Rubisco is evolving for improved catalytic efficiency and CO₂assimilation in plants

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: July 6, 2022

Abstract Rubisco is the primary entry point for carbon into biosphere. However, rubisco widely regarded as inefficient leading many to question whether enzyme can adapt become a better catalyst. Through phylogenetic investigation of molecular and kinetic evolution Form I we demonstrate that not stagnant. Instead, rbcL among 1% slowest evolving genes enzymes on Earth, accumulating one nucleotide substitution every 0.9 million years amino acid mutation 7.2 years. Despite this, catalysis continuing evolve toward improved CO 2 /O specificity, carboxylase turnover, carboxylation efficiency. Consistent with this adaptation, reveal increased leads concomitant improvement in leaf-level assimilation. Thus, continually catalytic efficiency assimilation plants.

Language: Английский

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Re-establishment of <em>Aechmea laxiflora</em> (Bromeliaceae, Bromelioideae) based on morphological and phylogenetic evidence, with notes on its geographical distribution

Botanical Sciences, Journal Year: 2024, Volume and Issue: 102(2), P. 534 - 560

Published: March 27, 2024

Background: Previous phylogenetic analyses suggested that Aechmea bracteata is not a monophyletic species, being each variety an individual lineage within the complex. Hypothesis: A analysis based on molecular data and morphological will provide evidence to support taxonomic recognition of A. var. pacifica as distinct species. Studies species: bracteata, related Study site dates: Mexico Northern South America; 17 populations from Southeastern Western Mexico. Analyses were performed between 2021 2023. Methods: linear morphometric was conducted with 85 herbarium specimens testing 28 quantitative three qualitative variables. Potential diagnostic traits reviewed in living specimens. two nDNA markers (ETS g3pdh) one cpDNA marker (trnL-F). total 373 records projected into biogeographical provinces Neotropics. Results: The allowed separate group, also, nine evaluated resulted statistically significant through univariate analysis. Five additional inflorescence leaves recognized. According both taxa present reciprocal monophyly, however, groups Central American showcasing potential hybrid origin. Geographically, Sierra Madre del Sur acts barrier taxa. Conclusions: Due gathered possible recognize endemic species Mexico, reestablishing basionym laxiflora.

Language: Английский

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Chloroplast Genome Variation and Phylogenetic Relationships of Autochthonous Varieties of Vitis vinifera from the Don Valley

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(18), P. 9928 - 9928

Published: Sept. 14, 2024

The autochthonous grape varieties of the Don Valley, situated in southern Russia, constitute a distinctive element regional cultural heritage. These have been adapted over centuries to region's specific local climatic and soil conditions. For most part, these are not imported from other countries. They closely related found Crimea North Caucasus. In this study, we obtained first complete, unfragmented sequences chloroplast genomes eight Valley one Crimea. We also performed comparative analysis their genomic features. size

Language: Английский

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Complete Plastid Genomes of Nine Species of Ranunculeae (Ranunculaceae) and Their Phylogenetic Inferences

Genes, Journal Year: 2023, Volume and Issue: 14(12), P. 2140 - 2140

Published: Nov. 27, 2023

The tribe Ranunculeae, Ranunculaceae, comprising 19 genera widely distributed all over the world. Although a large number of Sanger sequencing-based molecular phylogenetic studies have been published, very few performed on using genomic data to infer relationships within Ranunculeae. In this study, complete plastid genomes nine species (eleven samples) from Ceratocephala, Halerpestes, and Ranunculus were de novo assembled next-generation sequencing method. Previously published plastomes Oxygraphis other related family downloaded GenBank for comparative analysis. plastome each Ranunculeae has 112 genes in total, including 78 protein-coding genes, 30 transfer RNA four ribosomal genes. structure samples is conserved gene order arrangement. There are no inverted repeat (IR) region expansions only one IR contraction was found tested samples. This study also compared sequences across collinearity, codon usage, editing sites, nucleotide variability, simple sequence repeats, positive selection sites. Phylogeny available inferred by maximum-likelihood Bayesian inference methods, partitioning strategies tested. better resolved previous based showing potential value inferring phylogeny tribe.

Language: Английский

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Tracing the Maternal Line in Glacial–Interglacial Migrations of Populus tremuloides: Finding Trees for Future Sustainable Forests by Searching in the Past

Sustainability, Journal Year: 2024, Volume and Issue: 16(3), P. 949 - 949

Published: Jan. 23, 2024

Maintaining and planting sustainable forests is fundamental in perpetuating the essential functions of these ecosystems. A central aspect managing for future resilience consideration past migration evolution trees using genetic genomic data to ensure that functionally appropriate diversity conserved utilized. In our study, we generated compared from plastome better understand phylogeography molecular tree species Populus tremuloides (aspen). With analyses, found evidence divergence between northern southern sites. Additionally, deep incomplete sorting across Salicaceae was when examining insertion–deletion (indel) sites associated with DNA repair. By indels plastomic genes introns Salicaceae, a strong correlation abundance repair position transcript abundance. From findings, conclude previously ignored are understanding key metabolic processes improved aspen forest planning. Given propensity host high levels biodiversity, rapidly sequester carbon, absorb excess nitrogen, efficiently regulate snowmelt, improvements planning conservation will be highly impactful.

