expression in roots of sunflower plantlets treated with different plant hormones, chemicals and NaCl. By using Illumina cDNA libraries, available from public repositories, we measured the number of reads matching the retrotranscriptase domains isolated from a whole genome library of retrotransposons. LTR-retrotransposons resulted in general barely expressed, except for 4 elements, all belonging to the AleII lineage, which showed high transcription levels in roots of both control and treated plants. The expression of retrotransposons in treated plants was slightly higher than in the control. Transcribed elements belonged to specific chromosomal loci and were not abundant in the genome. A few elements resulted differentially expressed depending on the treatment. Results suggest that, although most retrotransposons are not expressed, the transcription of such elements is related to their abundance, to their position in the chromosome and to their lineage.

Influence of CNV on transcript levels of HvCBF genes at Fr-H2 locus revealed by resequencing in resistant barley cv. 'Nure' and expression analysis

Resequencing in resistant cultivar 'Nure' and structural comparison with the same region of susceptible 'Morex' was performed in order to gain a better insight into barley Frost-resistance-H2 locus. Accurate annotation showed copy number variation (CNV) in the proximal part of the locus. In 'Nure', two exact copies of the HvCBF4-HvCBF2A region and one of the HvCBF4-HvCBF2B segment were observed, while in 'Morex' the corresponding region harboured a single HvCBF4-HvCBF2A (22 kb) segment. Abundance and diversity of repetitive element classes, gene function gain/losses, regulatory motifs and SNPs in gene sequences were identified. An expression study of key HvCBFs with/without CNV on selected genotypes contrasting for frost resistance and estimated HvCBF4-HvCBF2B copy number (2-10 copies) was also performed. Under light stimulus at warm temperature (23 °C), CNV of HvCBF2A and HvCBF4 correlated with their expression levels and reported frost resistance of genotypes; moreover, expression levels of HvCBF2A and HvCBF14 were strongly correlated (r = 0.908, p < 0.01). On the other hand, frost resistance correlated to HvCBF14 expression (r = 0.871, p < 0.01) only after cold induction (6°C) in the dark. A complex interplay of HvCBFs expression levels under different light/temperature stimuli is discussed in light of CNV and presence/number of regulatory elements that integrate different signal transduction pathways.

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.

How an ancient, salt-tolerant fruit crop, Ficus carica L., copes with salinity: a transcriptome analysis

Although Ficus carica L. (fig) is one of the most resistant fruit tree species to salinity, no comprehensive studies are currently available on its molecular responses to salinity. Here we report a transcriptome analysis of F. carica cv. Dottato exposed to 100 mM sodium chloride for 7 weeks, where RNA-seq analysis was performed on leaf samples at 24 and 48 days after the beginning of salinization; a genome-derived fig transcriptome was used as a reference. At day 24, 224 transcripts were significantly up-regulated and 585 were down-regulated, while at day 48, 409 genes were activated and 285 genes were repressed. Relatively small transcriptome changes were observed after 24 days of salt treatment, showing that fig plants initially tolerate salt stress. However, after an early down-regulation of some cell functions, major transcriptome changes were observed after 48 days of salinity. Seven weeks of 100 mM NaCl dramatically changed the repertoire of expressed genes, leading to activation or reactivation of many cell functions. We also identified salt-regulated genes, some of which had not been previously reported to be involved in plant salinity responses. These genes could be potential targets for the selection of favourable genotypes, through breeding or biotechnology, to improve salt tolerance in fig or other crops.

The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)

Background

The genus Potentilla is closely related to that of Fragaria, the economically important strawberry genus. Potentilla micrantha is a species that does not develop berries but shares numerous morphological and ecological characteristics with Fragaria vesca. These similarities make P. micrantha an attractive choice for comparative genomics studies with F. vesca.

Findings

In this study, the P. micrantha genome was sequenced and annotated, and RNA-Seq data from the different developmental stages of flowering and fruiting were used to develop a set of gene predictions. A 327 Mbp sequence and annotation of the genome of P. micrantha, spanning 2674 sequence contigs, with an N50 size of 335,712, estimated to cover 80% of the total genome size of the species was developed. The genus Potentilla has a characteristically larger genome size than Fragaria, but the recovered sequence scaffolds were remarkably collinear at the micro-syntenic level with the genome of F. vesca, its closest sequenced relative. A total of 33,602 genes were predicted, and 95.1% of bench-marking universal single-copy orthologous genes were complete within the presented sequence. Thus, we argue that the majority of the gene-rich regions of the genome have been sequenced.

Conclusions

Comparisons of RNA-Seq data from the stages of floral and fruit development revealed genes differentially expressed between P. micrantha and F. vesca.The data presented are a valuable resource for future studies of berry development in Fragaria and the Rosaceae and they also shed light on the evolution of genome size and organization in this family.

