Phylogenomics and the evolution of hemipteroid insects

Proceedings of the National Academy of Sciences, Journal Year: 2018, Volume and Issue: 115(50), P. 12775 - 12780

Published: Nov. 26, 2018

Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among hemipteroid lineages. We provide maximum likelihood-based phylogenomic taxonomically comprehensive dataset comprising sequences 2,395 single-copy, protein-coding genes for 193 samples outgroups. These yield well-supported phylogeny insects. Monophyly each three orders (Psocodea, Thysanoptera, Hemiptera) is strongly supported, as most suborders families. Thysanoptera (thrips) supported sister to Hemiptera. However, in recent large-scale analysis sampling orders, trees from our data matrices support Psocodea (bark lice parasitic lice) group holometabolous (those complete metamorphosis). In contrast, four-cluster likelihood mapping these does this result. A molecular dating using 23 fossil calibration points suggests began diversifying before Carboniferous, 365 million years ago. also explore implications understanding timing diversification, evolution morphological traits, mitochondrial genome organization. results framework future studies group.

Language: Английский

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Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees

Bioinformatics, Journal Year: 2016, Volume and Issue: 32(21), P. 3246 - 3251

Published: July 4, 2016

Large multiple sequence alignments (MSAs), consisting of thousands sequences, are becoming more and common, due to advances in sequencing technologies. The MAFFT MSA program has several options for building large MSAs, but their performances have not been sufficiently assessed yet, because realistic benchmarking MSAs difficult. Recently, such assessments made possible through the HomFam ContTest benchmark protein datasets. Along with development these datasets, an interesting theory was proposed: chained guide trees increase accuracy structurally conserved regions. This challenges basis progressive alignment methods needs be examined by being compared other known including computationally intensive ones.We used HomFam, OXFam (an extended version OXBench) evaluate enabled MAFFT: (1) a method approximate trees, (2) (3) combination iterative refinement (4) less that uses rigorous tree consistency score. Other programs, Clustal Omega UPP, available were also included into comparison. effect 2 (chained trees) positive negative OXFam. Methods 3 4 increased scores consistently than three suggesting they safer use.http://mafft.cbrc.jp/alignment/software/ CONTACT: [email protected] information: Supplementary data at Bioinformatics online.

Language: Английский

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Giant virus diversity and host interactions through global metagenomics

Nature, Journal Year: 2020, Volume and Issue: 578(7795), P. 432 - 436

Published: Jan. 22, 2020

Abstract Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes sampling sites across the globe by building on rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity a parallel 10-fold expansion functional diversity. Analysis 58,023 major capsid proteins giant using metagenomic data revealed global distribution patterns cosmopolitan nature these viruses. The discovered encoded wide range putative roles photosynthesis diverse substrate transport processes, indicating host reprogramming probably common strategy NCLDVs. Furthermore, inferences horizontal gene transfer connected lineages eukaryotic hosts. We anticipate NCLDVs describe here will establish viruses—which associated most lineages—as important players ecosystems Earth’s biomes.

Language: Английский

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Structure of the bacterial ribosome at 2 Å resolution

eLife, Journal Year: 2020, Volume and Issue: 9

Published: Sept. 14, 2020

Using cryo-electron microscopy (cryo-EM), we determined the structure of Escherichia coli 70S ribosome with a global resolution 2.0 Å. The maps reveal unambiguous positioning protein and RNA residues, their detailed chemical interactions, modifications. Notable features include first examples isopeptide thioamide backbone substitutions in ribosomal proteins, former likely conserved all domains life. also extensive solvation small (30S) subunit, interactions A-site P-site tRNAs, mRNA, antibiotic paromomycin. models bacterial presented here now allow deeper phylogenetic analysis components including structural conservation to level solvation. high quality should enable future analyses basis for translation aid development robust tools cryo-EM modeling refinement.

Language: Английский

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Fungal diversity notes 840–928: micro-fungi associated with Pandanaceae

Fungal Diversity, Journal Year: 2018, Volume and Issue: 93(1), P. 1 - 160

Published: Sept. 27, 2018

Language: Английский

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Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: July 31, 2019

Abstract Single-stranded (ss) DNA viruses are a major component of the earth virome. In particular, circular, Rep-encoding ssDNA (CRESS-DNA) show high diversity and abundance in various habitats. By combining sequence similarity network phylogenetic analyses replication proteins (Rep) belonging to HUH endonuclease superfamily, we that machinery CRESS-DNA evolved, on three independent occasions, from Reps bacterial rolling circle-replicating plasmids. The emerged via recombination between such plasmids cDNA copies capsid genes eukaryotic positive-sense RNA viruses. Similarly, rep prokaryotic appear have evolved archaeal Our findings also suggest polyomaviruses papillomaviruses with dsDNA genomes parvoviruses Collectively, our results shed light complex evolutionary history class revealing its polyphyletic origins.

Language: Английский

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Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

mBio, Journal Year: 2020, Volume and Issue: 11(3)

Published: June 15, 2020

Microbes produce specialized compounds to compete or communicate with one another and their environment. Some of these compounds, such as antibiotics, are also useful in medicine biotechnology. Historically, most antibiotics have come from soil bacteria which can be isolated grown the lab. Though vast majority cannot isolated, we extract genetic information search it for genes compounds. These understudied offer a wealth potential discovery new important microbial products. Here, identified ability diverse novel range environments. This will other researchers who wish isolate certain Beyond use humans, understanding distribution function products is key communities effects on biogeochemical cycles.

Language: Английский

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Deacetylation of chitin oligomers increases virulence in soil-borne fungal pathogens

Nature Plants, Journal Year: 2019, Volume and Issue: 5(11), P. 1167 - 1176

Published: Oct. 21, 2019

Language: Английский

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A catalog of the diversity and ubiquity of bacterial microcompartments

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: June 21, 2021

Bacterial microcompartments (BMCs) are organelles that segregate segments of metabolic pathways which incompatible with surrounding metabolism. BMCs consist a selectively permeable shell, composed three types structurally conserved proteins, together sequestered enzymes vary among functionally distinct BMCs. Genes encoding shell proteins typically clustered those for the encapsulated enzymes. Here, we report number identifiable BMC loci has increased twenty-fold since last comprehensive census 2014, and doubled. The new expand range compartmentalized catalysis suggest there is more biochemistry yet to be discovered. Our catalog provides framework their identification, correlation bacterial niche adaptation, experimental characterization, development BMC-based nanoarchitectures biomedical bioengineering applications.

Language: Английский

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Complexity of avian evolution revealed by family-level genomes

Nature, Journal Year: 2024, Volume and Issue: 629(8013), P. 851 - 860

Published: April 1, 2024

Abstract Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and choice genomic regions 1–3 . Here we address these issues by analysing genomes 363 bird 4 (218 taxonomic families, 92% total). Using intergenic coalescent methods, present well-supported tree but also marked degree discordance. The confirms that Neoaves experienced rapid radiation at or near Cretaceous–Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective resolving difficult nodes. Remaining recalcitrant nodes involve are challenge model due either extreme DNA composition, variable substitution rates, incomplete lineage sorting complex evolutionary events such as ancient hybridization. Assessment effects different partitions showed high heterogeneity across genome. We discovered sharp increases population size, rates relative brain size following extinction event, supporting hypothesis emerging ecological opportunities catalysed diversification modern birds. resulting estimate offers fresh insights into birds provides taxon-rich backbone for future comparative studies.

Language: Английский

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