Language: Английский

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Widespread adaptive evolution in the photosystems of angiosperms provides new insight into the evolution of photosystem II repair.

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

Published: May 24, 2024

Abstract Oxygenic photosynthesis generates the initial energy source which fuels nearly all life on earth. At heart of process are photosystems, pigment binding multi-protein complexes that catalyse first step photochemical conversion light into chemical energy. Here, we investigate molecular evolution at single residue resolution plastid-encoded subunits photosystems across 773 angiosperm species. We show despite an extremely high level conservation, 7% residues in spanning photosystem subunits, exhibit hallmarks adaptive evolution. Through silico modelling these substitutions uncover impact changes properties focussing their effects co-factor and formation inter-subunit interfaces. further reveal has repeatedly destabilised interaction II its D1 subunit, thereby reducing energetic barrier for turn-over repair. Together, results provide new insight trajectory during radiation angiosperms.

Language: Английский

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From light into shadow: comparative plastomes in Petrocosmea and implications for low light adaptation

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Oct. 11, 2024

Plastids originated from an ancient endosymbiotic event and evolved into the photosynthetic organelles in plant cells. They absorb light energy carbon dioxide, converting them chemical oxygen, which are crucial for development adaptation. However, little is known about plastid genome to Petrocosmea, a member of Gesneriaceae family, comprises approximately 70 species with diverse environment, serve as ideal subject studying plastomes adapt light. In this study, we selected ten representative Petrocosmea environments, assembled their genomes, conducted comparative genomic analysis. We found that highly conserved both structure gene content. The phylogenetic relationships reconstructed based on genes were divided five clades, consistent results previous studies. vast majority protein-coding under purifying selection, only rps8 rps16 identified positive selection different environments. Notably, significant differences evolutionary rate observed NADH dehydrogenase, ATPase ribosome, RNA polymerase between Clade A other clades. Additionally, ycf1 several intergenic regions (trnH-psbA, trnK-rps16, rpoB-trnC, petA-psbJ, ccsA-trnL, rps16-trnQ, trnS-trnG) candidate barcodes emerging ornamental horticulture. newly genomes hypervariable regions, providing genetic resources markers promising Furthermore, our study suggested patterns related diversity environment Petrocosmea. This revealed scenario adaptation plants.

Language: Английский

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Widespread adaptive evolution in angiosperm photosystems provides insight into the evolution of photosystem II repair

The Plant Cell, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 15, 2024

Abstract Oxygenic photosynthesis generates the initial energy source that fuels nearly all life on Earth. At heart of process are photosystems, which pigment binding multiprotein complexes catalyze first step photochemical conversion light into chemical energy. Here, we investigate molecular evolution plastid-encoded photosystem subunits at single-residue resolution across 773 angiosperm species. We show despite an extremely high level conservation, 7% residues in spanning subunits, exhibit hallmarks adaptive evolution. Through silico modeling these substitutions, uncover impact changes predicted properties focusing their effects cofactor and intersubunit interface formation. By analyzing cohorts changes, reveal has repeatedly altered interaction between Photosystem II its D1 subunit a manner is to reduce energetic barrier for turnover repair. Together, results provide insight trajectory adaptation during

Language: Английский

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Taken to extremes: Loss of plastid rpl32 in Streptophyta and Cuscuta’s unconventional solution for its replacement

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: unknown, P. 108243 - 108243

Published: Nov. 1, 2024

The evolution of plant genomes is riddled with exchanges genetic material within one (endosymbiotic gene transfer/EGT) and between unrelated plants (horizontal transfer/HGT). These have left their marks on genomes. Parasitic special evolutionary niche provide ample examples for these processes because they are under a reduced pressure to maintain autotrophy thus conserve plastid On the other hand, close physical connections different hosts enabled them acquire from plants. Based an analysis extensive dataset including parasite Cuscuta campestris parasitic species, we identified unique history rpl32 genes coding essential ribosomal subunit in Cuscuta. Our suggests that was most likely sequestered by HGT member Oxalidales order serving as host ancestor subgenus Grammica. had suffered ancestral EGT predating genus subsequently relieved its constraint led loss genome. HGT-based acquisition supported high sequence similarity mature L32 protein species Grammica representatives Oxalidales, surprisingly conserved transit peptide, whose functionality experimentally verified. findings discussed view overall pattern events subunits Streptophyta.

Language: Английский

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