Highlighting type A RRs as potential regulators of the dkHK1 multi-step phosphorelay pathway in Populus

In previous studies, we highlighted a multistep phosphorelay (MSP) system in poplars composed of two hybrid-type Histidine aspartate Kinases, dkHK1a and dkHK1b, which interact with three Histidine Phosphotransfer proteins, dkHPt2, 7, and 9, which in turn interact with six type B Response Regulators. These interactions correspond to the dkHK1a-b/dkHPts/dkRRBs MSP. This MSP is putatively involved in an osmosensing pathway, as dkHK1a-b are orthologous to the Arabidopsis osmosensor AHK1, and able to complement a mutant yeast deleted for its osmosensors. Since type A RRs have been characterized as negative regulators in cytokinin MSP signaling due to their interaction with HPt proteins, we decided in this study to characterize poplar type A RRs and their implication in the MSP. For a global view of this MSP, we isolated 10 poplar type A RR cDNAs, and determined their subcellular localization to check the in silico prediction experimentally. For most of them, the in planta subcellular localization was as predicted, except for three RRAs, for which this experimental approach gave a more precise localization. Interaction studies using yeast two-hybrid and in planta BiFC assays, together with transcript expression analysis in poplar organs led to eight dkRRAs being singled out as partners which could interfere the dkHK1a-b/dkHPts/dkRRBs MSP identified in previous studies. Consequently, the results obtained in this study now provide an exhaustive view of dkHK1a-b partners belonging to a poplar MSP.

Different histories of two highly variable LTR retrotransposons in sunflower species

In the Helianthus genus, very large intra- and interspecific variability related to two specific retrotransposons of Helianthus annuus (Helicopia and SURE) exists. When comparing these two sequences to sunflower sequence databases recently produced by our lab, the Helicopia family was shown to belong to the Maximus/SIRE lineage of the Sirevirus genus of the Copia superfamily, whereas the SURE element (whose superfamily was not even previously identified) was classified as a Gypsy element of the Ogre/Tat lineage of the Metavirus genus. Bioinformatic analysis of the two retrotransposon families revealed their genomic abundance and relative proliferation timing. The genomic abundance of these families differed significantly among 12 Helianthus species. The ratio between the abundance of long terminal repeats and their reverse transcriptases suggested that the SURE family has relatively more solo long terminal repeats than does Helicopia. Pairwise comparisons of Illumina reads encoding the reverse transcriptase domain indicated that SURE amplification may have occurred more recently than that of Helicopia. Finally, the analysis of population structure based on the SURE and Helicopia polymorphisms of 32 Helianthus species evidenced two subpopulations, which roughly corresponded to species of the Helianthus and Divaricati/Ciliares sections. However, a number of species showed an admixed structure, confirming the importance of interspecific hybridisation in the evolution of this genus. In general, these two retrotransposon families differentially contributed to interspecific variability, emphasising the need to refer to specific families when studying genome evolution.

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.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-4050-6) contains supplementary material, which is available to authorized users.

Cultivar-specific transcriptome prediction and annotation in Ficus carica L

The availability of transcriptomic data sequence is a key step for functional genomics studies. Recently, a repertoire of predicted genes of a Japanese cultivar of fig (Ficus carica L.) was released. Because of the great phenotypic variability that can be found in this species, we decided to study another fig genotype, the Italian cv. Dottato, in order to perform comparative studies between the two cultivars and extend the pan genome of this species. We isolated, sequenced and assembled fig genomic DNA from young fruits of cv. Dottato. Then, putative gene sequences were predicted and annotated. Finally, a comparison was performed between cvs. Dottato and Horaishi predicted transcriptomes. Our data provide a resource (available at the Sequence Read Archive database under SRP109082) to be used for functional genomics of fig, in order to fill the gap of knowledge still existing in this species concerning plant development, defense and adaptation to the environment.

Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes

The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes—7 wild accessions and 8 cultivars—of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower.

Analysis of the repetitive component and retrotransposon population in the genome of a marine angiosperm, Posidonia oceanica (L.) Delile

Posidonia oceanica is a monocotyledonous marine plant that plays a crucial role in maintaining the Mediterranean environment. Despite its ecological importance, basic knowledge of the functional and structural genomics of this species is still limited, as it is for the other seagrasses. Here, for the first time, we report data on the repetitive component of the genome of this seagrass using a low coverage of Illumina sequences and different assembly approaches. A dataset of 19,760 assembled sequences, mostly belonging to the repetitive fraction of the genome, was produced and annotated. Based on mapping Illumina reads onto this dataset, the genome structure of P. oceanica and its repetitive component was inferred. A very large proportion of the genome is represented by long-terminal-repeat (LTR) retrotransposons of both the Copia and Gypsy superfamilies. Posidonia LTR-retrotransposons were classified and their sequences analysed. Gypsy elements belong to three main lineages, while Copia ones belong to seven lineages. Gypsy elements were more represented than Copia ones in the set of assembled sequences and in the genome. Analysis of sequence variability indicated that Gypsy lineages have experienced amplification in more recent times compared to Copia ones.

The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads

Background

Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage Illumina or 454 libraries.

Results

By varying sequencing technology (Illumina or 454), coverage (0.55 x-1.25 x), assemblers and assembly procedures, six different genomic databases were produced. The annotation of these databases showed that they were composed of different proportions of repetitive DNA families. The final assembly of the sequences belonging to the six databases produced a whole genome set of 283,800 contigs. The redundancy of each contig was estimated by mapping the whole genome set with a large Illumina read set and measuring the number of matched Illumina reads. The repetitive component amounted to 81% of the sunflower genome, that is composed mainly of numerous families of Gypsy and Copia retrotransposons. Also many families of non autonomous retrotransposons and DNA transposons (especially of the Helitron superfamily) were identified.

Conclusions

The results substantially matched those previously obtained by using a Sanger-sequenced shotgun library and a standard 454 whole-genome-shotgun approach, indicating the reliability of the proposed procedures also for other species. The repetitive sequences were collected to produce a database, SUNREP, that will be useful for the annotation of the sunflower genome sequence and for studying the genome evolution in dicotyledons.

