Heterogeneity of layer 4 in visual areas of rhesus macaque cortex.

Recently, single-cell RNA-sequencing (scRNA-seq) has enabled unprecedented insights to the cellular landscape of the brains of many different species, among them the rhesus macaque as a key animal model. Building on previous, broader surveys of the macaque brain, we closely examined five immediately neighboring areas within the visual cortex of the rhesus macaque: V1, V2, V4, MT and TEO. To facilitate this, we first devised a novel pipeline for brain spatial archive - the BrainSPACE - which enabled robust archiving and sampling from the whole unfixed brain. SnRNA-sequencing of ~100,000 nuclei from visual areas V1 and V4 revealed conservation within the GABAergic neuron subtypes, while seven and one distinct principle neuron subtypes were detected in V1 and V4, respectively, all most likely located in layer 4. Moreover, using small molecule fluorescence in situ hybridization, we identified cell type density gradients across V1, V2, V4, MT, and TEO appearing to reflect the visual hierarchy. These findings demonstrate an association between the clear areal specializations among neighboring areas with the hierarchical levels within the visual cortex of the rhesus macaque.

Whispering-Gallery Quantum-Well Exciton Polaritons in an Indium Gallium Arsenide Microdisk Cavity.

Despite appealing high-symmetry properties that enable strong spatial confinement and ultrahigh-Q, optical whispering-gallery modes of spherical and circular resonators have been absent from the field of quantum-well exciton polaritons. Here we observe whispering-gallery exciton polaritons in a gallium arsenide microdisk cavity filled with indium gallium arsenide quantum wells, the test bed materials of polaritonics. Strong coupling is evidenced in photoluminescence and resonant spectroscopy accessed through concomitant confocal microscopy and near-field optical techniques. Excitonic and optical resonances are tuned by varying temperature and disk radius, revealing Rabi splittings between 5 and 10 meV. A dedicated analytical quantum model for such circular whispering-gallery polaritons is developed, which reproduces the measured values. At high power, lasing is observed and accompanied by a blueshift of the emission consistent with the regime of polariton lasing. With experimental methods and theory now established, whispering-gallery-mode polaritons in round dielectric resonators appear as a new viable platform toward low loss polaritonics.

All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity.

Bread wheat (Triticum aestivum L.) is a major crop and its genome is one of the largest ever assembled at reference-quality level. It is 15 Gb, hexaploid, with 85% of transposable elements (TEs). Wheat genetic diversity was mainly focused on genes and little is known about the extent of genomic variability affecting TEs, transposition rate, and the impact of polyploidy. Multiple chromosome-scale assemblies are now available for bread wheat and for its tetraploid and diploid wild relatives. In this study, we computed base pair-resolved, gene-anchored, whole genome alignments of A, B, and D lineages at different ploidy levels in order to estimate the variability that affects the TE space. We used assembled genomes of 13 T. aestivum cultivars (6x = AABBDD) and a single genome for Triticum durum (4x = AABB), Triticum dicoccoides (4x = AABB), Triticum urartu (2x = AA), and Aegilops tauschii (2x = DD). We show that 5%-34% of the TE fraction is variable, depending on the species divergence. Between 400 and 13,000 novel TE insertions per subgenome were detected. We found lineage-specific insertions for nearly all TE families in di-, tetra-, and hexaploids. No burst of transposition was observed and polyploidization did not trigger any boost of transposition. This study challenges the prevailing idea of wheat TE dynamics and is more in agreement with an equilibrium model of evolution.

Wheat Ym2 originated from Aegilops sharonensis and confers resistance to soil-borne Wheat yellow mosaic virus infection to the roots.

Wheat yellow mosaic virus (WYMV) is a pathogen transmitted into its host's roots by the soil-borne vector Polymyxa graminis. Ym1 and Ym2 genes protect the host from the significant yield losses caused by the virus, but the mechanistic basis of these resistance genes remains poorly understood. Here, it has been shown that Ym1 and Ym2 act within the root either by hindering the initial movement of WYMV from the vector into the root and/or by suppressing viral multiplication. A mechanical inoculation experiment on the leaf revealed that the presence of Ym1 reduced viral infection incidence, rather than viral titer, while that of Ym2 was ineffective in the leaf. To understand the basis of the root specificity of the Ym2 product, the gene was isolated from bread wheat using a positional cloning approach. The candidate gene encodes a CC-NBS-LRR protein and it correlated allelic variation with respect to its sequence with the host's disease response. Ym2 (B37500) and its paralog (B35800) are found in the near-relatives, respectively, Aegilops sharonensis and Aegilops speltoides (a close relative of the donor of bread wheat's B genome), while both sequences, in a concatenated state, are present in several accessions of the latter species. Structural diversity in Ym2 has been generated via translocation and recombination between the two genes and enhanced by the formation of a chimeric gene resulting from an intralocus recombination event. The analysis has revealed how the Ym2 region has evolved during the polyploidization events leading to the creation of cultivated wheat.

