Agronomic Performance and Lignin Content of HCT Down-Regulated Alfalfa (Medicago sativa L.)

This article evaluates HCT down-regulated alfalfa plants for their forage composition and agronomic performance in the greenhouse and under field conditions

Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass)

Background: Seagrasses (Alismatales) are the only fully marine angiosperms. Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings. Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding. Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins. Conclusions: As an important marine angiosperm, the improved Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life

Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass)

BACKGROUND : Seagrasses (Alismatales) are the only fully marine angiosperms. Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings. METHODS : The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A highquality reference genome was assembled with the MECAT assembly pipeline combining PacBio longread sequencing and Hi-C scaffolding. RESULTS : In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 proteinencoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins. CONCLUSIONS : As an important marine angiosperm, the improved Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.The DOE-Joint Genome Institute, Berkeley, CA, USA, Community Sequencing Program 2019.http://f1000research.com/am2022BiochemistryGeneticsMicrobiology and Plant Patholog

Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes

Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum. Remarkably, despite that the two species diverged ~350 Mya, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications, and the resulting intragenomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species

Dynamic genome evolution in a model fern

The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

DATA AVAILABILITY : The DNA sequencing data for the C. nodosa genome assembly have been deposited in the NCBI database under BioProject PRJNA1041560 via the link https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1041560. All assemblies and annotations for all seagrass species discussed in the current paper can be found at https://bioinformatics.psb.ugent.be/gdb/seagrasses/. The transcriptome data (including raw data and clean data) and sequencing QC reports for C. nodosa can be found at https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Cymnodnscriptome_2, the transcriptome data and sequencing QC reports for P. oceanica can be found at https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Posocenscriptome_2, the transcriptome data and sequencing QC reports for T. testudinum can be found at https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Thatesnscriptome_4 and the transcriptome data for Z. marina are from ref. 15. For the public databases, the RFAM database v.14.7 can be downloaded at https://ftp.ebi.ac.uk/pub/databases/Rfam/14.7/, the UniProt database can be accessed from the web at http://www.uniprot.org and downloaded from http://www.uniprot.org/downloads and the NCBI nucleotide database can be accessed via https://www.ncbi.nlm.nih.gov/.We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the ‘savannahs of the sea’ are of major concern in times of climate change and loss of biodiversity.The DOE, JGI, Berkeley, California, USA, under the Community Sequencing Program 2018; the European Research Council under the European Union’s Horizon 2020 research and innovation programme ; Ghent University (Methusalem funding); the Deutsche Forschungsgemeinschaft (German Research Foundation); the Helmholtz School for Marine Data Science; partially supported by the project Marine Hazard, PON03PE_00203_1 (MUR, Italian Ministry of University and Research) and by the National Biodiversity Future Centre Program, Italian Ministry of University and Research, PNRR, Missione 4 Componente 2 Investimento 1.4; and Universiti Malaysia Terengganu.https://www.nature.com/nplants2024-07-26hj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-14:Life below wate

Analysis of genetic diversity in colonial bentgrass (Agrostis capillaris L.) and rough bluegrass (Poa trivialis L.) by using randomly amplified polymorphic DNA (RAPD) markers

Colonial bentgrass (Agrostis capillaris L.) is a cool-season perennial grass. It is of great importance because it is adapted to fairways and tees of golf courses, and it has good low temperature hardiness and medium shade tolerance. Rough bluegrass (Poa trivialis L.) is a cool-season grass grown for sports fields, home lawns, and also winter overseeding on warm-season turf in southern United States. Our objective was to analyze genetic variation among each 27 accessions of rough bluegrass and colonial bentgrass by using randomly amplified polymorphic DNA (RAPD) markers. For colonial bentgrass, the Jaccard's similarity coefficients ranged from 0.13 to 0.72 based on RAPD data. The unweighted pair group method with arithmetic average (UPGMA) dendrogram clearly separated 26 out of 27 accessions into 3 clusters. A high cophenetic correlation coefficient (r = 0.82) indicated a good fit between the RAPD data matrix and cophenetic matrix. For rough bluegrass, the Jaccard's similarity coefficients ranged from 0.07 to 0.74 based on RAPD data. The UPGMA dendrogram revealed that 26 out of 27 accessions were clustered in 4 different clusters. The cophenetic correlation (r) value of 0.90 indicated a very good fit between data matrix and the cluster analysis. The clustering patterns of principal components analysis (PCA) corresponded well with the dendrograms in both colonial bentgrass and rough bluegrass. Since there was no similarity coefficient value close to one between any two accessions there was no duplication of accessions in colonial bentgrass and rough bluegrass germplasm collection.</p

Biosynthesis of Cissus rotundifolia Stem-Mediated Titanium Dioxide Nanoparticles and Their Anticariogenic Activity against Streptococcus mutans and Lactobacillus sp.

IntroductionThe green synthesis of metal oxide nanoparticles using plant extracts has emerged as an eco-friendly method. Titanium dioxide nanoparticles (TiO2NPs) were synthesized using Cissus rotundifolia in this study. Titanium dioxide nanoparticles were utilized in restorative medicine for enhanced medicinal properties and in dental composites for their antimicrobial activities. Cissus rotundifolia is recognized as a medicinal plant due to its diverse properties, including mild laxatives, anti-inflammatory, and hyperglycemic activities. Materials and MethodsThe antimicrobial activity of the prepared nanoparticles against Lactobacillus Sp. and Streptococcus mutans was evaluated using agar well diffusion method. The bactericidal and bacteriostatic activity of the prepared TiO2NPs was examined using time-kill kinetic analysis. ResultsThe prepared nanoparticles exhibited potential antimicrobial activity against Lactobacillus sp. (12 mm) at the highest concentration of 100 µg/mL. The prepared nanoparticles also exhibited excellent bactericidal activity against Lactobacillus Sp. and mild bacteriostatic activity against Staphylococcus mutans at the highest concentration of 100 µg/mL. ConclusionThe synthesized TiO2NPs showed significant antimicrobial activity against dental pathogens. The observed anticariogenic activity shows the potential of nanoparticles for dental applications. Hence, the prepared nanoparticles can be used in the field of dentistry as an antimicrobial agent instead of synthetic drugs causing more side effects

Rhodium-Catalyzed Transannulation of 1,2,3-Triazoles to Polysubstituted Pyrroles

Rhodium-catalyzed transannulation of <i>N</i>-sulfonyl-1,2,3-triazoles with vinyl ether has been accomplished for the synthesis of various polysubstituted pyrroles. The present method allows the synthesis of mono-, di-, and trisubstituted pyrroles with appropriate substitutions. Furthermore, the developed methodology was applied in the formal synthesis of neolamellarin A, an antitumor agent