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Wellcome Open Research 2023We present a genome assembly from a specimen of (the silverweed cinquefoil; Streptophyta; eudicotyledons; Rosales; Potentilleae). The haploid genome sequence is 237...
We present a genome assembly from a specimen of (the silverweed cinquefoil; Streptophyta; eudicotyledons; Rosales; Potentilleae). The haploid genome sequence is 237 megabases in span. Most of the assembly is scaffolded into seven chromosomal pseudomolecules. The mitochondrial and plastid genomes have also been assembled and are 294.6 and 155.6 kilobases in length respectively.
PubMed: 38855725
DOI: 10.12688/wellcomeopenres.19908.1 -
Frontiers in Plant Science 2024The orchid genus comprises three species, all discovered in the 21 century. Each of these species is achlorophyllous, mycoheterotrophic and is known to be endemic to...
The orchid genus comprises three species, all discovered in the 21 century. Each of these species is achlorophyllous, mycoheterotrophic and is known to be endemic to Vietnam. The type species of the genus, , occurs in a single location in northern Vietnam within a lowland limestone karstic area. and , in contrast, are confined to mountains of southern Vietnam, far away from any limestone formations. Taxonomic placement of remained uncertain for the reason of inconclusive morphological affinities. At the same time, the genus has never been included into molecular phylogenetic studies. We investigate the phylogenetic relationships of two species of ( and ) based on three DNA datasets: (1) a dataset comprising two nuclear regions, (2) a dataset comprising two plastid regions, and (3) a dataset employing data on the entire plastid genomes. Our phylogenetic reconstructions support the placement of into the subtribe Orchidinae (tribe Orchideae, subfamily Orchidoideae). This leads to a conclusion that the previously highlighted similarities in the rhizome morphology between and certain mycoheterotrophic genera of the subfamilies Epidendroideae and Vanilloideae are examples of a convergence. is deeply nested within Orchidinae, and therefore the subtribe Vietorchidinae is to be treated as a synonym of Orchidinae. In the obtained phylogenetic reconstructions, is sister to the photosynthetic genus . is restricted to limestone mountains, which allows to speculate that association with limestone karst is plesiomorphic for . Flower morphology is concordant with the molecular data in placing into Orchidinae and strongly supports the assignment of the genus to one of the two major clades within this subtribe. Within this clade, however, shows no close structural similarity with any of its genera; in particular, the proximity between and has never been proposed. Finally, we assembled the plastid genome of , which is 65969 bp long and contains 45 unique genes, being one of the most reduced plastomes in the subfamily Orchidoideae. The plastome of lacks any rearrangements in comparison with the closest studied autotrophic species, and possesses substantially contracted inverted repeats. No signs of positive selection acting on the protein-coding plastid sequences were detected.
PubMed: 38855461
DOI: 10.3389/fpls.2024.1393225 -
Frontiers in Plant Science 2023The hyperdiverse orchid genus is the second largest genus of flowering plants and exhibits a pantropical distribution with a center of diversity in tropical Asia. The...
The hyperdiverse orchid genus is the second largest genus of flowering plants and exhibits a pantropical distribution with a center of diversity in tropical Asia. The only section with a center of diversity in Australasia is sect. . However, the phylogenetic placement, interspecific relationships, and spatio-temporal evolution of this section remain largely unclear. To infer broad-level relationships within , and interspecific relationships within sect. , a genome skimming dataset was generated for 89 samples, which yielded 70 plastid coding regions and a nuclear ribosomal DNA cistron. For 18 additional samples, Sanger data from two plastid loci (K and 1) and nuclear ITS were added using a supermatrix approach. The study provided new insights into broad-level relationships in , including phylogenetic evidence for the non-monophyly of sections , , , , , , , , , and . Section and sect. formed a highly supported clade that was resolved as a sister group to the remainder of the genus. Divergence time estimations based on a relaxed molecular clock model placed the origin of in the Early Oligocene (ca. 33.2 Ma) and sect. in the Late Oligocene (ca. 23.6 Ma). Ancestral range estimations based on a BAYAREALIKE model identified the Australian continent as the ancestral area of the sect. The section underwent crown diversification from the mid-Miocene to the late Pleistocene, predominantly in continental Australia. At least two independent long-distance dispersal events were inferred eastward from the Australian continent to New Zealand and to New Caledonia from the early Pliocene onwards, likely mediated by predominantly westerly winds of the Southern hemisphere. Retraction and fragmentation of the eastern Australian rainforests from the early Miocene onwards are likely drivers of lineage divergence within sect. facilitating allopatric speciation.
