scholarly journals Evolution and expression of LEAFY genes in ferns and lycophytes

EvoDevo ◽  
2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Carolina Rodríguez-Pelayo ◽  
Barbara A. Ambrose ◽  
Alejandra Vasco ◽  
Juan F. Alzate ◽  
Natalia Pabón-Mora
Keyword(s):  
Functional Data ◽  
Large Scale ◽  
Developmental Stages ◽  
Phylogenetic Analyses ◽  
Seed Plant ◽  
Meristem Identity ◽  
Multiple Species ◽  
Species Specific ◽  
Selaginella Moellendorffii ◽  
Ferns And Lycophytes

Abstract Background The LEAFY (LFY) transcription factors are present in algae and across land plants. The available expression and functional data of these genes in embryophytes suggest that LFY genes control a plethora of processes including the first zygotic cell division in bryophytes, shoot cell divisions of the gametophyte and sporophyte in ferns, cone differentiation in gymnosperms and floral meristem identity in flowering plants. However, their putative plesiomorphic role in plant reproductive transition in vascular plants remains untested. Results We perform Maximum Likelihood (ML) phylogenetic analyses for the LFY gene lineage in embryophytes with expanded sampling in lycophytes and ferns. We recover the previously identified seed plant duplication that results in LEAFY and NEEDLY paralogs. In addition, we recover multiple species-specific duplications in ferns and lycophytes and large-scale duplications possibly correlated with the occurrence of whole genome duplication (WGD) events in Equisetales and Salviniales. To test putative roles in diverse ferns and lycophytes we perform LFY expression analyses in Adiantum raddianum, Equisetum giganteum and Selaginella moellendorffii. Our results show that LFY genes are active in vegetative and reproductive tissues, with higher expression in early fertile developmental stages and during sporangia differentiation. Conclusions Our data point to previously unrecognized roles of LFY genes in sporangia differentiation in lycophytes and ferns and suggests that functions linked to reproductive structure development are not exclusive to seed plant LFY homologs.

scholarly journals Evolution of gene expression across species and specialized zooids in Siphonophora

2021 ◽  
Author(s):  
Catriona Munro ◽  
Felipe Zapata ◽  
Mark Howison ◽  
Stefan Siebert ◽  
Casey W Dunn
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Gene Trees ◽  
Species Trees ◽  
Examine Gene Expression ◽  
Specialized Tissue ◽  
Species Specific

Background: Siphonophores are complex colonial animals, consisting of asexually-produced bodies (called zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to investigate gene expression patterns in five zooids and one specialized tissue (pneumatophore) across seven siphonophore species. Analyses of gene expression across species present several challenges, including identification of comparable expression changes on gene trees with complex histories of speciation, duplication, and loss. Here, we conduct three analyses of expression. First, we examine gene expression within species. Then, we conduct classical analyses examining expression patterns between species. Lastly, we introduce Speciation Branch Filtering, which allows us to examine the evolution of expression in a phylogenetic framework. Results: Within and across species, we identified hundreds of zooid-specific and species-specific genes, as well as a number of putative transcription factors showing differential expression in particular zooids and developmental stages. We found that gene expression patterns tended to be largely consistent in zooids with the same function across species, but also some large lineage-specific shifts in gene expression. Conclusions: Our findings show that patterns of gene expression have the potential to define zooids in colonial organisms. We also show that traditional analyses of the evolution of gene expression focus on the tips of gene phylogenies, identifying large-scale expression patterns that are zooid or species variable. The new explicit phylogenetic approach we propose here focuses on branches (not tips) offering a deeper evolutionary perspective into specific changes in gene expression within zooids along all branches of the gene (and species) trees.

scholarly journals Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation

2019 ◽  
Vol 20 (12) ◽  
pp. 3101 ◽  
Author(s):  
Saurabh Gupta ◽  
Yanni Dong ◽  
Paul P. Dijkwel ◽  
Bernd Mueller-Roeber ◽  
Tsanko S. Gechev
Keyword(s):  
Phylogenetic Analyses ◽  
Cellular Damage ◽  
Antioxidant Genes ◽  
Regulatory Modules ◽  
Genome Wide ◽  
Selaginella Lepidophylla ◽  
Detoxification Systems ◽  
Antioxidant Defense Systems ◽  
Species Specific ◽  
Selaginella Moellendorffii

