A spinach genome assembly with remarkable completeness,and its use for rapid identification of candidate genes for agronomic traits

Spinach (Spinacia oleracea) is grown as a nutritious leafy vegetable worldwide. To accelerate spinach breeding efficiency, a high-quality reference genome sequence with great completeness and continuity is needed as a basic infrastructure. Here, we used long-read and linked-read technologies to construct a de novo spinach genome assembly, designated SOL_r1.1, which was comprised of 287 scaffolds (total size: 935.7 Mb; N₅₀ = 11.3 Mb) with a low proportion of undetermined nucleotides (Ns = 0.34%) and with high gene completeness (BUSCO complete 96.9%). A genome-wide survey of resistance gene analogues identified 695 genes encoding nucleotide-binding site domains, receptor-like protein kinases, receptor-like proteins and transmembrane-coiled coil domains. Based on a high-density double-digest restriction-site associated DNA sequencing-based linkage map, the genome assembly was anchored to six pseudomolecules representing ∼73.5% of the whole genome assembly. In addition, we used SOL_r1.1 to identify quantitative trait loci for bolting timing and fruit/seed shape, which harbour biologically plausible candidate genes, such as homologues of the FLOWERING LOCUS T and EPIDERMAL PATTERNING FACTOR-LIKE genes. The new genome assembly, SOL_r1.1, will serve as a useful resource for identifying loci associated with important agronomic traits and for developing molecular markers for spinach breeding/selection programs.     

Clostridium perfringens Alpha-Toxin Induces Gm1a Clustering and Trka Phosphorylation in the Host Cell Membrane

Clostridium perfringens alpha-toxin elicits various immune responses such as the release of cytokines, chemokines, and superoxide via the GM1a/TrkA complex. Alpha-toxin possesses phospholipase C (PLC) hydrolytic activity that contributes to signal transduction in the pathogenesis of gas gangrene. Little is known about the relationship between lipid metabolism and TrkA activation by alpha-toxin. Using live-cell fluorescence microscopy, we monitored transbilayer movement of diacylglycerol (DAG) with the yellow fluorescent protein-tagged C1AB domain of protein kinase C-γ (EYFP-C1AB). DAG accumulated at the marginal region of the plasma membrane in alpha toxin-treated A549 cells, which also exhibited GM1a clustering and TrkA phosphorylation. Annexin V binding assays showed that alpha-toxin induced the exposure of phosphatidylserine on the outer leaflet of the plasma membrane. However, H148G, a variant toxin which binds cell membrane and has no enzymatic activity, did not induce DAG translocation, GM1a clustering, or TrkA phosphorylation. Alpha-toxin also specifically activated endogenous phospholipase Cγ-1 (PLCγ-1), a TrkA adaptor protein, via phosphorylation. U73122, an endogenous PLC inhibitor, and siRNA for PLCγ-1 inhibited the formation of DAG and release of IL-8. GM1a accumulation and TrkA phosphorylation in A549 cells treated with alpha-toxin were also inhibited by U73122. These results suggest that the flip-flop motion of hydrophobic lipids such as DAG leads to the accumulation of GM1a and TrkA. We conclude that the formation of DAG by alpha-toxin itself (first step) and activation of endogenous PLCγ-1 (second step) leads to alterations in membrane dynamics, followed by strong phosphorylation of TrkA.     