PubMed: 38854888
DOI: 10.3389/fpls.2023.1219354 -
Wellcome Open Research 2024We present a genome assembly from a diploid female (the Annual Mercury; Tracheophyta; Magnoliopsida; Malpighiales; Euphorbiaceae). The genome sequence is 453.2...
We present a genome assembly from a diploid female (the Annual Mercury; Tracheophyta; Magnoliopsida; Malpighiales; Euphorbiaceae). The genome sequence is 453.2 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules, including the X chromosome. The organelle genomes have also been assembled, and the mitochondrial genome is 435.28 kilobases in length, while the plastid genome is 169.65 kilobases in length.
PubMed: 38854694
DOI: 10.12688/wellcomeopenres.21004.1 -
PhytoKeys 2024This study addresses the longstanding absence of a comprehensive phylogenetic backbone for the apple tribe Maleae, a deficiency attributed to limited taxon and marker...
Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of and its allies in the Old World.
This study addresses the longstanding absence of a comprehensive phylogenetic backbone for the apple tribe Maleae, a deficiency attributed to limited taxon and marker sampling. We conducted an extensive taxon sampling, incorporating 563 plastomes from a diverse range of 370 species encompassing 26 presently recognized genera. Employing a range of phylogenetic inference methods, including RAxML and IQ-TREE2 for Maximum Likelihood (ML) analyses, we established a robust phylogenetic framework for the Maleae tribe. Our phylogenomic investigations provided compelling support for three major clades within Maleae. By integrating nuclear phylogenetic data with morphological and chromosomal evidence, we propose an updated infra-tribal taxonomic system, comprising subtribe Malinae Reveal, subtribe Lindleyinae Reveal, and subtribe Vauqueliniinae B.B.Liu (). Plastid phylogenetic analysis also confirmed the monophyly of most genera, except for , , sensu lato, and . In addition, we present a comprehensive taxonomic synopsis of and its morphological allies in the Old World, recognizing 27 species and ten varieties within , three species and two varieties within , and two species and three varieties within . Furthermore, we also lectotypified 12 names and made two new combinations, (J.E.Vidal) B.B.Liu and (P.L.Chiu ex Z.H.Chen & X.F.Jin) B.B.Liu.
PubMed: 38854497
DOI: 10.3897/phytokeys.242.117481 -
BioRxiv : the Preprint Server For... May 2024The heteromeric acetyl-CoA carboxylase (ACC) has four subunits assumed to form an elusive catalytic complex and are involved in allosteric and transcriptional...
The heteromeric acetyl-CoA carboxylase (ACC) has four subunits assumed to form an elusive catalytic complex and are involved in allosteric and transcriptional regulation. The ACC represents almost all ACCs from pathogenic bacteria making it a key antibiotic development target to fight growing antibiotic resistance. Furthermore, it is a model for cyanobacterial and plant plastid ACCs as biofuel engineering targets. Here we report the catalytic ACC complex surprisingly forms tubes rather than dispersed particles. The cryo-EM structure reveals key protein-protein interactions underpinning efficient catalysis and how transcriptional regulatory roles are masked during catalysis. Discovering the protein-protein interaction interfaces that facilitate catalysis, allosteric and transcriptional regulation provides new routes to engineering catalytic activity and new targets for drug discovery.
PubMed: 38854064
DOI: 10.1101/2024.05.28.596234 -
BMC Plant Biology Jun 2024The phosphorylation of the Light-Harvesting Complex of photosystem II (LHCII) driven by STATE TRANSITION 7 (STN7) kinase is a part of one of the crucial regulatory...
BACKGROUND
The phosphorylation of the Light-Harvesting Complex of photosystem II (LHCII) driven by STATE TRANSITION 7 (STN7) kinase is a part of one of the crucial regulatory mechanisms of photosynthetic light reactions operating in fluctuating environmental conditions, light in particular. There are evidenced that STN7 can also be activated without light as well as in dark-chilling conditions. However, the biochemical mechanism standing behind this complex metabolic pathway has not been deciphered yet.
RESULTS
In this work, we showed that dark-chilling induces light-independent LHCII phosphorylation in runner bean (Phaseolus coccineus L.). In dark-chilling conditions, we registered an increased reduction of the PQ pool which led to activation of STN7 kinase, subsequent LHCII phosphorylation, and possible LHCII relocation inside the thylakoid membrane. We also presented the formation of a complex composed of phosphorylated LHCII and photosystem I typically formed upon light-induced phosphorylation. Moreover, we indicated that the observed steps were preceded by the activation of the oxidative pentose phosphate pathway (OPPP) enzymes and starch accumulation.
CONCLUSIONS
Our results suggest a direct connection between photosynthetic complexes reorganization and dark-chilling-induced activation of the thioredoxin system. The proposed possible pathway starts from the activation of OPPP enzymes and further NADPH-dependent thioredoxin reductase C (NTRC) activation. In the next steps, NTRC simultaneously activates ADP-glucose pyrophosphorylase and thylakoid membrane-located NAD(P)H dehydrogenase-like complex. These results in starch synthesis and electron transfer to the plastoquinone (PQ) pool, respectively. Reduced PQ pool activates STN7 kinase which phosphorylates LHCII. In this work, we present a new perspective on the mechanisms involving photosynthetic complexes while efficiently operating in the darkness. Although we describe the studied pathway in detail, taking into account also the time course of the following steps, the biological significance of this phenomenon remains puzzling.
Topics: Phaseolus; Phosphorylation; Light; Thylakoids; Photosystem I Protein Complex; Cold Temperature; Light-Harvesting Protein Complexes; Photosystem II Protein Complex; Plant Proteins; Starch; Pentose Phosphate Pathway; Enzyme Activation; Photosynthesis; Stress, Physiological; Protein Serine-Threonine Kinases
PubMed: 38849759
DOI: 10.1186/s12870-024-05169-3 -
MLife Dec 2023Photosynthetic microalgae like hold enormous potential as sustainable, light-driven biofactories for the production of high-value natural products such as terpenoids....
Photosynthetic microalgae like hold enormous potential as sustainable, light-driven biofactories for the production of high-value natural products such as terpenoids. is distinguished as a particularly robust host with extensive genomic and transgenic resources available. Its capacity to grow in wastewater, brackish, and sea waters, coupled with advances in microalgal metabolic engineering, genome editing, and synthetic biology, provides an excellent opportunity. In the present work, we demonstrate how can be engineered to produce the diterpene casbene-an important intermediate in the biosynthesis of pharmacologically relevant macrocyclic diterpenoids. Casbene accumulated after stably expressing and targeting the casbene synthase from (DgTPS1) to the algal chloroplast. The engineered strains yielded production titers of up to 0.12 mg g total dry cell weight (DCW) casbene. Heterologous overexpression and chloroplast targeting of two upstream rate-limiting enzymes in the 2-C-methyl- d-erythritol 4-phosphate pathway, 1-deoxy- d-xylulose-5-phosphate synthase and geranylgeranyl diphosphate synthase genes, further enhanced the yield of casbene to a titer up to 1.80 mg g DCW. The results presented here form a basis for further development and production of complex plant diterpenoids in microalgae.
PubMed: 38818264
DOI: 10.1002/mlf2.12097 -
BMC Genomic Data May 2024Oreomecon nudicaulis, commonly known as mountain poppy, is a significant perennial herb. In 2022, the species O. nudicaulis, which was previously classified under the...
Oreomecon nudicaulis, commonly known as mountain poppy, is a significant perennial herb. In 2022, the species O. nudicaulis, which was previously classified under the genus Papaver, was reclassified within the genus Oreomecon. Nevertheless, the phylogenetic status and chloroplast genome within the genus Oreomecon have not yet been reported. This study elucidates the chloroplast genome sequence and structural features of O. nudicaulis and explores its evolutionary relationships within Papaveraceae. Using Illumina sequencing technology, the chloroplast genome of O. nudicaulis was sequenced, assembled, and annotated. The results indicate that the chloroplast genome of O. nudicaulis exhibits a typical circular quadripartite structure. The chloroplast genome is 153,903 bp in length, with a GC content of 38.87%, containing 84 protein-coding genes, 8 rRNA genes, 38 tRNA genes, and 2 pseudogenes. The genome encodes 25,815 codons, with leucine (Leu) being the most abundant codon, and the most frequently used codon is AUU. Additionally, 129 microsatellite markers were identified, with mononucleotide repeats being the most abundant (53.49%). Our phylogenetic analysis revealed that O. nudicaulis has a relatively close relationship with the genus Meconopsis within the Papaveraceae family. The phylogenetic analysis supported the taxonomic status of O. nudicaulis, as it did not form a clade with other Papaver species, consistent with the revised taxonomy of Papaveraceae. This is the first report of a phylogenomic study of the complete chloroplast genome in the genus Oreomecon, which is a significant genus worldwide. This analysis of the O. nudicaulis chloroplast genome provides a theoretical basis for research on genetic diversity, molecular marker development, and species identification, enriching genetic information and supporting the evolutionary relationships among Papaveraceae.
Topics: Phylogeny; Genome, Chloroplast; Genomics; Papaveraceae; Microsatellite Repeats; Chloroplasts; Base Composition; Evolution, Molecular; RNA, Transfer
PubMed: 38816818
DOI: 10.1186/s12863-024-01236-8 -
BMC Plant Biology May 2024RNA editing in chloroplast and mitochondrion transcripts of plants is an important type of post-transcriptional RNA modification in which members of the multiple...
BACKGROUND
RNA editing in chloroplast and mitochondrion transcripts of plants is an important type of post-transcriptional RNA modification in which members of the multiple organellar RNA editing factor gene family (MORF) play a crucial role. However, a systematic identification and characterization of MORF members in Brassica napus is still lacking.
RESULTS
In this study, a total of 43 MORF genes were identified from the genome of the Brassica napus cultivar "Zhongshuang 11". The Brassica napus MORF (BnMORF) family members were divided into three groups through phylogenetic analysis. BnMORF genes distributed on 14 chromosomes and expanded due to segmental duplication and whole genome duplication repetitions. The majority of BnMORF proteins were predicted to be localized to mitochondria and chloroplasts. The promoter cis-regulatory element analysis, spatial-temporal expression profiling, and co-expression network of BnMORF genes indicated the involvement of BnMORF genes in stress and phytohormone responses, as well as growth and development.
CONCLUSION
This study provides a comprehensive analysis of BnMORF genes and lays a foundation for further exploring their physiological functions in Brassica napus.
Topics: Brassica napus; Multigene Family; Phylogeny; Plant Proteins; Gene Expression Regulation, Plant; Genes, Plant; RNA Editing; Gene Expression Profiling; Chloroplasts
PubMed: 38816808
DOI: 10.1186/s12870-024-05177-3