Abiotic stress is one of the major threats to plant crop yield and productivity. When plants are exposed to stress, production of reactive oxygen species (ROS) increases, which could lead to extensive cellular damage and hence crop loss. During evolution, plants have acquired antioxidant defense systems which can not only detoxify ROS but also adjust ROS levels required for proper cell signaling. Ascorbate peroxidase (APX), glutathione peroxidase (GPX), catalase (CAT) and superoxide dismutase (SOD) are crucial enzymes involved in ROS detoxification. In this study, 40 putative APX, 28 GPX, 16 CAT, and 41 SOD genes were identified from genomes of the resurrection species Boea hygrometrica, Selaginella lepidophylla, Xerophyta viscosa, and Oropetium thomaeum, and the mesophile Selaginella moellendorffii. Phylogenetic analyses classified the APX, GPX, and SOD proteins into five clades each, and CAT proteins into three clades. Using co-expression network analysis, various regulatory modules were discovered, mainly involving glutathione, that likely work together to maintain ROS homeostasis upon desiccation stress in resurrection species. These regulatory modules also support the existence of species-specific ROS detoxification systems. The results suggest molecular pathways that regulate ROS in resurrection species and the role of APX, GPX, CAT and SOD genes in resurrection species during stress.

scholarly journals A multi-bioassay integrated approach to assess antifouling potential of extracts from the Mediterranean sponge Ircinia oros

2021 ◽  
Author(s):  
Lucia De Marchi ◽  
Carlo Pretti ◽  
Alessia Cuccaro ◽  
Matteo Oliva ◽  
Federica Tardelli ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Integrated Approach ◽  
Common Species ◽  
Marine Diatom ◽  
Cellular Damage ◽  
Inhibition Of Growth ◽  
Aliivibrio Fischeri ◽  
The Mediterranean ◽  
Ircinia Oros ◽  
Species Specific

AbstractThe phylum Porifera and their symbionts produce a wide variety of bioactive compounds, playing a central role in their ecology and evolution. In this study, four different extracts (obtained by non-polar and semi-polar extraction methodologies) of the Mediterranean sponge Ircinia oros were tested through a multi-bioassay integrated approach to assess their antifouling potential. Tests were performed using three common species, associated with three different endpoints: the marine bacterium Aliivibrio fischeri (inhibition of bioluminescence), the marine diatom Phaeodactylum tricornutum (inhibition of growth), and different development stages of the brackish water serpulid Ficopomatus enigmaticus (gametes: sperm motion, vitality inhibition and cellular damage; larvae: development; adults: AChE (acetylcholinesterase)-inhibitory activity). The effects of extracts were species specific and did not vary among different extraction methodologies. In particular, no significant reduction of bioluminescence of A. fischeri was observed for all tested samples. By contrast, extracts inhibited P. tricornutum growth and had toxic effects on different F. enigmaticus’ developmental stages. Our results suggest that the proposed test battery can be considered a suitable tool as bioactivity screening of marine natural products.

scholarly journals The Effect of an Anthropogenic Magnetic Field on the Early Developmental Stages of Fishes—A Review

2021 ◽  
Vol 22 (3) ◽  
pp. 1210
Author(s):  
Krzysztof Formicki ◽  
Agata Korzelecka-Orkisz ◽  
Adam Tański
Keyword(s):  
Magnetic Fields ◽  
Developmental Stages ◽  
Negative Influence ◽  
Pigment Cells ◽  
Egg Activation ◽  
Industrial Equipment ◽  
Positive Effects ◽  
Early Developmental Stages ◽  
Species Specific ◽  
Early Developmental

The number of sources of anthropogenic magnetic and electromagnetic fields generated by various underwater facilities, industrial equipment, and transferring devices in aquatic environment is increasing. These have an effect on an array of fish life processes, but especially the early developmental stages. The magnitude of these effects depends on field strength and time of exposure and is species-specific. We review studies on the effect of magnetic fields on the course of embryogenesis, with special reference to survival, the size of the embryos, embryonic motor function, changes in pigment cells, respiration hatching, and directional reactions. We also describe the effect of magnetic fields on sperm motility and egg activation. Magnetic fields can exert positive effects, as in the case of the considerable extension of sperm capability of activation, or have a negative influence in the form of a disturbance in heart rate or developmental instability in inner ear organs.

