In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental and genetic factors. To gain insights into this specialized reproductive development program we used short- and long-read RNA-sequencing (RNA-seq) to study the temporal dynamics of transcript abundance in immuno-cytologically staged barley (Hordeum vulgare) anthers and meiocytes. We show that the most significant transcriptional changes in anthers occur at the transition from pre-meiosis to leptotene–zygotene, which is followed by increasingly stable transcript abundance throughout prophase I into metaphase I–tetrad. Our analysis reveals that the pre-meiotic anthers are enriched in long non-coding RNAs (lncRNAs) and that entry to meiosis is characterized by their robust and significant down regulation. Intriguingly, only 24% of a collection of putative meiotic gene orthologs showed differential transcript abundance in at least one stage or tissue comparison. Argonautes, E3 ubiquitin ligases, and lys48 specific de-ubiquitinating enzymes were enriched in prophase I meiocyte samples. These developmental, time-resolved transcriptomes demonstrate remarkable stability in transcript abundance in meiocytes throughout prophase I after the initial and substantial reprogramming at meiosis entry and the complexity of the regulatory networks involved in early meiotic processes.

In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental and genetic factors. To gain insights into this specialised reproductive development programme we used short- and long-read RNA-sequencing (RNA-seq) to study the temporal dynamics of transcript abundance in immuno-cytologically staged barley (Hordeum vulgare) anthers and meiocytes. We show that the most significant transcriptional changes occur at the transition from pre-meiosis to leptotene–zygotene, which is followed by largely stable transcript abundance throughout prophase I. Our analysis reveals that the developing anthers and meiocytes are enriched in long non-coding RNAs (lncRNAs) and that entry to meiosis is characterized by their robust and significant down regulation. Intriguingly, only 24% of a collection of putative meiotic gene orthologues showed differential transcript abundance in at least one stage or tissue comparison. Changes in the abundance of numerous transcription factors, representatives of the small RNA processing machinery, and post-translational modification pathways highlight the complexity of the regulatory networks involved. These developmental, time-resolved, and dynamic transcriptomes increase our understanding of anther and meiocyte development and will help guide future research.One sentence summaryAnalysis of RNA-seq data from meiotically staged barley anthers and meiocytes highlights the role of lncRNAs within a complex network of transcriptional and post-transcriptional regulation accompanied by a hiatus in differential gene expression during prophase I.The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Robbie Waugh (robbie.waugh@hutton.ac.uk)

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12Pasteuria penetrans is a gram-positive endospore forming bacterial parasite of Meloidogyne spp. the 13 most economically damaging genus of plant parasitic nematodes globally. The obligate antagonistic 14 nature of P. penetrans makes it an attractive candidate biological control agent. However, deployment 15 of P. penetrans for this purpose is inhibited by a lack of understanding of its metabolism and the 16 molecular mechanics underpinning parasitism of the host, in particular the initial attachment of the 17 endospore to the nematode cuticle. Several attempts to assemble the genomes of species within this 18 genus have been unsuccessful. Primarily this is due to the obligate parasitic nature of the bacterium 19which makes obtaining genomic DNA of sufficient quantity and quality which is free from 20 contamination challenging. Taking advantage of recent developments in whole genome amplification, 21 long read sequencing platforms, and assembly algorithms, we have developed a protocol to generate 22 large quantities of high molecular weight genomic DNA from a small number of purified endospores. 23We demonstrate this method via genomic assembly of P. penetrans. This assembly reveals a reduced 24 genome of 2.64Mbp estimated to represent 86% of the complete sequence; its reduced metabolism 25 reflects widespread reliance on the host and possibly associated organisms. Additionally, apparent 26 expansion of transposases and prediction of partial competence pathways suggest a high degree of 27 genomic plasticity. Phylogenetic analysis places our sequence within the Bacilli, and most closely 28 related to Thermoactinomyces species. Seventeen predicted BclA-like proteins are identified which 29 may be involved in the determination of attachment specificity. This resource may be used to develop 30 in vitro culture methods and to investigate the genetic and molecular basis of attachment specificity. 31 32 33