β-blockade with nebivolol for prevention of acute ischaemic events in elderly patients with heart failure

Aim. This subanalysis of the Study of the Effects of Nebivolol Intervention on Outcomes and Hospitalisation in Seniors with Heart Failure (SENIORS) investigates whether treatment with nebivolol, a β-blocker with nitric oxide-releasing properties, can provide additional benefits besides its effects on heart failure (HF), by reducing cardiac ischaemic events in patients with HF of ischaemic aetiology. Material and methods. A double-blind, randomised, placebo-controlled, multicentre trial of nebivolol in 2128 elderly patients. For this analysis, data were extracted for 2128 elderly (≥70 years) HF patients in whom coronary artery disease (CAD) was the underlying aetiology (68,2 %; 717 placebo-treated patients and 735 assigned to nebivolol). The main endpoint was the composite of cardiac ischaemic events at 2 year follow-up: death/hospitalisation for myocardial infarction, unstable angina or sudden death, as originally identified in the case report form. Results. At follow-up, nebivolol treatment was associated with a one-third reduction in the risk of ischaemic events, the composite endpoint occurring in 15,9 % of placebo and 10,7 % of nebivolol-treated patients (HR 0,68; 95 % CI 0,51 to 0,90; p=0,008). This effect was independent of age, gender and ejection fraction. No difference in this composite endpoint was observed in the subgroup of patients of non-ischaemic aetiology. Conclusion. Nebivolol was effective in reducing cardiac ischaemic events in patients with HF of ischaemic aetiology. The prevention of ischaemic events can be an additional beneficial effect of β-blockade in HF patients with underlying CAD.

Neuronal localization of M2 muscarinic receptor immunoreactivity in the rat amygdala

Muscarinic cholinergic neurotransmission in the amygdala is critical for memory consolidation in emotional/motivational learning tasks, but little is known about the neuronal distribution of different receptor subtypes. Immunohistochemistry was used in the present investigation to localize the m2 receptor (M2R). Differential patterns of M2R-immunoreactivity (M2R-ir) were observed in the somata and neuropil of the various amygdalar nuclei. Neuropilar M2R-ir was strongest in rostral portions of the basolateral nuclear complex (BLC). M2R-positive (M2R+) somata were seen in low numbers in all nuclei of the amygdala. Most M2R+ neurons associated with the BLC were in the lateral nucleus and external capsule. These cells were nonpyramidal neurons that contained glutamatic acid decarboxylase (GAD), somatostatin (SOM), and neuropeptide Y (NPY), but not parvalbumin (PV), calretinin (CR), or cholecystokinin (CCK). Little or no M2R-ir was observed in GAD+, PV+, CR+, or CCK+ axons in the BLC, but it was seen in some SOM+ axons and many NPY+ axons. M2R-ir was found in a small number of spiny and aspiny neurons of the central nucleus that were mainly located along the lateral and ventral borders of its lateral subdivision. Many of these cells contained SOM and NPY. M2R+ neurons were also seen in the medial nucleus, including a distinct subpopulation of neurons that surrounded its anteroventral subdivision. The latter neurons were negative for all neuronal markers analyzed. The intercalated nuclei (INs) were associated with two types of large M2R+ neurons, spiny and aspiny. The small principal neurons of the INs were M2R-negative. The somata and dendrites of the large spiny neurons, which were actually found in a zone located just outside of the rostral INs, expressed SOM and NPY, but not GAD. These findings indicate that acetylcholine can modulate a variety of discrete neuronal subpopulations in various amygdalar nuclei via M2Rs, especially neurons that express SOM and NPY.

Postsynaptic targets of GABAergic basal forebrain projections to the basolateral amygdala

Recent studies indicate that the basolateral amygdala, like the neocortex and hippocampus, receives GABAergic inputs from the basal forebrain in addition to the well-established cholinergic inputs. Since the neuronal targets of these inputs have yet to be determined, it is difficult to predict the functional significance of this innervation. The present study addressed this question in the rat by employing anterograde tract tracing combined with immunohistochemistry at the light and electron microscopic levels of analysis. Amygdalopetal axons from the basal forebrain mainly targeted the basolateral nucleus (BL) of the amygdala. The morphology of these axons was heterogeneous and included GABAergic axons that contained vesicular GABA transporter protein (VGAT). These axons, designated type 1, exhibited distinctive large axonal varicosities that were typically clustered along the length of the axon. Type 1 axons formed multiple contacts with the cell bodies and dendrites of parvalbumin-containing (PV+) interneurons, but relatively few contacts with calretinin-containing and somatostatin-containing interneurons. At the ultrastructural level of analysis, the large terminals of type 1 axons exhibited numerous mitochondria and were densely packed with synaptic vesicles. Individual terminals formed broad symmetrical synapses with BL PV+ interneurons, and often formed additional symmetrical synapses with BL pyramidal cells. Some solitary type 1 terminals formed symmetrical synapses solely with BL pyramidal cells. These results suggest that GABAergic neurons of the basal forebrain provide indirect disinhibition, as well as direct inhibition, of BL pyramidal neurons. The possible involvement of these circuits in rhythmic oscillations related to emotional learning, attention, and arousal is discussed.

