Anri Chomentowska's research works | Yale University and other places

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Overview of Cistanthe cachinalensis and its genome. (a) Cistanthe cachinalensis is a desert annual C3 + crassulacean acid metabolism (CAM) plant that blooms robustly in years with higher‐than‐usual precipitation, along with other mass‐blooming species in its (b) native Atacama Desert region in Northern Chile. Points on the map are filtered occurrence data from the Global Biodiversity Information Facility (2022). (c) The genus Cistanthe is in the family Montiaceae, highlighted in the orange branches of a cladogram of the suborder Portulacineae and sister lineage Molluginaceae. (d) Syntenic depth analyses of C. cachinalensis and Portulaca amilis genomes show that 34% and 37% of the P. amilis and C. cachinalensis genomes had two syntenic regions, respectively. This suggests that these taxa share an ancestral whole‐genome duplication. (e) The syntenic blocks between the two genomes that include core CAM genes are visualized in red, whereas the rest are visualized in gray. One gene that did not map to a similar region to the rest of its block from P. amilis was PPC‐1E1c (visualized in green), the copy of the phosphoenolpyruvate carboxylase gene used in CAM in C. cachinalensis and P. amilis.

Crassulacean acid metabolism (CAM) physiology in Cistanthe cachinalensis. (a) CO2 assimilation rate (μmol m⁻² s⁻¹) measured across six timepoints over 24 h (time elapsed shown in seconds) in an individual under drought at the pre‐flowering (vegetative) stage (red), a separate individual under a well‐watered treatment at the pre‐flowering stage (blue), and four additional individuals under a well‐watered treatment at the post‐flowering stage (magenta). Error bars are ±SD taken directly from the LI‐6800 machine, which was used to measure the assimilation rate for the drought/pre‐flowering and watered/pre‐flowering lines (n = 1 for both lines), and ±SD calculated from the four assimilation rate measurements taken for the watered/post‐flowering line (n = 4). Time period with lights off (10 h) is shaded in gray. (b) Titratable acidity (in μ equivalents of H⁺; ΔH⁺ μmol g⁻¹ FW) assayed among leaf samples of C. cachinalensis in (1) well‐watered treatment and drought treatment (pre‐flowering individuals), as well as in (2) pre‐ and post‐flowering stages (grown under well‐watered conditions). This shows nocturnal acid accumulation (the difference between dawn and dusk collection per sample), which is a measure of CAM activity. Boxplots show median and interquartile range (whiskers = 1.5 × interquartile range). Asterisks indicate significance from Wilcoxon signed‐rank sum exact test (*, P < 0.1; ***, P < 0.001).

Core crassulacean acid metabolism (CAM) gene expression patterns in Cistanthe cachinalensis. (a) A simplified schematic of the CAM molecular pathway, showing the nighttime carboxylation and daytime decarboxylation in a mesophyll cell. Core enzymes are shown in orange (except for PEPC, shown in red, for emphasis). CBB, Calvin–Benson–Bassham; MDH, malate dehydrogenase; NADP‐ME, nicotinamide adenine dinucleotide phosphate‐dependent malic enzyme; OAA, oxaloacetate; PEP, phosphoenolpyruvate; PEPC, phosphoenolpyruvate carboxylase; PPCK, phosphoenolpyruvate carboxylase kinase; PPDK, pyruvate, phosphate dikinase; β‐CA, beta carbonic anhydrase. (b) Normalized abundance of PPC‐1E1c (gene g11025 in our annotation) across time (in transcripts per million). Upper panel compares drought vs watered, and lower panel compares pre‐flowering vs post‐flowering. Three or four biological replicates per time point; error bars indicate SE. (c) Normalized abundance of cNAD‐MDH (g17299), cpNADP‐ME (g11158), and PPDK (g22207) genes.

Expression profiles of 11 photosynthesis pathway genes differentially expressed in both experiments in Cistanthe cachinalensis. Normalized abundances of these genes are plotted across time (in transcripts per million), and grouped by photosynthetic pathway identity (as defined by Gilman et al., 2022). In each set of plots, the left panels show the results for the watered vs drought treatment experiment; the right panels show the results for the pre‐flowering vs post‐flowering stage experiment. Three or four biological replicates for each treatment × time point or stage × time point, and error bars indicate SE. AMY, alpha‐amylase; BAM, beta‐amylase; GLN, glutamine synthetase; LUX, LUX ARRHYTHMO; PHS, alpha‐glucan phosphorylase; RBCS, ribulose bisphosphate carboxylase (RuBisCO) small subunit; SBE, 1,4‐alpha‐glucan‐branching enzyme; SCL, Scarecrow‐like; SWEET, bidirectional sugar transporter; VHA, V‐type proton ATPase.

A high‐quality genome of the Atacama Desert plant Cistanthe cachinalensis and its photosynthetic behavior related to drought and life history

May 2025

76 Reads

[...]

