Rubisco is evolving for improved catalytic efficiency and CO ₂ assimilation in plants

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(11)

Published: March 5, 2024

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 uncover evolutionary trajectory in angiosperms. We show that rbcL among 1% slowest-evolving genes enzymes on Earth, accumulating one nucleotide substitution every 0.9 My amino acid mutation 7.2 My. Despite this, catalysis has been continually evolving toward improved CO 2 /O specificity, carboxylase turnover, carboxylation efficiency. Consistent with this adaptation, increased led concomitant improvement leaf-level assimilation. Thus, slowly but catalytic efficiency assimilation plants.

Language: Английский

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Comparative Analysis of Plastome Sequences of Seven Tulipa L. (Liliaceae Juss.) Species from Section Kolpakowskianae Raamsd. Ex Zonn and Veldk.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(14), P. 7874 - 7874

Published: July 18, 2024

Tulipa L. is a genus of significant economic, environmental, and cultural importance in several parts the world. The exact number species remains uncertain due to inherent taxonomic challenges. We utilized next-generation sequencing technology sequence assemble plastid genomes seven collected Kazakhstan conducted comparative analysis. total annotated genes was 136 all studied species, 114 which were unique, including 80 protein-coding, 30 tRNA, 4 rRNA genes. Nine regions (petD, ndhH, ycf2-ycf3, ndhA, rpl16, clpP, ndhD-ndhF, rpoC2, ycf1) demonstrated nucleotide variability, suggesting their potential as molecular markers. A 1388 SSRs identified plastomes, with mononucleotide repeats being most abundant (60.09%), followed by dinucleotide (34.44%), tetranucleotide (3.90%), trinucleotide (1.08%), pentanucleotide (0.22%), hexanucleotide (0.29%). Ka/Ks values protein-coding ranged from 0 3.9286, majority showing <1. Phylogenetic analysis based on complete genome gene sequences divided into three major clades corresponding subgenera. results obtained this study may contribute understanding phylogenetic relationships taxonomy species.

Language: Английский

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Molecular marker development and phylogenetic analysis of Aconitum species based on chloroplast genomes

Industrial Crops and Products, Journal Year: 2024, Volume and Issue: 221, P. 119386 - 119386

Published: Aug. 7, 2024

Language: Английский

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Decoding the Chloroplast Genome of Bitterwood (Picrasma quassioides): Structure, Variability, and Evolutionary Relationships

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

The chloroplast genome of Picrasma quassioides, a medicinally significant plant in traditional Asian medicine, was sequenced and analyzed to understand its genetic architecture evolutionary relationships within Simaroubaceae. High-throughput sequencing revealed 160,013-bp circular with typical quadripartite structure, encoding 132 genes including 87 protein-coding genes, 37 tRNA 8 rRNA genes. Comparative analysis other Simaroubaceae species identified distinct patterns nucleotide diversity between single-copy repeat regions, while examination IR boundaries dynamic processes. Analysis 101 SSR loci 48 sequences provided insights into organization potential molecular markers for identification. Selective pressure across 78 demonstrated predominant purifying selection (average K a/K s ratio 0.23), evidence positive specific Phylogenetic reconstruction using 77 confirmed Simaroubaceae's monophyly close relationship Rutaceae. These findings advance our understanding evolution providing tools authentication breeding this valuable medicinal species. comprehensive genomic characterization establishes foundation investigating the basis therapeutic properties P. quassioides facilitating conservation.

Language: Английский

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IRplus: An Augmented Tool to Detect Inverted Repeats in Plastid Genomes

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(10)

Published: Oct. 1, 2023

High-throughput sequencing methods have increased the accessibility of plastid genomes, which are crucial for clarifying phylogenetic relationships. Current large efforts require software tools routine display their distinctive quadripartite structure, is denoted by four junction sites. By concentrating on these junctions and close vicinity, IRscope has emerged as standard tool detection this structure creating simplified comparative graphical maps genomes. Here, we provide an augmented version (IRplus) that encompasses a novel set functions such integrated error detection, flexible color schemes, upgraded method to detect inverted repeats in genomic sequences. Spanning across plant tree life, IRplus allows quick visualization various sets genomes features, next smooth interoperability with other widely used annotation file formats platforms. The can be accessed at https://irscope.shinyapps.io/IRplus/, source codes freely available https://github.com/AmiryousefiLab/IRplus.

