Molecular Mechanisms Underlying Phenotypically Plastic Variation And Adaptation In Alternanthera Philoxeroides

Alligator weed (Alternanthera philoxeroides (Mart.) Griseb.) is an invasive weed in China, which is native to South America but has now invaded almost all temperate and tropical areas of the world, including most provinces of South China. Alligator weed can exploit both aquatic and terrestrial habitats in the introduced region. Individuals growing in different habitats exhibit extensive ecophysiological and morphological distinctions, but show very little genetic variation within and among populations. It has thus been proposed that phenotypic plasticity, rather than the existence of locally adapted ecotypes, allows the invasive alligator weed to colonize a wide range of habitats with different water availability. However, the mechanisms underpinning the wide range of phenotypic variation and rapid adaptation to changing environments remain uncharacterized.Integrative approaches involving field survey, common garden experiments, transcriptome profiling, and genome-wide DNA methylation analysis were conducted in this study to investigate the possible molecular mechanisms involved in plastic variation in phenotypes, and to identify the complex relationships existing between the mechanisms that produce variable morphological, physiological and behavioral traits during development, as well as the adaptive significance of phenotypic plasticity in ecological contexts. The main results are as follows:1) A large-scale functional genomic dataset of alligator weed was generated using the high-throughput next-generation sequencing technology and de novo assembly methods. Approximate55.15million reads were obtained, trimmed, and assembled into144,082unigenes, with an average length of346bp and an N50of552bp. Sequence similarity analyses against different public databases found39,589unigenes that could be annotated with gene descriptions, conserved protein domains, or gene ontology terms.7,296unigenes were assigned to putative metabolic pathways. This database provides extensive coverage of genes and major metabolic pathways involved in vegetative growth of alligator weed, and can serve as an important public information platform for gene expression and functional genomic studies in alligator weed.2) Ecological genetic analyses based on DNA fingerprint and common garden experiments indicated nearly no genetic differentiation among populations from different habitats, which is consistent with the dominance of asexual reproduction in alligator weed. Instead, alligator weed showed notable phenotypic plasticity in a collection of functional traits, including storage root allocation, stem diameter, stem pith cavity, and internode length. Transcriptome profiling provided convincing evidence that phenotypic variations of alligator weed mostly took place by altering gene expression and eventually altering ontogenetic trajectory in response to environmental changes, with7803unigenes displaying altered patterns of expression at different time points of aquatic and upland treatments. The functional distribution of differentially expressed genes included reactive oxygen species metabolism, signaling, cell wall modification and carbohydrate metabolism. Genes associated with aerenchyma formation, stem internode elongation and adventitious root development were significantly up-regulated by pond treatment. Genes related to cell wall thicking, secondary cell wall biogenesis, and osmotic solute biosynthesis showed a significant ’up-down’ pattern of expression with the expression levels peaking at3h after aquatic treatment and dropping quickly thereafter.3) Genome-wide methylation profiling using methylationsensitive amplified fragment length polymorphism (MSAP) revealed considerable DNA methylation polymorphisms within and between natural populations. Plants of different source populations not only underwent significant morphological changes in common garden environments, but also underwent a genome-wide epigenetic reprogramming in response to different treatments. Plants raised in the same common garden, no matter whether they came from aquatic or upland habitats, exhibited a high level of DNA methylation similarity, demonstrating the environmental sensitivity and flexibility of the epigenetic regulatory system. This research not only provided evidence of the correlation between epigenetic reprogramming and the reversible phenotypic response of alligator weed to particular environmental factors, but might also help explain why genetically identical organisms can have dramatically different phenotypes in different environments.4) Comparative analyses of variation in morphological traits, osmotic potential, and the expression pattern of ESK1, CESA8and MS1between alligator weed and its native congener (A. sessilis), as well as the alien congener(A. pungens), revealed that alligator weed not only exhibits greater phenotypic plasticity than A. sessilis and A. pungens, but also possesses a more effective mechanism for osmotic adjustment. The expression level of genes involved in cell wall thicking, secondary cell wall biogenesis, and osmotic solute biosynthesis displayed a consistent variation tendency with the cellular osmotic potential, suggesting the potential role of these genes in the adjustment of water potential and turgor pressure.Living organisms have developed various strategies to adapt to environmental changes. In contrast to the long-term strategy of generating new traits by selection, phenotypically plastic variation provides an efficient short-term strategy for organisms living in changing environments to sense their environment and to respond to it rapidly and flexibly. The results of this study provided evidence that, although cued by the external environment, most phenotypically plastic responses of alligator weed are mediated by alterations in the internal environment via concomitant changes in gene expression and interaction. Information on how gene expression is regulated in response to environmental change would thus provide clues to the molecular mechanisms underlying phenotypic alteration in response to environmental stimuli. Epigenetic modifications provide a plausible mechanism for the putative link between environmental variation and alterations in gene expression. Studying epigenetic complexes in the real environment would allow us not only to get greater insights into the molecular mechanisms underlying phenotypic plasticity, but also to establish an integrated understanding of the molecular machinery that interfaces the genotype and the environment.