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: DNA methylation has been considered a stable epigenetic mark but may respond to fluctuating environments. However, it is unclear how they behave in natural environments. Here, we analyzed seasonal patterns of genome-wide DNA methylation in a single clone from a natural population of the perennial Arabidopsis halleri . The genome-wide pattern of DNA methylation was primarily stable, and most of the repetitive regions were methylated across the year. Although the proportion was small, we detected seasonally methylated cytosines (SeMCs) in the genome. SeMCs in the CHH context were detected predominantly at repetitive sequences in intergenic regions. In contrast, gene-body CG methylation (gbM) itself was generally stable across seasons, but the levels of gbM were positively associated with seasonal stability of RNA expression of the genes. These results suggest the existence of two distinct aspects of DNA methylation in natural environments: sources of epigenetic variation and epigenetic marks for stable gene expression., Competing Interests: The authors declare that they have no conflicts of interests.

Seasonal developmental plasticity, which consists of season-dependent alternations of developmental processes, has evolved to produce optimal phenotypes depending on specific periods in a year. For example, many phenological events in plants, such as flowering, fruiting, bud blast, bud formation, and growth cessation, are often controlled seasonally. Although temperature and photoperiod are the two major seasonal cues for such responses, the importance of phase lag between annual oscillations of the two signals has been unexplored, despite its universal nature in the context of seasonal environments. In this article, the phase-lag calendar hypothesis (New Phytologist, 210, 2016, 399), especially the one between temperature and photoperiod, is explained using meteorological data obtained from central Japan as an example. We set forth to show how, for a narrow window in time of a couple of weeks in a year, simple threshold responses to these two signals that differ in annual oscillation phases are enough to make developmental plasticity to be expressed as phenological events. The properties of the underlying mechanisms of the events in different seasons are further predicted, and the responses are compared with reported empirical examples. Because many organisms have evolved under the phase lag between photoperiod and temperature, the developmental plasticity in response to the phase lag should be evaluated for diverse organisms., (© 2018 Japanese Society of Developmental Biologists.)

Sequencing of RNA by next generation sequencers, RNA-Seq, is revolutionizing virus detection. In addition to the unbiased detection of various viruses from wild plants in natural environments, RNA-Seq also allows for the parallel collection of host plant transcriptome data. Host transcriptome data are highly valuable for studying the responses of hosts to viral infections, as well as viral host manipulation. When detecting viruses using RNA-Seq, it is critical to choose appropriate methods for the removal of rRNA from total RNA. Although viruses with polyadenylated genomes can be detected by RNA-Seq following mRNA purification using oligo-dT beads, viruses with non-polyadenylated genomes are not effectively detected. However, such viruses can be detected by RNA-Seq using the rRNA selective depression method. The high-throughput and cost-effective method of RNA-Seq library preparation which is described here allows us to detect a broad range of viruses in wild plants.

Background: It is essential to understand and predict the effects of changing environments on plants. This review focuses on the sexual reproduction of plants, as previous studies have suggested that this trait is particularly vulnerable to climate change, and because a number of ecologically and evolutionarily relevant genes have been identified., Scope: It is proposed that studying gene functions in naturally fluctuating conditions, or gene functions in natura, is important to predict responses to changing environments. First, we discuss flowering time, an extensively studied example of phenotypic plasticity. The quantitative approaches of ecological and evolutionary systems biology have been used to analyse the expression of a key flowering gene, FLC, of Arabidopsis halleri in naturally fluctuating environments. Modelling showed that FLC acts as a quantitative tracer of the temperature over the preceding 6 weeks. The predictions of this model were verified experimentally, confirming its applicability to future climate changes. Second, the evolution of self-compatibility as exemplifying an evolutionary response is discussed. Evolutionary genomic and functional analyses have indicated that A. thaliana became self-compatible via a loss-of-function mutation in the male specificity gene, SCR/SP11. Self-compatibility evolved during glacial-interglacial cycles, suggesting its association with mate limitation during migration. Although the evolution of self-compatibility may confer short-term advantages, it is predicted to increase the risk of extinction in the long term because loss-of-function mutations are virtually irreversible., Conclusions: Recent studies of FLC and SCR have identified gene functions in natura that are unlikely to be found in laboratory experiments. The significance of epigenetic changes and the study of non-model species with next-generation DNA sequencers is also discussed.