TaRECQ4 contributes to maintain both homologous and homoeologous recombination during wheat meiosis.

Introduction: Meiotic recombination (or crossover, CO) is essential for gamete fertility as well as for alleles and genes reshuffling that is at the heart of plant breeding. However, CO remains a limited event, which strongly hampers the rapid production of original and improved cultivars. RecQ4 is a gene encoding a helicase protein that, when mutated, contributes to improve recombination rate in all species where it has been evaluated so far. Methods: In this study, we developed wheat (Triticum aestivum L.) triple mutant (TM) for the three homoeologous copies of TaRecQ4 as well as mutants for two copies and heterozygous for the last one (Htz-A, Htz-B, Htz-D). Results: Phenotypic observation revealed a significant reduction of fertility and pollen viability in TM and Htz-B plants compared to wild type plants suggesting major defects during meiosis. Cytogenetic analyses of these plants showed that complete absence of TaRecQ4 as observed in TM plants, leads to chromosome fragmentation during the pachytene stage, resulting in problems in the segregation of chromosomes during meiosis. Htz-A and Htz-D mutants had an almost normal meiotic progression indicating that both TaRecQ4-A and TaRecQ4-D copies are functional and that there is no dosage effect for TaRecQ4 in bread wheat. On the contrary, the TaRecQ4-B copy seems knocked-out, probably because of a SNP leading to a Threonine>Alanine change at position 539 (T539A) of the protein, that occurs in the crucial helicase ATP bind/DEAD/ResIII domain which unwinds nucleic acids. Occurrence of numerous multivalents in TM plants suggests that TaRecQ4 could also play a role in the control of homoeologous recombination. Discussion: These findings provide a foundation for further molecular investigations into wheat meiosis regulation to fully understand the underlying mechanisms of how TaRecQ4 affects chiasma formation, as well as to identify ways to mitigate these defects and enhance both homologous and homoeologous recombination efficiency in wheat.

Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly.

Until recently, achieving a reference-quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5-Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high-confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat.

New insights into homoeologous copy number variations in the hexaploid wheat genome.

Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so-called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post-polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat.

Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats.

Structural variations (SVs) such as copy number and presence-absence variations are polymorphisms that are known to impact genome composition at the species level and are associated with phenotypic variations. In the absence of a reference genome sequence, their study has long been hampered in wheat. The recent production of new wheat genomic resources has led to a paradigm shift, making possible to investigate the extent of SVs among cultivated and wild accessions. We assessed SVs affecting genes and transposable elements (TEs) in a Triticeae diversity panel of 45 accessions from seven tetraploid and hexaploid species using high-coverage shotgun sequencing of sorted chromosome 3B DNA and dedicated bioinformatics approaches. We showed that 23% of the genes are variable within this panel, and we also identified 330 genes absent from the reference accession Chinese Spring. In addition, 60% of the TE-derived reference markers were absent in at least one accession, revealing a high level of intraspecific and interspecific variability affecting the TE space. Chromosome extremities are the regions where we observed most of the variability, confirming previous hypotheses made when comparing wheat with the other grasses. This study provides deeper insights into the genomic variability affecting the complex Triticeae genomes at the intraspecific and interspecific levels and suggests a phylogeny with independent hybridization events leading to different hexaploid species.

Worldwide phylogeography and history of wheat genetic diversity.

Since its domestication in the Fertile Crescent ~8000 to 10,000 years ago, wheat has undergone a complex history of spread, adaptation, and selection. To get better insights into the wheat phylogeography and genetic diversity, we describe allele distribution through time using a set of 4506 landraces and cultivars originating from 105 different countries genotyped with a high-density single-nucleotide polymorphism array. Although the genetic structure of landraces is collinear to ancient human migration roads, we observe a reshuffling through time, related to breeding programs, with the appearance of new alleles enriched with structural variations that may be the signature of introgressions from wild relatives after 1960.

Impact of transposable elements on genome structure and evolution in bread wheat.

BACKGROUND: Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes. RESULTS: The overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid. CONCLUSIONS: Even though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes.