Skip to main content
ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Sunflower and Plant Biology Research » Research » Publications at this Location » Publication #313477

Title: RNA Sequencing Characterizes Transcriptomes Differences in Cold Response Between Northern and Southern Alternanthera philoxeroides and Highlight Adaptations Associated With Northward Expansion

item LIU, DASHENG - Shandong Institute
item Horvath, David
item MANDADI, KRANTHI - Texas A&M University
item LI, PENG - Shandong Institute
item LIU, WENMING - Shandong University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/9/2019
Publication Date: 1/28/2019
Citation: Liu, D., Horvath, D., Li, P., Liu, W. 2019. RNA sequencing characterizes transcriptomes differences in cold response between northern and southern Alternanthera philoxeroides and highlight adaptations associated with northward expansion. Frontiers in Plant Science. 10:24.

Interpretive Summary: Alligatorweed is an invasive weed in many parts of the world and can negatively impact navigation and flooding potential in the waterways it infests including the US. Very few genes from alligatorweed have been sequenced, making it difficult to identify genes that could help explain why it is so invasive. Recently, alligator weed was found nearly 5 degrees in latitude north of its predicted northern limit in China. We used new sequencing technologies to investigate differences in how individuals from these northward-expanding populations differed from individuals in the central established range of this weed in China. Not only did this work provide sequences for tens of thousands of genes from this invasive weed, but it also provided insights into how genetic adaptations to cold have allowed it to spread northward. Specifically, we determined that genetic changes resulted in repression of photosynthesis in the cold – thus likely preventing damage caused by oxidative stress might be responsible for adaptation of the northern individuals that has allowed their northward expansion. Additionally, we identified a small number of mutations, one of which is in a gene known to control the response of plants to cold environments, to be present in all of the northern individuals, but to be absent in all of the southern individuals.

Technical Abstract: Invasive plant, alligatorweed has recently increased its range northwards in China, and it is unknown if the range expansion has a genetic or epigenetic basis. It is invasive on at least three continents. Despite its world-wide invasiveness, less than 100 genes have been sequenced from this species and made publicly available. We have used a next generation RNA sequencing approach to examine gene expression in 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 via a common garden method. Our study presents the first transcription sequence for alligatorweed. 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. We also 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 and we relate these differences to cold adaptation. However, alterations in genes controlling the C-REPEAT/DRE BINDING FACTOR (CBF) regulon were not indicated.