Gene Expression Reaction Norms Unravel the Molecular and Cellular Processes Underpinning the Plastic Phenotypes of Alternanthera Philoxeroides in Contrasting Hydrological Conditions

Abstract

Alternanthera philoxeroides is an amphibious invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation. Little is known about the molecular basis underlying environment-induced phenotypic changes. Variation in transcript abundance in A. philoxeroides was characterized throughout the time-courses of pond and upland treatments using RNA-Sequencing. Seven thousand eight hundred and five genes demonstrated variable expression in response to different treatments, forming 11 transcriptionally coordinated gene groups. Functional enrichment analysis of plastically expressed genes revealed pathway changes in hormone-mediated signaling, osmotic adjustment, cell wall remodeling, and programmed cell death, providing a mechanistic understanding of the biological processes underlying the phenotypic changes in A. philoxeroides. Both transcriptional modulation of environmentally sensitive loci and environmentally dependent control of regulatory loci influenced the plastic responses to the environment. Phenotypic responses and gene expression patterns to contrasting hydrological conditions were compared between A. philoxeroides and its alien congener Alternanthera pungens. The terricolous A. pungens displayed limited phenotypic plasticity to different treatments. It was postulated based on gene expression comparison that the interspecific variation in plasticity between A. philoxeroides and A. pungens was not due to environmentally-mediated changes in hormone levels but to variations in the type and relative abundance of different signal transducers and receptors expressed in the target tissue.

Allelopathic Effects of Aqueous Extracts of Alternanthera philoxeroides on the Growth of Zoysia matrella

“…Biological invasions can severely affect indigenous biological diversity, natural resources [2], and even global ecosystem balance [3][4], as the invasive species are often more competitive than the native species. Alternanthera philoxeroides, a perennial invasive aquatic plant, can rapidly outcompete indigenous species and occupy their aquatic or terrestrial niche to become the dominant species [5]. The country of origin of A. philoxeroides is Brazil.…”

Analysis of the Role of the Drought-Induced Gene DRI15 and Salinity-Induced Gene SI1 in Alternanthera philoxeroides Plasticity Using a Virus-Based Gene Silencing Tool

“…Alternanthera philoxeroides is a notoriously invasive weed, and is difficult to prevent from its damages ( Sainty et al, 1998 ; Pan et al, 2006 ; Fan et al, 2013 ). To date, the researches in the underlying molecular mechanisms of A. philoxeroides , exclude taxonomy and ecology and the integrated management is only limited to analyses of genome-wide DNA methylation and gene expression ( Gao et al, 2010 , 2015 ), due to insufficient molecular approaches. In this study, we successfully developed a simple and highly effective method in A. philoxeroides , the pgR107 VIGS system, using the ApPDS marker gene.…”

Differentially Expressed microRNAs and Target Genes Associated with Plastic Internode Elongation in Alternanthera philoxeroides in Contrasting Hydrological Habitats

“…In the pond treatment, the potted plants were completely submerged in a series of plastic tanks containing tap water to a depth of 50 cm. Plants were supplied with 1 L water per day in the upland treatment and the soil was kept well-drained ( Gao et al, 2015 ). The length and diameter of the fifth internode from top of 10 individuals were measured under each treatment, at 0, 1, 3, 6, 12, and 120 h from the start of treatments.…”

“…Clean reads that could not be assigned to the aforementioned RNA classes were used to predict potential novel microRNAs in A. philoxeroides . Due to the non-availability of the genome sequence of A. philoxeroides , the transcriptome of A. philoxeroides ( Gao et al, 2015 ) was used to predict novel microRNAs. MIREAP 4 was used to examine the hairpin structure, the Dicer cleavage site and the minimum free energy of candidate sequences according to the following parameters: (i) minimal microRNA reference sequence length of 20 nt and maximal microRNA reference sequence length of 24 nt; (ii) maximal copy number of microRNAs on the reference was 20; (iii) maximal free energy allowed for a microRNA precursor was -18 kcal/mol; (iv) maximal space between the microRNA and microRNA ∗ was 300 nt; (v) minimal base pairs of microRNA and microRNA ∗ was 16; (vi) maximal bulge of microRNA and microRNA ∗ was 4; (vii) maximal asymmetry of the microRNA/microRNA ∗ duplex was 4; and (viii) flank sequence length of microRNA precursor was 20.…”

“…The genetically identical but phenotypically distinct plants of A. philoxeroides provide a suitable model for us to rule out genetic contributions to observed differences, to explore the correlations between environmental stimuli, epigenetic modification and phenotypic variation. Previously, we have investigated the gene expression reaction norms of A. philoxeroides in contrasting hydrological conditions, and identified 11 transcriptionally coordinated gene groups associated with environment-induced phenotypic variation in A. philoxeroides ( Gao et al, 2015 ). We have also examined genome-wide DNA methylation patterns of A. philoxeroides in natural and manipulated habitats, and found that plants of different source populations not only underwent significant morphological changes in common garden environments, but also underwent genome-wide DNA methylation alterations in response to different water treatments, demonstrating a correlation between epigenetic reprogramming and the reversible phenotypic response of A. philoxeroides to particular environmental factors ( Gao et al, 2010 ; Deng et al, 2014 ).…”