GSE63585
Alternanthera philoxeroides Transcriptome or Gene expression
Research conducted, including the rationale: Alligatorweed is an invasive perennial primarily aquatic weed that can also grow terrestrially and thus has potential to become problematic in agricultural settings. It is invasive on at least three continents. Despite its invasiveness, less than 100 genes have been sequenced from this species. Alligatorweed has recently increased its range northwards in China, and it is unknown if the range expansion has a genetic or epigenetic basis. We have used a next generation RNA sequencing approach to examine gene expression in a three individuals from the northern edge of its range and from the central portion of its range in China to look for different responses to cold temperatures using a common garden approach. We identified numerous differences in gene expression associated with the cold response between these two populations. Gene set and sub-network enrichment analysis indicated differences in the response of photosynthetic processes and oxidative stress responses were different between the two populations. However, alterations in genes controlling the C-REPEAT/DRE BINDING FACTOR (CBF) regulon were not indicated. Additionally, we assembled over 75,000 genes of which over 65,000 had long open reading frames with similarity to sequences from arabidopsis. Single nucleotide polymorphisms unique to the northern and southern individuals were identified, and several of these were in genes such as RESPONSIVE TO DEHYDRATION 21 that could impact the cold response of the plants. Overall design: Samples were collected from cold-treated plants from each populations  (The "central" populations collected in Shanghai and "Northern" population collected in Jinan,Shandong in China) with three biological replicates from each population.