A system to grow tomato plants infected by Meloidogyne javanica under constant temperatures of 18, 21, 24, 27 and 30°C was developed and used to assess how temperature and the application of the biological control bacterium Pasteuria penetrans affected plant growth, the nematode population and endospore production. Each plant was inoculated with 300 second-stage juveniles (J2) with four or five spores of P. penetrans attached to their cuticles or with 300 nematodes without P. penetrans. Increasing soil temperature increased tomato growth, the number of endospores per female, and the number of galls of M. javanica at the end of 38 days. Increasing temperatures up to 27°C also increased the number of egg masses produced by M. javanica. Presence of P. penetrans reduced the numbers of galls and egg masses at all temperatures by up to 52.2% and 61.4% at 27 and 30°C, respectively. Pasteuria penetrans reduced the M. javanica population even at soil temperatures of 18 and 21°C. However, temperatures of 27 and 30°C enhanced nematode control and the production of P. penetrans endospores is faster. The system developed in this work is simple and efficient for growing plants under constant temperatures and can be used for different purposes.

A culture collection of 41 bacteria isolated from the rhizosphere of cultivated barley (Hordeum vulgare L. ssp. vulgare) was produced and is archived at Plant Sciences, University of Dundee (UK). Associated data include information regarding genes implicated in nitrogen fixation, hydrogen cyanide channels and phosphate solubilisation, and whole genome sequences

Flowering plants reproduce sexually by combining a haploid male and female gametophyte during fertilization. Male gametophytes are localized in the anthers, each containing reproductive (meiocyte) and non-reproductive tissue necessary for anther development and maturation. Meiosis, where chromosomes pair and exchange their genetic material during a process called recombination, is one of the most important and sensitive stages in breeding, ensuring genetic diversity. Most anther development studies have focussed on transcript variation, but very few have been correlated with protein abundance. Taking advantage of a recently published barley anther transcriptomic dataset (BAnTr) and a newly developed sensitive mass spectrometry-based approach to analyse barley anther proteome, we conducted high-resolution mass spectrometry analysis of barley anthers, collected at 6 time points and representing their development from pre-meiosis to metaphase. Each time point was carefully staged using immunocytology, providing a robust and accurate staging mirroring our previous transcriptomic dataset (BAnTr). We identified more than 6,100 non-redundant proteins including 82 known and putative meiotic proteins. Although the protein abundance was relatively stable throughout prophase I, we were able to quantify the dynamic variation of 336 proteins. We present the first quantitative comparative proteomics study of barley anther development during meiotic prophase I when the important process of homologous recombination is taking place.

Pasteuria spp. are endospore forming bacteria which act as natural antagonists to many of the most economically significant plant parasitic nematodes (PPNs). Highly speciesspecific nematode suppression may be observed in soils containing a sufficiently high density of Pasteuria spp. spores. This suppression is enacted by the bacteria via inhibition of root invasion and sterilization of the nematode host. Molecular methods for the detection of Pasteuria spp. from environmental DNA (eDNA) have been described; however, these methods are limited in both scale and in depth. We report the use of small subunit rRNA gene metabarcoding to profile Pasteuria spp. and nematode communities in parallel. We have investigated Pasteuria spp. population structure in Scottish soils using eDNA from two sources: soil extracted DNA from the second National Soil Inventory of Scotland (NSIS2); and nematode extracted DNA collected from farms in the East Scotland Farm Network (ESFN). We compared the Pasteuria spp. community culture to both nematode community structure and the physiochemical properties of soils. Our results indicate that Pasteuria spp. populations in Scottish soils are broadly dominated by two sequence variants. The first of these aligns with high identity to Pasteuria hartismeri, a species first described parasitizing Meloidogyne ardenensis, a nematode parasite of woody and perennial plants in northern Europe. The second aligns with a Pasteuria-like sequence which was first recovered from a farm near Edinburgh which was found to contain bacterial feeding nematodes and Pratylenchus spp. encumbered by Pasteuria spp. endospores. Further, soil carbon, moisture, bulk density, and pH showed a strong correlation with the Pasteuria spp. community composition. These results indicate that metabarcoding is appropriate for the sensitive, specific, and semi-quantitative profiling of Pasteuria species from eDNA.