FLIP: FLuorescence Imaging Pipeline for field-based chlorophyll fluorescence images

Photosynthesis is one of the most important biological reactions on earth providing oxygen and food for humanity. As global populations rise and arable land decreases, crops need to become more efficient at photosynthetic processes, particularly utilizing absorbed light energy. Chlorophyll fluorescence imaging is a rapid, non-destructive measurement that can provide information on the efficiency of the light-dependent reactions and carbon reactions of photosynthesis. Over the years chlorophyll fluorescence imaging systems have been developed and improved to capture two critical measurements: minimum fluorescence (F0) and maximum fluorescence (FM). These systems have primarily been utilized in controlled chamber or greenhouse settings focused at the single leaf or small plant level. To improve plant photosynthesis, fluorescence imaging data needs to be obtained from field-grown plants to capture canopy spatial effects. Previously developed software to extract F0 and FM from controlled, leaf level images do not capture the complexity of the light-dependent reactions from field-grown plants. New software is needed that accounts for the canopy spatial effects from images of field-grown plants. FLIP: fluorescence imaging pipeline, was designed specifically for the TERR-REF field scanalyzer located at the University of Arizona's Maricopa Agricultural Center located in Maricopa, Arizona but could be adapted for other field deployed fluorescence imaging systems. FLIP utilizes open source tools to convert binary images, apply a multi-threshold to extract the fluorescence data from the plant canopy, calculate photosynthetic efficiency, and assign those values to the appropriate experimental plot. © 2021Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

The <em>Spirodela polyrhiza</em> genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle.

The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Here we select Spirodela polyrhiza for whole-genome sequencing. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications

Genome sequencing and analysis of the model grass Brachypodium distachyon

Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops