Open Tree of Life
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Reproduction is a fundamental aspect of life that affects all levels of biology, from genomes and development to population dynamics and diversification. The first Tree of Sex database synthesized a vast diversity of reproductive strategies and their intriguing distribution throughout eukaryotes. A decade on, we are reviving this initiative and greatly expanding its scope to provide the most comprehensive integration of knowledge on eukaryotic reproduction to date. In this perspective, we first identify important gaps in our current knowledge of reproductive strategies across eukaryotes. We then highlight a selection of questions that will benefit most from this new Tree of Sex project, including those related to the evolution of sex, modes of sex determination, sex chromosomes, and the consequences of various reproductive strategies. Finally, we outline our vision for the new Tree of Sex database and the consortium that will create it (treeofsex.org). The new database will cover all Eukaryota and include a wide selection of biological traits. It will also incorporate genomic data types that were scarce or non-existent at the time of the first Tree of Sex initiative. The new database will be publicly accessible, stable, and self-sustaining, thus greatly improving the accessibility of reproductive knowledge to researchers across disciplines for years to come. Lastly, the consortium will persist after the database is created to serve as a collaborative framework for research, prioritizing ethical standards in the collection, use, and sharing of reproductive data. The new Tree of Sex consortium is open, and we encourage all who are interested in this topic to join us.
- Klíčová slova
- asexual reproduction, biodiversity, database, ontology, sex chromosomes, sex determination, sexual reproduction,
- MeSH
- biologická evoluce * MeSH
- Eukaryota * fyziologie genetika MeSH
- procesy určující pohlaví MeSH
- rozmnožování * genetika MeSH
- Publikační typ
- časopisecké články MeSH
We present a genome assembly from a female specimen of Boloria aquilonaris (Cranberry Fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The assembly contains two haplotypes with total lengths of 415.84 megabases and 390.14 megabases. Most of haplotype 1 (99.86%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.17 kilobases.
- Klíčová slova
- Boloria aquilonaris, Cranberry Fritillary, Lepidoptera, chromosomal, genome sequence,
- Publikační typ
- časopisecké články MeSH
This paper is focused on the modification of commercial resin by using biobased fillers during stereolithography (SLA) 3D printing. This research aims to create a composite material with a matrix made of commercially available photosensitive resin modified with a filler based on secondary raw materials and materials formed as by-products in the processing of biological materials. The research determines the effect of different fillers on the tensile properties and hardness of samples printed using SLA 3D printing, and it also investigates their integrity using SEM analysis. This study aims to evaluate the feasibility of using these fillers for producing 3D-printed parts with SLA technology. The results of this study open up new possibilities for designing modified composite materials based on additive SLA 3D-printing technology using biological fillers. Within the framework of research activities, a positive effect on tensile properties and an improved interfacial interface between the matrix and the filler was demonstrated for several tested fillers. Significant increases in tensile strength of up to 22% occurred in composite systems filled with cotton flakes (CF), miscanthus (MS), walnut (WN), spruce tree (SB), wheat (WT) and eggshells (ES). Significant potential for further research activities and added value was shown by most of the tested bio-fillers. A significant contribution of the current research is the demonstration of the improved mechanical performance of photosensitive resin modified with natural fillers.
- Klíčová slova
- 3D printing, additive manufacturing technologies, biological fillers, composite, mechanical properties, stereolithography (SLA),
- Publikační typ
- časopisecké články MeSH
We present a genome assembly of the diplonemid Rhynchopus euleeides (Euglenozoa; Diplonemea; Diplonemea; Diplonemidae). The genome sequence is 199.0 megabases long, with most of the assembly scaffolded into 88 chromosomal pseudomolecules. The multipartite mitochondrial genome and the 2.0 megabase genome of Ca. Syngnamydia salmonis, a bacterial endosymbiont of R. euleeides, were also sequenced and assembled.
- Klíčová slova
- Diplonemea, Euglenozoa, Rhynchopus euleeides, bacterial endosymbionts, chromosomal, genome sequence,
- Publikační typ
- časopisecké články MeSH
We present a genome assembly from an individual male specimen of the small dung beetle, Aphodius sticticus (Arthropoda; Insecta; Coleoptera; Scarabaeidae). The genome sequence has a total length of 628.40 megabases. Most of the assembly (98.96%) is scaffolded into 11 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 20.8 kilobases in length.
- Klíčová slova
- Aphodius sticticus, Coleoptera, chromosomal, genome sequence, small dung beetle,
- Publikační typ
- časopisecké články MeSH
Plant specialized metabolites play key roles in diverse physiological processes and ecological interactions. Identifying structurally novel metabolites, as well as discovering known compounds in new species, is often crucial for answering broader biological questions. The Piper genus (Piperaceae family) is known for its special phytochemistry and has been extensively studied over the past decades. Here, we investigated the alkaloid diversity of Piper fimbriulatum, a myrmecophytic plant native to Central America, using a metabolomics workflow that combines untargeted LC-MS/MS analysis with a range of recently developed computational tools. Specifically, we leverage open MS/MS spectral libraries and metabolomics data repositories for metabolite annotation, guiding isolation efforts toward structurally new compounds (i.e., dereplication). As a result, we identified several alkaloids belonging to five different classes and isolated one novel seco-benzylisoquinoline alkaloid featuring a linear quaternary amine moiety which we named fimbriulatumine. Notably, many of the identified compounds were never reported in Piperaceae plants. Our findings expand the known alkaloid diversity of this family and demonstrate the value of revisiting well-studied plant families using state-of-the-art computational metabolomics workflows to uncover previously overlooked chemodiversity. To contextualize our findings within a broader biological context, we employed a workflow for automated mining of literature reports of the identified alkaloid scaffolds and mapped the results onto the angiosperm tree of life. By doing so, we highlight the remarkable alkaloid diversity within the Piper genus and provide a framework for generating hypotheses on the biosynthetic evolution of these specialized metabolites. Many of the computational tools and data resources used in this study remain underutilized within the plant science community. This manuscript demonstrates their potential through a practical application and aims to promote broader accessibility to untargeted metabolomics approaches.