Neuronal localization of 5-HT type 2A receptor immunoreactivity in the rat basolateral amygdala

Although it is well established that there are alterations in type 2A 5-HT receptors (5-HT2ARs) in the basolateral nuclear complex of the amygdala (BLC) in several neuropsychiatric disorders, very little is known about the neuronal localization of these receptors in this brain region. Single-labeling and dual-labeling immunohistochemical techniques were utilized in the rat to address this question. Three different 5-HT2AR antibodies were used, each producing distinct but overlapping patterns of immunostaining. Two of three 5-HT2AR antibodies mainly stained pyramidal projection neurons in the BLC. The third antibody only stained pyramidal cells in the dorsolateral subdivision of the lateral amygdalar nucleus. With one of the antibodies, the most intensely stained neurons were a population of large nonpyramidal neurons whose morphology and distribution closely resembled those shown in previous studies to project to the mediodorsal thalamic nucleus (MD). This was confirmed in the present study using a technique that combined 5-HT2AR immunohistochemistry with fluorogold retrograde tract-tracing. Two of three 5-HT2AR antibodies stained large numbers of parvalbumin-containing interneurons in the BLC. One of these two antibodies also stained a subpopulation of somatostatin-containing neurons. None of the 5-HT2AR antibodies stained significant numbers of the other two main interneuronal subpopulations, the large cholecystokinin-positive neurons or the small interneurons that exhibit extensive colocalization of calretinin and cholecystokinin. Since each of the three antibodies was raised against a distinct immunizing antigen, they may recognize different conformations of 5-HT2AR in different neuronal domains. The expression of 5-HT2ARs in pyramidal cells and parvalbumin-positive interneurons in the BLC is consistent with the results of previous electrophysiological studies, and suggests that 5-HT may produce excitation of several neuronal populations in the BLC via 5-HT2ARs.

Differential expression of Kv3.1b and Kv3.2 potassium channel subunits in interneurons of the basolateral amygdala

The expression of Kv3.1 and Kv3.2 voltage-gated potassium channel subunits appears to be critical for high-frequency firing of many neuronal populations. In the cortex these subunits are mainly associated with fast-firing GABAergic interneurons containing parvalbumin or somatostatin. Since the basolateral nuclear complex of the amygdala contains similar interneurons, it is of interest to determine if these potassium channel subunits are expressed in these same interneuronal subpopulations. To investigate this issue, peroxidase and dual-labeling fluorescence immunohistochemistry combined with confocal laser scanning microscopy was used to determine which interneuronal subpopulations in the basolateral nuclear complex of the rat amygdala express Kv3.1b and Kv3.2 subunits. Antibodies to parvalbumin, somatostatin, calretinin, and cholecystokinin were used to label separate subsets of basolateral amygdalar interneurons. Examination of immunoperoxidase preparations suggested that the expression of both channels was restricted to nonpyramidal interneurons in the basolateral amygdala. Somata and proximal dendrites were intensely-stained, and axon terminals arising from presumptive basket cells and chandelier cells were lightly stained. Immunofluorescence observations revealed that parvalbumin+ neurons were the main interneuronal subpopulation expressing the Kv3.1b potassium channel subunit in the basolateral amygdala. More than 92-96% of parvalbumin+ neurons were Kv3.1b+, depending on the nucleus. These parvalbumin+/Kv3.1b+ double-labeled cells constituted 90-99% of all Kv3.1b+ neurons. Parvalbumin+ neurons were also the main interneuronal subpopulation expressing the Kv3.2 potassium channel subunit. More than 67-78% of parvalbumin+ neurons were Kv3.2+, depending on the nucleus. However, these parvalbumin+/Kv3.2+ double-labeled cells constituted only 71-81% of all Kv3.2+ neurons. Most of the remaining neurons with significant levels of the Kv3.2 subunit were somatostatin+ interneurons. These Kv3.2-containing somatostatin+ interneurons constituted 27-50% of the somatostatin+ population, depending on the nucleus in question. These data suggest that both fast-firing and burst-firing parvalbumin+ interneurons in the basolateral amygdala express the Kv3.1b subunit. The significance of Kv3.2 expression in some parvalbumin+ and somatostatin+ interneurons remains to be determined.

Localization of the CB1 type cannabinoid receptor in the rat basolateral amygdala: high concentrations in a subpopulation of cholecystokinin-containing interneurons

The neuronal localization of the CB1 cannabinoid receptor in the rat basolateral amygdala was studied using peroxidase and fluorescence immunohistochemical techniques. All nuclei of the basolateral amygdala contained a large number of lightly stained pyramidal neurons and a small number of more intensely stained non-pyramidal neurons. Most of the latter cells had medium-sized to large multipolar somata and three to four aspiny dendrites, but some exhibited smaller oval somata. The axon initial segments of some of these non-pyramidal neurons exhibited large swollen varicosities in colchicine-injected animals, suggesting that much of the CB1 receptor protein is transported down the axons of these cells. Double-labeling studies using immunofluorescence histochemistry combined with confocal laser scanning microscopy revealed that the great majority of non-pyramidal neurons with CB1 receptor immunoreactivity belonged to a cholecystokinin-containing subpopulation. Whereas none of the other subpopulations of non-pyramidal neurons (exhibiting immunoreactivity for calretinin, parvalbumin, or somatostatin) expressed high levels of CB1 receptor immunoreactivity, a small percentage of these cells exhibited low levels of immunoreactivity. The results indicate that cannabinoids may modulate the activity of pyramidal projection neurons as well as a subpopulation of cholecystokinin-containing non-pyramidal neurons in the basolateral amygdala. Previous studies indicate that most of the latter are inhibitory interneurons that utilize GABA as a neurotransmitter. The intense staining of the cholecystokinin-containing interneurons and the evidence that large amounts of CB1 receptor protein are transported down the axons of these cells suggests that, as in the hippocampus, cannabinoids may inhibit the release of GABA from the axon terminals of these neurons.

