Persistent infection, wherein a pathogen is continually present in a host individual, is widespread in virus-host systems. However, little is known regarding how seasonal environments alter virus-host interaction during such metastability. We observed a lineage-to-lineage infection of the host plant Arabidopsis halleri with Turnip mosaic virus for 3 years without severe damage. Virus dynamics and virus-host interactions within hosts were highly season dependent. Virus accumulation in the newly formed leaves was temperature dependent and was suppressed during winter. Transcriptome analyses suggested that distinct defence mechanisms, i.e. salicylic acid (SA)-dependent resistance and RNA silencing, were predominant during spring and autumn, respectively. Transcriptomic difference between infected and uninfected plants other than defence genes appeared transiently only during autumn in upper leaves. However, the virus preserved in the lower leaves is transferred to the clonal offspring of the host plants during spring. In the linage-to-linage infection of the A. halleri-TuMV system, both host clonal reproduction and virus transmission into new clonal rosettes are secured during the winter-spring transition. How virus and host overwinter turned out to be critical for understanding a long-term virus-host interaction within hosts under temperate climates, and more generally, understanding seasonality provides new insight into ecology of plant viruses.

Scaevola taccada is characterized by dimorphic fruits, with one type having cork and pulp (C-morph) and the other type having only pulp (NC-morph). Although within-individual dimorphism has not been observed, both morphs can occur at the same sites. The cork floats on seawater, and the pulp is eaten by birds. Thus, the morphs may have different seed dispersal abilities, via sea currents and birds, respectively. This study aimed to determine the functional characteristics of the dimorphic fruits. First, the potential seed dispersal ability of sea currents and birds was compared between the two fruits morphs by conducting a floating test and by measuring the proportions of different parts of the fruits, respectively. Next, the frequencies of the two morphs across different substrates (beaches, rocks, and cliffs) in the southern islands around Japan were analyzed. Most C-morph fruits remained floating for more than 180 days in a seawater tank, whereas all NC-morph fruits sank after approximately 1 week. The NC-morph fruits had a more pulp volume and less indigestible material than the C-morph fruits. Although both types of plants were found on many islands and all substrates, the C-morph was dominant on beaches, whereas the NC-morph was most frequent on cliffs. The frequencies of the morphs on different substrates might be influenced by the differences in their seed dispersal abilities. The two morphs may differ in fitness on different substrates. These findings improve our understanding of plant adaptations for dispersal.

: 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.