- Klíčová slova
- Piper fimbriulatum, Piperaceae, Wikidata, alkaloids, angiosperms, computational metabolomics, mass spectrometry, technical advance,
- MeSH
- alkaloidy * metabolismus chemie MeSH
- chromatografie kapalinová MeSH
- metabolomika * metody MeSH
- Piper * metabolismus chemie MeSH
- tandemová hmotnostní spektrometrie MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- alkaloidy * MeSH
Gene expression regulation during tissue development is extremely complex. A key mechanism of gene regulation is the recognition of regulatory motifs, also known as cis-regulatory elements (CREs), by various proteins in gene promoter regions. Localization of these motifs near the transcription start site (TSS) or translation start site (ATG) is crucial for transcription initiation and rate. Transcription levels of individual genes, regulated by these motifs, can vary significantly across tissues and developmental stages, especially in processes like sexual reproduction. However, the precise localization and visualization of these motifs in relation to gene expression in specific tissues can be challenging. Here, we introduce a freely available tool called GOLEM (Gene regulatOry eLEMents; https://golem.ncbr.muni.cz), which enables users to precisely locate any motif of interest with respect to TSS or ATG within the relevant plant genomes across the plant Tree of Life (Chara, Marchantia, Physcomitrium, Azolla, Ceratopteris, Amborella, Oryza, Zea, Solanum and Arabidopsis). The visualization of the motifs is performed with respect to the transcript levels of particular genes in leaves and male reproductive tissues and can be compared with genome-wide distribution regardless of the transcription level. Additionally, genes with specific CREs at defined positions and high expression in selected tissues can be exported for further analysis. GOLEM's functionality is illustrated by its application to conserved motifs (e.g. TATA-box, ABRE, I-box, and TC-element), hormone-responsive elements (GCC-box, ARR10_binding motif), as well as to male gametophyte-related motifs (e.g., LAT52, MEF2, and DOF_core).
- Klíčová slova
- GOLEM, Gene regulatOry eLEMents, TSS, gametophyte, motif localization, plant genes, promoter elements, technical advance,
- MeSH
- Arabidopsis genetika MeSH
- genom rostlinný genetika MeSH
- počátek transkripce MeSH
- promotorové oblasti (genetika) * genetika MeSH
- pyl * genetika MeSH
- regulace genové exprese u rostlin genetika MeSH
- software * MeSH
- Publikační typ
- časopisecké články MeSH
Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.
We present a genome assembly from an individual female Spicauda simplicius (the Plain Longtail butterfly; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 610.1 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.54 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,506 protein coding genes.
- Klíčová slova
- Lepidoptera, Plain Longtail butterfly, Spicauda simplicius, chromosomal, genome sequence,
- Publikační typ
- časopisecké články MeSH
Canopy accession strategies reveal much about tree life histories and forest stand dynamics. However, the protracted nature of ascending to the canopy makes direct observation challenging. We use a reconstructive approach based on an extensive tree ring database to study the variability of canopy accession patterns of dominant tree species (Abies alba, Acer pseudoplatanus, Fagus sylvatica, Picea abies) in temperate mountain forests of Europe and elucidate how disturbance histories, climate, and topography affect canopy accession. All four species exhibited high variability of radial growth histories leading to canopy accession and indicated varying levels of shade tolerance. Individuals of all four species survived at least 100 years of initial suppression. Fir and particularly beech, however, survived longer periods of initial suppression, exhibited more release events, and reached the canopy later on average, with a larger share of trees accessing the canopy after initially suppressed growth. These results indicate the superior shade tolerance of beech and fir compared to spruce and maple. The two less shade-tolerant species conversely relied on faster growth rates, revealing their competitive advantage in non-suppressed conditions. Additionally, spruce from higher-elevation spruce-dominated forests survived shorter periods of initial shading and exhibited fewer releases, with a larger share of trees reaching the canopy after open canopy recruitment (i.e. in absence of suppression) and no subsequent releases compared to spruce growing in lower-elevation mixed forests. Finally, disturbance factors were identified as the primary driver of canopy accession, whereby disturbances accelerate canopy accession and consequently regulate competitive interactions. Intensifying disturbance regimes could thus promote shifts in species composition, particularly in favour of faster-growing, more light-demanding species.
- Klíčová slova
- Disturbance, Growth release, Irradiance, Radial growth, Shade tolerance, Suppression,
- MeSH
- Acer * MeSH
- buk (rod) * fyziologie MeSH
- jedle * MeSH
- lesy MeSH
- lidé MeSH
- smrk * MeSH
- stromy MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Evropa MeSH