Colocalization of calcium-binding proteins and GABA in neurons of the rat basolateral amygdala

The basolateral amygdala contains subpopulations of non-pyramidal neurons that express the calcium-binding proteins parvalbumin, calbindin-D28k (calbindin) or calretinin. Although little is known about the exact functions of these proteins, they have provided useful markers of specific neuronal subpopulations in studies of the neuronal circuitry of the cerebral cortex and other brain regions. The purpose of the present study was to investigate whether basolateral amygdalar non-pyramidal neurons containing parvalbumin, calbindin, or calretinin exhibit immunoreactivity for GABA, and to determine if calretinin is colocalized with parvalbumin or calbindin in the rat basolateral amygdala. Pyramidal neurons were distinguished from non-pyramidal neurons on the basis of staining intensity. Using immunofluorescence confocal laser scanning microscopy, as well as the 'mirror technique' on immunoperoxidase-stained sections, it was found that there was virtually no colocalization of calretinin with parvalbumin or calbindin, but that the great majority of basolateral amygdalar non-pyramidal neurons containing parvalbumin, calbindin, or calretinin exhibited GABA immunoreactivity. Calbindin-positive neurons constituted almost 60% of the GABA-containing population in both subdivisions of the basolateral nucleus and more than 40% of the GABA-containing population in the lateral nucleus. Parvalbumin-positive neurons constituted 19-43% of GABA-immunoreactive neurons in the basolateral amygdala, depending on the nucleus. Calretinin-positive non-pyramidal neurons constituted about 20% of the GABA-positive neuronal population in each nucleus of the basolateral amygdala. These findings indicate that non-pyramidal neurons containing parvalbumin, calbindin, or calretinin comprise the majority of GABA-containing neurons in the basolateral amygdala, and that the calretinin subpopulation is distinct from non-pyramidal subpopulations containing parvalbumin and calbindin. These separate neuronal populations may play unique roles in the inhibitory circuitry of the amygdala.

Projections of the lateral entorhinal cortex to the amygdala: a Phaseolus vulgaris leucoagglutinin study in the rat

In addition to providing a gateway to the hippocampus, the entorhinal cortex has significant projections to the amygdala. In the present investigation, the organization of the projections of the lateral entorhinal cortex to the amygdala was studied in the rat using the sensitive anterograde tracer Phaseolus vulgaris leucoagglutinin. Each of the three main subdivisions of the lateral entorhinal cortex provided a characteristic projection to the amygdala that mainly arose from the deep cortical layers. The projections from the dorsolateral and ventrolateral entorhinal areas were much stronger than those arising from the ventromedial entorhinal area. The primary targets of the dorsolateral and ventrolateral entorhinal areas were the basolateral amygdala, lateral capsular subdivision of the central nucleus and caudal portions of the cortical nuclear complex. The dorsolateral entorhinal area projects mainly to the lateral part of the basal nucleus, while the ventrolateral entorhinal area projects mainly to its medial part. A transitional region at the rostral pole of the ventrolateral entorhinal cortex has additional strong projections to the lateral subdivision of the central nucleus, medial amygdaloid nucleus and the intra-amygdaloid portion of the bed nucleus of the stria terminalis. The results of the present study indicate that the amygdala is one of the principal targets of the entorhinal cortex. The correspondence between the topography of entorhino-hippocampal connections and entorhino-amygdaloid connections suggests that the amygdaloid projection arising in each of the three main subdivisions of the entorhinal cortex conveys information processed in different septotemporal portions of the hippocampal formation. These entorhinal projections, which probably convey complex relational (including contextual) information to the amygdala, are in a position to produce different behavioral responses by activating different portions of the amygdaloid nuclear complex.

Immunohistochemical localization of the beta 2 and beta 3 subunits of the GABAA receptor in the basolateral amygdala of the rat and monkey

The basolateral amygdala has a strong intrinsic inhibitory system mediated by GABAA receptors and is the main site of the anxiolytic actions of benzodiazepines. In an effort to identify the anatomical substrates for these transmitter and drug actions, immunohistochemical techniques were used to analyse the neuronal localization of the beta 2 and beta 3 receptor subunits of the GABAA-benzodiazepine receptor complex in the rat and monkey basolateral amygdala. The overall pattern of GABAA-benzodiazepine receptor immunoreactivity was very similar in both species. The density of the immunoreactivity in the neuropil varied in different nuclei of the basolateral amygdaloid complex. In both species the neuropil of the lateral nucleus exhibited the most robust staining. Immunoreactivity was also seen in neuronal perikarya and dendrites where it was localized to the cytoplasm and/or surface membrane. The cell type with the strongest immunoreactivity was a subpopulation of small non-pyramidal neurons that had numerous thin dendrites. Other larger non-pyramidal neurons were also stained. Pyramidal neurons in the rat and monkey basolateral amygdala exhibited light to moderate perikaryal staining that varied in different nuclei. The results of this study indicate that the pattern of GABAA-benzodiazepine receptor immunoreactivity in the neuropil of the rat and monkey basolateral amygdala closely resembled the distribution of benzodiazepine receptors localized in previous radioligand autoradiographic studies. The finding of intense immunoreactivity in subpopulations of non-pyramidal neurons suggests the existence of disinhibitory mechanisms which may be important for the activation of basolateral amygdaloid projection neurons.