A conserved non-reproductive GnRH system in chordates

Gonadotropin-releasing hormone (GnRH) is a neuroendocrine peptide that plays a central role in the vertebrate hypothalamo-pituitary axis. The roles of GnRH in the control of vertebrate reproductive functions have been established, while its non-reproductive function has been suggested but less well understood. Here we show that the tunicate Ciona intestinalis has in its non-reproductive larval stage a prominent GnRH system spanning the entire length of the nervous system. Tunicate GnRH receptors are phylogenetically closest to vertebrate GnRH receptors, yet functional analysis of the receptors revealed that these simple chordates have evolved a unique GnRH system with multiple ligands and receptor heterodimerization enabling complex regulation. One of the gnrh genes is conspicuously expressed in the motor ganglion and nerve cord, which are homologous structures to the hindbrain and spinal cord of vertebrates. Correspondingly, GnRH receptor genes were found to be expressed in the tail muscle and notochord of embryos, both of which are phylotypic axial structures along the nerve cord. Our findings suggest a novel non-reproductive role of GnRH in tunicates. Furthermore, we present evidence that GnRH-producing cells are present in the hindbrain and spinal cord of the medaka, Oryzias latipes, thereby suggesting the deep evolutionary origin of a non-reproductive GnRH system in chordates.     

Determination of the freshwater mark in otoliths of Japanese eel elvers using microstructure and Sr/Ca ratios

The microstructure, in particular checks within the otolith edge, of Anguilla japonica glass-eels and elvers and changes in otolith Sr/Ca ratios were examined to ascertain the environmental history of the eels, especially with regard to the time when glass-eels entered the river, and as a benchmark for count daily increments. The percentage of glass eels and elvers with checks and the mean number of checks within the otoliths of glass-eels caught at four localities, Tosa Bay off Tosa City, the mouth of the Gokase River, the mouth of the Saigo River and the dam of the Tsuri River were 0% (0), 15.0% (0.2), 51.6% (1.0) and 100.0% (4.2), respectively. The Sr/Ca ratios and Sr content peaked in the region where checks were formed and the values decreased rapidly towards the edge of the checks; on the other hand, these decreased gradually in the otolith when checks were not formed. These checks were estimated to be formed by stress when the glass-eels were affected by ambient fresh water within the river. The innermost check was called the freshwater mark in the present study and this mark may be useful as a benchmark in studying the growth history of the eel before and after entering freshwater.     

Note on <Emphasis Type="Italic">Cordyceps brongniartii</Emphasis> Shimazu collected from the wild in Japan

We collected Cordyceps brongniartii from the wild associated with coleopteran larvae for the first time in Japan. Morphological comparisons of C. brongniartii with the type specimen showed slight morphological difference, whereas it showed considerable differences from those collected in the wild in China. PCR-RFLP and ITS sequence analyses corroborated the teleomorph–anamorph relationship between C. brongniartii and Beauveria brongniartii.     

Anatomical observation of polyphenol changes in epidermal cells during the development of <Emphasis Type=Italic>Quercus acutissima</Emphasis>–<Emphasis Type=Italic>Scleroderma verrucosum</Emphasis> ectomycorrhizae

Quercus acutissima seedlings were cultivated in growth pouches and inoculated with Scleroderma verrucosum in order to assess the changes in polyphenol contents in epidermal cells during ECM development. Semithin sections stained with metachromatic Toluidine Blue O (TBO) were compared among non-inoculated lateral roots, early mantled lateral roots, and mycorrhizal roots with a mature mantle. Hyphae adhered closely or were embedded in mucilage-like materials on the epidermis. Epidermal cells and root hairs of the non-inoculated second-order lateral roots developing from the taproot harbored polyphenolic compounds that were stained by TBO. At non-inoculated stage, the average numbers of epidermal cells stained entirely (PC2), stained partially (PC1) or remaining unstained (PC0) were 16.5 ± 0.7, 0 ± 0, and 0 ± 0, respectively. At the early mantled stage, the numbers were 6.5 ± 1.6, 5.2 ± 1.4, and 4.2 ± 1.0, and at the mycorrhizal stage, it was 0 ± 0, 0 ± 0, and 32.8 ± 1.3 for PC2, PC1, and PC0, respectively. Total phenolic content in the root tips at each developmental stage declined with ECM development. The early mantled stage involved a dynamic process of polyphenol localization. However, some epidermal cells and endodermal cells of the proximal zone accumulated polyphenols. Eventually, polyphenolic compounds, which were found abundantly in the epidermal cells and root hairs of the non-inoculated lateral roots of the host, disappeared at the mycorrhization process with the symbiont.