Language: Английский

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An Integrative Framework Reveals Widespread Gene Flow During the Early Diversification of Malvaceae S.L

Published: Jan. 1, 2025

Language: Английский

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Ecological speciation with gene flow followed initial large‐scale geographic speciation in the enigmatic afroalpine giant senecios (Dendrosenecio)

New Phytologist, Journal Year: 2025, Volume and Issue: 246(5), P. 2307 - 2323

Published: Feb. 1, 2025

Summary Mountains have highly heterogeneous environments that generate ample opportunities for lineage differentiation through ecological adaptation, geographic isolation and secondary contact. The of the afroalpine vegetation fragments on East African mountain tops makes them an excellent system to study speciation. initial diversification within endemic genus Dendrosenecio was shown occur via allopatric divergence among four isolated groups, but potential role speciation these groups gene flow in remained uncertain. Here we extend sampling use phylogenomics assess importance genus. Then, population genomics, demographic modelling habitat analyses are used two sister species occurring Mount Kenya. We found sympatric Mt Kenya occupy distinct microhabitats, our support they originated situ with flow. In addition, obtained signals admixture history between groups. Taken together, results suggest shaped main lineages, while ecologically mediated occurred a single mountain.

Language: Английский

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DNA barcoding of the invasive alien aquatic weed Heteranthera reniformis Ruiz and Pavon using chloroplast DNA markers

Limnology, Journal Year: 2025, Volume and Issue: unknown

Published: April 2, 2025

Abstract Morphology-based species identification may not be accurate and necessitates extensive taxonomic knowledge. Regarding Heteranthera reniformis Ruiz Pavon, an invasive alien in Japan, it is difficult to find appropriate information on molecular data. DNA barcoding a convenient method of identifying based the nucleotide diversity conserved sequences. In this study, we aim assess suitability chloroplast maturase K ( matK ) ribulose-1,5-bisphosphate carboxylase large rbcL as barcode markers by collecting data comparing them with related available gene bank. Both exhibited 100% success rate their amplification sequencing, sizes 833 bp 552 bp, respectively. The subsequent sequence analysis confirmed biological homology closely species. highest 99.52% was found H. callifolia . Moreover, showed higher 99% seven same family. This study highlights utility both regions primers elucidating fundamental aspects plant.

Language: Английский

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Comparative Plastome Analysis of Apocynaceae with de novo Sequencing of Thevetia peruviana: Insights into Evolution and Phylogeny

Tropical Plant Biology, Journal Year: 2025, Volume and Issue: 18(1)

Published: May 13, 2025

Language: Английский

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Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 25(1), P. 257 - 257

Published: Dec. 23, 2023

Paeonia delavayi var. lutea, angustiloba, and ludlowii are Chinese endemics that belong to the Paeoniaceae family have vital medicinal ornamental value. It is often difficult classify plants based on their morphological characteristics, limited genomic information has strongly hindered molecular evolution phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, annotated chloroplast genomes P. ludlowii. The these strains were comparatively analyzed, relationships divergence times inferred. These three exhibited a typical quadripartite structure 152,687–152,759 bp in length. Each genome contains 126–132 genes, including 81–87 protein-coding 37 transfer RNAs, 8 ribosomal RNAs. addition, had 61–64 SSRs, with mononucleotide repeats being most abundant. codon bias patterns species tend use codons ending A/U. Six regions high variability identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, ycf1) can be used as DNA markers for taxonomic analysis. Ka/Ks ratio indicates positive selection rps18 gene associated self-replication. analysis 99 from Saxifragales clarified revealed monophyletic groups sisters delavayi. Divergence time estimation two evolutionary divergences early Oligocene Miocene. Afterward, they underwent rapid adaptive radiation Pliocene Pleistocene when formed. results study enrich reveal new insights into phylogeny

Language: Английский

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