Understanding the genetic bases of local adaptation in dominant conifer species is critical in predicting the impacts of rapid climate change on forest ecosystems. However, the genetic basis of adaptation is not yet fully understood due to the huge and complex genomes of conifers and the unavailability to date of suitable crossing material. In this study, we constructed a linkage map for Abies sachalinensis (2 n = 24) and investigated quantitative trait loci (QTLs) associated with local adaptation along an altitudinal gradient. A segregating population of 239 seedlings was produced from a cross between two F hybrids (high-altitude × low-altitude genotypes). QTL mapping of phenological and growth traits was performed using a pseudo-testcross strategy with linkage maps based on 1251 single-nucleotide polymorphism (SNP) and three simple sequence repeat (SSR) markers. Two maps consisting of 12 linkage groups with an average marker interval of ca. 3 cM were constructed for each parent. The total lengths of the maps were 1861 and 1949 cM. A permutation test identified four significant QTLs and 11 additional suggestive QTLs, with high logarithm of odds (LOD) scores (> 3.0). This is the first highly saturated linkage map produced for Abies taxa. Our results suggest that spring bud phenology is controlled by several QTLs with moderate effects. The use of the mapping population created by crossing two hybrids (high × low altitude genotypes) and numerous SNP markers enabled us to investigate the genetic basis of adaptive traits in conifer species. [ABSTRACT FROM AUTHOR]

Pelargonium zonate spot virus (PZSV) was identified from two wild Brassicaceae plant species, Arabidopsis halleri and Rorippa indica, in central Japan using RNA-Seq and RT-PCR. The deduced amino acid sequences of RNA-dependent RNA polymerase and coat protein were highly similar to those of previously reported PZSV isolates, with 96.6-98.2% and 93.7-98.0% identity, respectively. Mechanical inoculation revealed the pathogenicity of the PZSV isolate to Nicotiana benthamiana and Brassica oleracea. To the best of our knowledge, this is the first report of PZSV from Japan. [ABSTRACT FROM AUTHOR]

Frequency-dependent prey choice by natural enemies may influence the coexistence of multiple prey types, but little is known about whether frequency-dependent foraging choice occurs in herbivory on plants showing resistance polymorphism within a single population. Here we examined frequency-dependent foraging by a crucifer-feeding leaf beetle, Phaedon brassicae, on trichome-producing (hairy) and trichomeless (glabrous) plants coexisting within a natural population of the perennial herb Arabidopsis halleri subsp. gemmifera. Larvae of P. brassicae fed on hairy leaves showed slower growth than those fed on glabrous leaves. Although adult beetles consumed similar amounts of leaves when they were fed either hairy or glabrous leaves in no-choice conditions, our choice experiment showed that adult beetles fed at less than the proportionally expected level on hairy leaves compared to glabrous leaves when the hairy leaves were less or equally abundant. Both types of leaves were consumed at the proportionally expected levels when the hairy leaves were more abundant than the glabrous leaves. In a natural population, the leaf damage on the hairy plants was negatively correlated with the local proportion of the glabrous plants in a 1-m diameter patch across 2 years, while correlations between the leaf damage on the glabrous plants and their proportion differed between the 2 years. Additionally, we found five glucosinolates in leaves of A. halleri, but their accumulation did not differ between hairy and glabrous plants. Our experimental results indicate that hairy plants incur less herbivory by P. brassicae when glabrous plants are abundant. The field pattern provides evidence suggestive of frequency-dependent herbivory acting on hairy plants. The present study highlights one of the putative mechanisms of maintaining plant resistance polymorphism. [ABSTRACT FROM AUTHOR]