Projections of the medial and lateral prefrontal cortices to the amygdala: a Phaseolus vulgaris leucoagglutinin study in the rat

The projections of different subfields of the medial and lateral prefrontal cortices to the amygdala were studied in the rat using the sensitive Phaseolus vulgaris leucoagglutinin anterograde tract tracing technique. Injections into the infralimbic cortex produced anterograde labeling in the lateral capsular subdivision of the central nucleus, superficial (corticomedial) amygdaloid nuclei, lateral and accessory basal nuclei, and the anterior amygdaloid area. Injections into the caudal portion of the infralimbic cortex produced additional labeling in the intermediate subdivision of the central nucleus. The prelimbic cortex had projections to the medial portion of the magnocellular basal nucleus and adjacent portions of the lateral nucleus and lateral capsular subdivision of the central nucleus. The medial precentral cortex had projections to the rostromedial part of the magnocellular basal nucleus and adjacent portions of the lateral capsular subdivision of the central nucleus. Injections into the lateral orbital and ventral agranular insular cortices produced labeled fibers in the rostral part of the superficial amygdala, lateral capsular subdivision of the central nucleus, and the lateral and accessory basal nuclei. The dorsal agranular insular area had projections to several different subdivisions of the central nucleus as well as to the rostrolateral magnocellular basal nucleus; the latter projections were complementary to those originating in the prelimbic area. The present study indicates that each portion of the prefrontal cortex has a distinctive projection to the amygdala. The ventral areas of the lateral and medial prefrontal cortices, which receive olfactory projections, are the only prefrontal cortical areas with projections to the olfactory-related superficial amygdaloid nuclei. The more dorsally situated prefrontal areas, the dorsal agranular insular area and prelimbic cortex, have complementary projections to the basal nucleus, suggesting that they modulate separate prefrontal cortico-striatal-pallid circuits. The specificity of prefrontal cortico-amygdaloid projections is indicative of their involvement in discrete functions.

Cortico-cortical and cortico-amygdaloid projections of the rat occipital cortex: a Phaseolus vulgaris leucoagglutinin study

The efferent projections of the occipital cortex of the rat were investigated using the Phaseolus vulgaris leucoagglutinin anterograde tract tracing technique. Particular attention was focused on projections to the amygdala and amygdalopetal cortical areas. The primary visual cortex had projections to the medial and lateral portions of occipital area 2 and other cortical regions, but no projections to the amygdala or amygdalopetal cortical areas. The only occipital area that had direct projections to the amygdala was the most ventral portion of lateral occipital area 2, located just dorsal to temporal area 2. This occipitotemporal junction region, which received projections from secondary visual cortical areas but not from the primary visual cortex, had projections to the lateral nucleus, magnocellular basal nucleus, and lateral capsular subdivision of the central nucleus of the amygdala. Occipital area 2 had projections to seven amygdalopetal cortical regions: temporal area 2, temporal area 3, frontal area 2, ventrolateral orbitofrontal area, occipitotemporal junction region, lateral entorhinal area, and the perirhinal cortex. Projections to the perirhinal cortex targeted regions located adjacent to the parietal cortex and caudal temporal cortex, but not regions adjacent to the rostral temporal cortex. Other cortical regions receiving projections from medial and lateral portions of occipital area 2 included the presubiculum, retrosplenial areas, and caudal portions of the parietal cortical areas 1 and 2. The results of the present investigation, in conjunction with previous anatomical and neurobehavioral studies, support the concept that rodent cortical visual pathways, like those of primates, consist of a dorsal system involved with visuospatial functions and a ventral system involved with object recognition. As in primates, the ventral pathway projects to the temporal-perirhinal region in a cascading manner; only highly processed information from tertiary visual cortical areas reaches the amygdala. Unlike primates, however, cortical areas in the rat brain that receive highly processed visual information appear to be regions of multisensory convergence.

Synaptology of prefrontal cortical projections to the basolateral amygdala: an electron microscopic study in the rat

Prefrontal projections to the magnocellular basal amygdaloid nucleus (Bmg) of the rat were investigated using Phaseolus vulgaris leucoagglutinin (PHA-L) as an anterograde tracer. Electron microscopic examination revealed that most axon terminals in Bmg labeled by PHA-L injections into the prelimbic area contained round synaptic vesicles and made asymmetric synapses. The great majority of labeled terminals (93%) made synaptic contact with dendritic spines; a few contacts (7%) were seen with thin dendrites. These findings indicate that the main postsynaptic targets of PFC afferents to Bmg are spiny pyramidal neurons, the projection neurons of the basolateral amygdala. The morphology of the synapses suggests that they are excitatory.

