Predicting photosynthetic pathway from anatomy using machine learning

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 15, 2023

SUMMARY - Plants with Crassulacean acid metabolism (CAM) have long been associated a specialized anatomy, including succulence and thick photosynthetic tissues. Firm, quantitative boundaries between non-CAM CAM plants yet to be established – if they indeed exist. Using novel computer vision software measure we combined new measurements published data across flowering plants. We then used machine learning phylogenetic comparative methods investigate relationships anatomy. found significant differences in tissue anatomy differing phenotypes. Machine based classification was over 95% accurate differentiating from had 70% recall of distinct Phylogenetic least squares regression threshold analyses revealed that evolution significantly correlated increased mesophyll cell size, thicker leaves, decreased intercellular airspace. Our findings suggest may aid the discovery species evolutionary trajectory strong, obligate requires continual anatomical specialization.

Language: Английский

---

Crassulacean acid metabolism (CAM) at the crossroads: a special issue to honour 50 years of CAM research by Klaus Winter

Annals of Botany, Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 19, 2023

A spectacular feature of the botanical world is succulent flora, which presents a diversity life forms from fascinating to strange (Figs 123).Succulence describes fleshy tissue with high water content, yet as character state highly variable, ranging slightly planar leaves grossly corpulent stems cacti and aloes (Fig. 2; Grace, 2019;Peréz-Lopéz et al., 2023).The associated function also shows marked variation, salt storage, mechanical support and, in majority succulents, storage organic acids used crassulacean acid metabolism (CAM).Succulence hypothesized be essential for CAM photosynthetic pathway because it allows large amounts assimilated carbon form malate, assists process by trapping CO 2 released during day (Males, 2017; Borland 2018;Edwards, 2019).In typical photosynthesis, plants open stomata at night fix inorganic into malic using phosphoenolpyruvate (PEP) carboxylase (see figs 1 Chomthong Griffiths, 2023, this issue explanatory diagrams).The then stored vacuoles.During day, close, decarboxylated raise concentrations within levels that suppress wasteful photorespiration.Rubisco refixes trapped closed stomata, fixation products are synthesized sugars starch same biochemistry C 3 photosynthesis.Because over much transpiration low thus exhibit water-use efficiencies (WUE) photosynthesis.High WUE enables survival dry locations, include arid semi-arid landscapes, soil-less environments such epiphyte habitat on tree branches or lithophyte habit rock faces.CAM abundant well dispersed across world's flora occurring ferns, gymnosperms, monocots eudicots.As examined (Gilman 2023), photosynthesis independently evolved 60 times vascular plants, making one best examples evolutionary convergence complex trait living world.The repeated evolution has resulted hundreds genera close 18 000 species some degree CAM, numerous being recognized iconic

Language: Английский

---

Mesophyll-Specific Circadian Dynamics of CAM Induction in the Ice Plant Unveiled by Single-Cell Transcriptomics

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 8, 2024

Abstract Crassulacean acid metabolism (CAM) is an evolutionary modification of the C3 photosynthetic carbon dioxide fixation pathway used by approximately 7% terrestrial plants to live in drought-prone environments. Facultative CAM species, such as Mesembryanthemum crystallinum (common ice plant), possess unique ability switch from photosynthesis response high-salinity and water-deficit stress. Here we characterized environmentally-triggered transition plant using single nucleus RNA sequencing (snRNA-seq) identify its putative regulators, supported a novel high-quality assembled annotated genome. Analysis snRNA-seq datasets leaves transitioning between collected at dawn dusk revealed substantial transcriptional changes mesophyll cells onset induction. Notably, our findings sub-cell types engaged either or dusk. Cell trajectory inference analysis reconstructed both 24-hour cycles, enabling direct comparison gene expression profiles these pathways. This comparative study uncovered divergent patterns key circadian clock genes cell trajectories, pointing connection regulation

Language: Английский

---

Sequencing complex plants on a budget: The development of Kalanchoë blossfeldiana as a C₃, CAM comparative tool

Plants People Planet, Journal Year: 2024, Volume and Issue: 6(6), P. 1314 - 1328

Published: May 13, 2024

Societal Impact Statement Research efforts in plant biology have often been focused on sequenced and well‐studied ‘model’ organisms. Despite the advent of relatively inexpensive genome sequencing, most taxonomic groups are underrepresented, with few species that ‘represent’ diversity whole genera. This study describes an economical guide to sequencing a non‐model organism, which may be useful reducing cost more within genera across life. method was used develop Kalanchoë blossfeldiana as resource for comparing C 3 water‐conserving mode photosynthesis known Crassulacean acid metabolism (CAM) same plant. Summary increasing number well‐annotated genomes life, there densely sampled than couple sequences representing Here, we economic approach full‐genome could sequence many genus. We made use Nanopore rapid kit assist assembly, dramatically cost. Here applied this cost‐effectively genomic resources , commercially important ornamental, Acid Metabolism (CAM), can induced. present physiological biochemical characterisation Kalanchoe its nuclear chloroplastic comparative CAM dusk transcriptome. apply complex tetraploid genome, making relative chromosomal scaffolding reduce assembly ploidy, provide future gene expression studies. highlight limitations, e.g. need deeper accurately resolve structure haplotypes without using scaffolding. The demonstrates merits K. system studying has identified substantial changes transcriptome between young mature leaves response age‐induced CAM, shows absence abiotic stress, induction still involves engagement drought abscisic (ABA) pathways.

Language: Английский

---

Integrative analysis of CAM photosynthesis reveals its impact on primary metabolism in Yucca

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 3, 2024

Abstract Crassulacean Acid Metabolism (CAM) is an adaptation that temporally separates carbon uptake at night from photosynthesis during the day. CAM has evolved repeatedly across vascular plants, perhaps, in part, because it does not involve any novel gene functions and instead relies on regulatory modification of existing C 3 pathways. The co-option established processes corresponding alteration metabolic flux likely to impact other primary pathways such as nitrogen metabolism photorespiration. However, majority research date focused a handful genes core pathway. Understanding complex downstream effects associated with emergence essential explaining its convergent evolution well efforts engineer concentrating mechanisms crops. In this study, we integrate genomic, transcriptomic, proteomic, metabolomic data compare between species Yucca aloifolia closely related species, Y. filamentosa . Despite substantial differences metabolite abundance multiple pathways, including citrate metabolism, observe relatively few expression outside Additionally, minimal correlation protein mRNA expression, suggesting significant post-transcriptional regulation species. Our findings provide insights into shifts highlight complexity biological levels.

Language: Английский

---