The pineapple genome and the evolution of CAM photosynthesis

Abstract

Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water use efficiency, and the second most important tropical fruit after banana in terms of international trade. We sequenced the genomes of pineapple varieties ‘F153’ and ‘MD2’, and a wild pineapple relative A. bracteatus accession CB5. The pineapple genome has one fewer ancient whole genome duplications than sequenced grass genomes and, therefore, provides an important reference for elucidating gene content and structure in the last common ancestor of extant members of the grass family (Poaceae). Pineapple has a conserved karyotype with seven pre rho duplication chromosomes that are ancestral to extant grass karyotypes. The pineapple lineage has transitioned from C3 photosynthesis to CAM with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues using beta-carbonic anhydrase (βCA) for initial capture of CO2. Promoter regions of all three βCA genes contain a CCA1 binding site that can bind circadian core oscillators. CAM pathway genes were enriched with cis-regulatory elements including the morning (CCACAC) and evening (AAAATATC) elements associated with regulation of circadian-clock genes, providing the first link between CAM and the circadian clock regulation. Gene-interaction network analysis revealed both activation and repression of regulatory elements that control key enzymes in CAM photosynthesis, indicating that CAM evolved by reconfiguration of pathways preexisting in C3 plants. Pineapple CAM photosynthesis is the result of regulatory neofunctionalization of preexisting gene copies and not acquisition of neofunctionalized genes via whole genome or tandem gene duplication.

The Genome of a Southern Hemisphere Seagrass Species (Zostera muelleri)

“…3; Supplemental Figs. S1 and S2), consistent with recent observations (Ming et al, 2015). These results support that Tau occurred after the divergence of the Alismatales from the main monocot lineage, consistent with a previous study, and that the existing age estimation needs to be investigated further.…”

Phosphorylation of Phosphoenolpyruvate Carboxylase Is Essential for Maximal and Sustained Dark CO2 Fixation and Core Circadian Clock Operation in the Obligate Crassulacean Acid Metabolism Species Kalanchoë fedtschenkoi

“…Based on our currently incomplete understanding of the molecular-genetic blueprint for CAM (Hartwell et al, 2016), C 3 species are believed to possess ancestral copies of all of the genes required for CAM (Cushman and Bohnert, 1999;Aubry et al, 2011;Ming et al, 2015). In principle, for CAM to evolve from the C 3 ancestral state in a leaf succulent CAM species such as Kalanchoë fedtschenkoi, the corresponding metabolic enzymes, metabolite transporters, and their cognate regulatory proteins must increase in abundance in leaf mesophyll cells and come under tight temporal control such that certain metabolic steps are confined to the dark period, and others are confined to the light (Cushman and Bohnert, 1999;Borland et al, 2009;Abraham et al, 2016;Brilhaus et al, 2016;Hartwell et al, 2016).…”

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

“…For simplicity, TEs other than LTR-RT, including both non-LTR-RTs and DNA transposons, are called non-LTR in this study. In plants, LTR-RTs contribute significantly to genome size expansion due to their high copy number and large size (Rensing et al, 2008;Schnable et al, 2009;Nystedt et al, 2013;Ming et al, 2015). For example, retrotransposons contribute to approximately 75% of the size of the maize (Zea mays) genome (Schnable et al, 2009).…”