Neuropeptide Y and somatostatin-like immunoreactivity in neurons of the monkey amygdala

Neurons in the monkey amygdala exhibiting neuropeptide Y-like immunoreactivity and somatostatin-like immunoreactivity were identified using an avidin-biotin immunohistochemical technique. Differential co-existence of the two peptides was demonstrated using two-color immunoperoxidase and adjacent section methods. Numerous neuropeptide Y-positive neurons were observed in the basolateral and superficial amygdaloid nuclei. A moderate number of neuropeptide Y-positive neurons was seen in the medial subdivision of the central nucleus, but only a few neurons were observed in the lateral subdivision. Numerous somatostatin-positive neurons were stained in all major amygdaloid nuclei and always outnumbered neuropeptide Y-positive cells. All amygdaloid nuclei contained numerous peptide-positive fibers whose density varied depending on the nucleus. Approximately 90% of neuropeptide Y-positive neurons also exhibited somatostatin-like immunoreactivity. The percentage of somatostatin-positive neurons that exhibited neuropeptide-Y immunoreactivity varied in different nuclei. In the superficial amygdaloid nuclei, medial subdivision of the central nucleus and most portions of the basolateral nuclei the predominant cell type stained with both the neuropeptide Y and somatostatin antibodies was a spine-sparse non-pyramidal neuron. In the dorsal portion of the lateral nucleus, however, most peptide-positive neurons had spiny dendrites. Only the cell bodies and proximal dendrites of somatostatin-positive neurons in the lateral subdivision of the central nucleus were immunostained. This study demonstrates that specific cell populations in the primate amygdala contain neuropeptide Y, somatostatin or both peptides. Most peptide-positive neurons in the basolateral and superficial amygdaloid nuclei appear to be local circuit neurons that contribute to the dense plexus of peptide-positive axons in these regions. The finding of neurons with spiny dendrites in the dorsal part of the lateral nucleus suggests that these cells may be functionally different from peptide-positive neurons in other portions of the basolateral amygdala. The lateral subdivision of the central nucleus is distinguished from other amygdaloid nuclei by containing a large population of somatostatin-positive neurons that do not exhibit neuropeptide Y immunoreactivity.

Cholecystokinin corticostriatal pathway in the rat: evidence for bilateral origin from medial prefrontal cortical areas

The anterograde tracer Phaseolus vulgaris-leucoagglutinin was used to examine the organization of the projections to the striatum from medial prefrontal and frontal cortical areas in the rat with reference to their relation to cholecystokinin-like immunoreactivity in the striatum. Medial prefrontal cortical areas projected bilaterally, with an ipsilateral predominance, to the striatum. Most of the positive fibres were found in medial and ventral areas of the caudate-putamen and in the nucleus accumbens. Labelled fibres formed distinct patch-like arrangements throughout the dorsomedial striatum, whereas more ventrally the fibres were densely packed and spread to lateral areas. Almost no fibres were found in the dorsolateral aspects of the caudate-putamen. Cholecystokinin-like immunoreactivity in the striatum was diffusely distributed in the medial aspects, in fine punctate elements as well as in patches of fibres. Overlapping of corticostriatal clusters of fibres, from medial prefrontal cortex, with cholecystokinin-immunoreactive patches was found at all rostrocaudal levels studied, but predominantly in rostral areas. The overlap was present both in the ipsilateral and the contralateral side. Often the cluster of corticostriatal fibres was completely and precisely overlaid by a cholecystokinin-immunoreactive patch. At more caudal planes the overlap was only partial and in some instances cholecystokinin-positive patches "avoided" zones of dense corticostriatal fibre terminations. Frontal cortex injections of tracer gave rise to a network of fibres in the lateral aspects of the striatum, sparing the medial areas. No overlap with cholecystokinin-immunoreactive patches was found in these cases. These results suggest that a large number of cholecystokinin-containing striatal fibres originate in medial prefrontal cortical areas.

A sexually dimorphic population of CRF neurons in the medial preoptic area

The neuropeptide corticotropin-releasing factor (CRF) is thought to mediate the induction of a constellation of behavioral, endocrine, and autonomic responses which are important for an animal's adaptation to stressful events. We have found that the anteroventral periventricular preoptic nucleus (AVPv) and medial preoptic nucleus (MPN) of colchicine-injected female rats contained numerous intensely stained CRF-immunoreactive neurons. The AVPv/MPN in males contained very few CRF-immunoreactive neurons per section, even in colchicine-injected animals. This sexually dimorphic population of CRF-immunoreactive neurons in the AVPv may play some role in the sex-related differences in hormonal responses to stress and/or in the control of female reproductive events.

Corticoamygdaloid and corticocortical projections of the rat temporal cortex: a Phaseolus vulgaris leucoagglutinin study

The projections of the rat temporal cortex to the amygdala and cerebral cortex were studied using the sensitive anterograde tracer, Phaseolus vulgaris leucoagglutinin. These studies revealed that the core of temporal area 1 had no projections to the amygdala but did send efferents to several cortical fields that projected to the amygdala, including temporal area 2, temporal area 3, the lateral occipital area 2, and a cortical zone along the dorsal, rostral and caudal borders of temporal area 1 ("Tel fringe"). The temporal area 1 fringe cortex had light projections to the amygdala that were confined to the dorsolateral subdivision of the lateral amygdaloid nucleus. Temporal area 2 and the caudal portion of temporal area 3 had projections to both the dorsolateral and ventromedial subdivisions of the lateral nucleus; the projection from temporal area 2 targeted mainly the ventromedial subdivision, whereas the projection from the caudal portion of temporal area 3 terminated primarily in the dorsolateral subdivision. The rostral portion of temporal area 3 had projections to both subdivisions of the lateral nucleus and to the basal magnocellular nucleus. Temporal areas 2 and 3 also had light projections to the lateral capsular subdivision of the central amygdaloid nucleus. Temporal cortical areas exhibited extensive reciprocal connections with each other. Temporal areas with amygdaloid projections also had extensive projections to the perirhinal cortex. The results of the present investigation, in conjunction with other studies of temporal cortical connections, suggest that all temporal regions projecting to the amygdala are multimodal sensory areas. The core of temporal area 1, which is probably the primary auditory area, apparently has no direct projections to the amygdala. The differential projections of different temporal areas to the amygdala suggests the existence of several distinct multimodal pathways arranged in a parallel configuration.

Effects of injection of anti-luteinizing hormone (LH)-releasing hormone serum and anti-gonadotropin-releasing hormone-associated peptide serum into neonatal rats on LH and follicle-stimulating hormone cells

Relatively little is known regarding the potential importance of LHRH and of gonadotropin-releasing hormone-associated peptide (GAP) on the postnatal development of gonadotrophs. We investigated the effects of administration of anti (A)-LHRH serum or A-GAP serum to neonatal rats on the development of LH and FSH immunoreactivity in anterior pituitary gland (APG) cells. Serum (sheep non-immune [NSS], sheep A-LHRH, sheep A-LHRH/GAP [which bound LHRH and GAP], rabbit non-immune [NRS], or rabbit A-GAP) was injected s.c. into neonatal female and male rats on Days 1 and 3 or Days 1, 3, 5, and 7 after birth. Pups were killed on Day 5 or 9, two days after the last injection. The percentages of APG cells immunoreactive for LH or FSH increased from Day 1 to Day 5 and did not change between Days 5 and 9 in female pups treated with NSS or NRS. There was a trend for the percentages of LH and FSH cells to increase from Day 1 to Days 5 and 9 in male pups treated with NSS or NRS, but the increases were not statistically significant. In both females and males, treatment with antisera that recognized LHRH reduced the percentage of FSH cells on Day 5 and the percentages of LH and FSH cells on Day 9. Treatment with A-GAP was without effect in both sexes. There were similar percentages of LH and FSH cells in females and a lower percentage of FSH than of LH cells in males in the Day 5 and 9 controls.(ABSTRACT TRUNCATED AT 250 WORDS)

Immunocytochemical staining of neuropeptide Y (NPY) in the insular lobe of the monkey: a light microscopic study

Neuropeptide Y (NPY) has been detected immunocytochemically in cerebral cortex and subcortical white matter of the primate frontal, parietal, temporal, and occipital lobes. Because little is known about NPY in the primate insular lobe and because peptides play an important role in normal neuronal functioning and alterations in brain peptides are associated with certain neurological diseases, we studied the presence, distribution, and structural characteristics of NPY-immunostained elements at the light microscopic level in the insula of Macaca fascicularis. We used free-floating sections, rabbit anti-porcine NPY serum, and the avidin and biotinylated peroxidase complex technique. Neuropeptide Y-immunostained neurons were demonstrated in layers II, III, and V/VI, and in the adjoining subcortical white matter. Immunostaining was localized to neuronal somata, neuronal processes, and a delicate plexus in the neuropil. The majority of NPY-immunostained neurons were non-pyramidal, had round somata 10-20 microns in major transverse diameter, and two or three neuronal processes. Computer-aided quantitative analysis of the length, breadth, and area of NPY-stained neurons was performed. Our findings are consistent with observations by others on the presence, laminar distribution, and structural characteristics of NPY-immunostained elements at the light microscopic level in other cerebral lobes of non-human primates.

Identification of putative nitric oxide producing neurons in the rat amygdala using NADPH-diaphorase histochemistry

Putative nitric oxide-containing neurons in the rat amygdala were studied using reduced nicotinamide adenine dinucleotide phosphate diaphorase histochemistry. All nuclei of the amygdala contained subpopulations of diaphorase-positive neurons, but the staining intensity of different subpopulations varied. Intensely stained neurons exhibited labeling of the cell body and the entire dendritic arborization. The lateral nucleus had the greatest concentration of intensely labeled cells. Many intensely labeled neurons were located along nuclear boundaries and fiber bundles. In addition to neuronal staining, there was a differential staining of the neuropil in different amygdaloid nuclei. In the basolateral and cortical nuclei the diaphorase-positive cells were non-pyramidal neurons that resembled those containing somatostatin and neuropeptide Y. The distribution and neuronal morphology of labeled neurons in the central nucleus and anterior amygdaloid area suggests that diaphorase-positive cells in these areas may be cholinergic. Recent studies have shown that the enzyme responsible for neuronal diaphorase activity is actually the synthetic enzyme for the newly discovered neurotransmitter nitric oxide. Since there is evidence that nitric oxide plays an important role in excitotoxic neuronal degeneration, the neurons identified in the present study may be involved in degenerative diseases of the amygdala.

Biocytin injections produce selective neuronal labeling in the rat CNS

Large injections of biocytin into the lateral ventricle or brain resulted in the labeling of particular neuronal subpopulations in the rat CNS. Localization was accomplished using the avidin-biotin-peroxidase technique. In many cases the staining of neurons was totally complete and resembled that obtained with the Golgi technique. Regions containing labeled cells included the olfactory bulb, cerebral cortex, hippocampus, amygdala, striatum, hypothalamus, superior and inferior colliculi, cerebellar cortex, and dorsal horn of the spinal cord. Only particular cell types were labeled in each of these regions. The results of this study suggest that there is selective uptake and/or retention of biocytin, or a biotinylated metabolite of biocytin, by subpopulations of CNS neurons.