Crassulacean acid metabolism (CAM) photosynthesis has independently evolved many times in arid‐adapted plant lineages. Cistanthe cachinalensis (Montiaceae), a desert annual, can upregulate CAM facultatively upon stress such as drought. Few studies, however, consider life history stages when measuring CAM activity or its facultative onset. To test the effect of drought and flowering on photosynthetic activity, we assayed Cistanthe individuals in fully watered and drought conditions, as well as fully watered individuals at pre‐flowering and flowering life stages. We assembled and annotated a chromosome‐scale genome of C. cachinalensis and compared it with the genome of Portulaca amilis and analyzed differential gene expression. Results show significantly upregulated CAM in drought conditions as compared to fully watered conditions; furthermore, flowering individuals showed slightly higher CAM activity as compared to pre‐flowering plants, even when fully watered. Differential gene expression analyses provide preliminary support for the possible coregulation of CAM expression and reproduction. We emphasize the potentially missed significance of life history in the CAM literature and consider how the CAM biochemical module could become co‐opted into other plant behaviors and responses, such as the shift to reproduction or flowering in annuals.

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Figure 2. CAM physiology in Cistanthe longiscapa. (a) CO2 assimilation rate (μmol m -2 s -1 ) measured 365 across six timepoints over 24 hours (time elapsed shown in seconds) in an individual under drought (red) 366 and another under a well-watered treatment (blue). Time period with lights off (10 hours) is shaded in gray. 367 Error bars are ± standard deviation taken directly from the LI-6800 machine which was used to measure 368 the assimilation rate. (b) Titratable acidity (in μ equivalents of H + ; ΔH + µmol g -1 FW ) assayed among leaf 369 samples of C. longiscapa in 1. well-watered treatment and drought treatment (vegetative/pre-flowering 370 individuals), as well as in 2. pre-flowering and post-flowering stages (grown under well-watered 371 conditions). This shows nocturnal acid accumulation (the difference between dawn and dusk collection per 372 sample) which is a measure of CAM activity. Boxplots show median and interquartile range (whiskers = 373 1.5 × interquartile range). Asterisks indicate significance from Wilcoxon rank sum exact test ("***", 374 P < 0.001; "*", P < 0.1). 375

Figure 3. Core CAM gene expression patterns. (a) A simplified schematic of the CAM molecular 411 pathway, showing the nighttime carboxylation and daytime decarboxylation in a mesophyll cell. Core 412 enzymes are shown in orange (except for PEPC, shown in red, for emphasis). β-CA, beta carbonic 413 anhydrase; CBB, Calvin-Bensen-Bassham; MDH, malate dehydrogenase; NADP-ME, NADP-dependent 414 malic enzyme; OAA, oxaloacetate; PPCK, phosphoenolpyruvate carboxylase kinase; PPDK, pyruvate, 415 phosphate dikinase; PEP, Phosphoenolpyruvate; PEPC, PEP carboxylase. (b) Normalized abundance of 416 PPC-1E1c (gene g11025 in our annotation) across time (in TPM, transcripts per million). Top panel 417 compares Drought versus Watered, bottom compares Pre-Flowering versus Post-Flowering. Three or four 418 biological replicates per each timepoint; error bars indicate interquartile range. (c) Normalized abundance 419 of C. longiscapa copies of cNAD-MDH (g17299), cpNADP-ME (g11158), and PPDK (g22207) genes. 420

A high-quality genome of the mass-blooming desert plant Cistanthe longiscapa and its photosynthetic behavior related to drought and life history

November 2024

69 Reads

[...]

Crassulacean acid metabolism (CAM) photosynthesis has independently evolved many times in arid-adapted plant lineages. Cistanthe longiscapa (Montiaceae), a desert mass-blooming annual, can upregulate CAM facultatively upon stress such as drought. Few studies, however, consider life history stages when measuring CAM activity or its facultative onset. To test the effect of drought and flowering on photosynthetic activity, we assayed Cistanthe individuals in fully-watered and drought conditions, as well as fully-watered individuals at pre-flowering and flowering life stages. We assembled and annotated a chromosome-scale genome of C. longiscapa and compared it with the genome of Portulaca amilis and analyzed differential gene expression. Results show significantly upregulated CAM in drought conditions as compared to fully-watered conditions; furthermore, flowering individuals showed slightly higher CAM activity as compared to pre-flowering plants, even when fully-watered. Differential gene expression analyses provide preliminary support for the possible co-regulation of CAM expression and reproduction. We emphasize the potentially missed significance of life history in the CAM literature, and consider how the CAM biochemical module could become co-opted into other plant behaviors and responses, such as the shift to reproduction or flowering in annuals.

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Anri Chomentowska’s research while affiliated with Yale University and other places

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