scholarly journals Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

2021 ◽  
Author(s):  
Cecilia Di Bernardi ◽  
Camilla Wikenros ◽  
Eva Hedmark ◽  
Luigi Boitani ◽  
Paolo Ciucci ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Multiple Species ◽  
Species Specific

scholarly journals Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Science ◽  
2021 ◽  
pp. eabf2946
Author(s):  
Louis du Plessis ◽  
John T. McCrone ◽  
Alexander E. Zarebski ◽  
Verity Hill ◽  
Christopher Ruis ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Transmission Dynamics ◽  
Genetic Lineage ◽  
Size Dependent ◽  
Spatio Temporal ◽  
The Uk ◽  
Lineage Structure ◽  
And Control ◽  
Lineage Diversity

The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, while lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

scholarly journals Interacting effects of insect and ungulate herbivory on Scots pine growth

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Michelle Nordkvist ◽  
Maartje J. Klapwijk ◽  
La rs Edenius ◽  
Christer Björkman
Keyword(s):  
Plant Growth ◽  
Scots Pine ◽  
Growth Response ◽  
Insect Herbivory ◽  
Additive Effects ◽  
Significant Interaction Effect ◽  
Ungulate Herbivory ◽  
Pine Trees ◽  
Multiple Species ◽  
Species Specific

AbstractMost plants are subjected to damage from multiple species of herbivores, and the combined impact on plant growth can be non-additive. Since plant response to herbivores tends to be species specific, and change with repeated damage, the outcome likely depend on the sequence and number of attacks. There is a high likelihood of non-additive effects on plant growth by damage from mammals and insects, as mammalian herbivory can alter insect herbivore damage levels, yet few studies have explored this. We report the growth response of young Scots pine trees to sequential mammal and insect herbivory, varying the sequence and number of damage events, using an ungulate-pine-sawfly system. Combined sawfly and ungulate herbivory had both additive and non-additive effects on pine growth—the growth response depended on the combination of ungulate browsing and sawfly defoliation (significant interaction effect). Repeated sawfly herbivory reduced growth (compared to single defoliation) on un-browsed trees. However, on browsed trees, depending on when sawfly defoliation was combined with browsing, trees exposed to repeated sawfly herbivory had both higher, lower and the same growth as trees exposed to a single defoliation event. We conclude that the sequence of attacks by multiple herbivores determine plant growth response.

scholarly journals Cloning, Characterization, and RNA Interference Effect of the UDP-N-Acetylglucosamine Pyrophosphorylase Gene in Cnaphalocrocis medinalis

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 464
Author(s):  
Yuan-Jin Zhou ◽  
Juan Du ◽  
Shang-Wei Li ◽  
Muhammad Shakeel ◽  
Jia-Jing Li ◽  
...  
Keyword(s):  
Developmental Disorders ◽  
Developmental Stages ◽  
Phylogenetic Analyses ◽  
Digital Pcr ◽  
Cnaphalocrocis Medinalis ◽  
Chitin Synthesis ◽  
Reading Frame ◽  
Rnai Technology ◽  
Glyphodes Pyloalis ◽  
Key Enzyme

The rice leaf folder, Cnaphalocrocis medinalis is a major pest of rice and is difficult to control. UDP-N-acetylglucosamine pyrophosphorylase (UAP) is a key enzyme in the chitin synthesis pathway in insects. In this study, the UAP gene from C. medinalis (CmUAP) was cloned and characterized. The cDNA of CmUAP is 1788 bp in length, containing an open reading frame of 1464 nucleotides that encodes 487 amino acids. Homology and phylogenetic analyses of the predicted protein indicated that CmUAP shared 91.79%, 87.89%, and 82.75% identities with UAPs of Glyphodes pyloalis, Ostrinia furnacalis, and Heortia vitessoides, respectively. Expression pattern analyses by droplet digital PCR demonstrated that CmUAP was expressed at all developmental stages and in 12 tissues of C. medinalis adults. Silencing of CmUAP by injection of double-stranded RNA specific to CmUAP caused death, slow growth, reduced feeding and excretion, and weight loss in C. medinalis larvae; meanwhile, severe developmental disorders were observed. The findings suggest that CmUAP is essential for the growth and development of C. medinalis, and that targeting the CmUAP gene through RNAi technology can be used for biological control of this insect.

scholarly journals Bark traits, decomposition and flammability of Australian forest trees

2017 ◽  
Vol 65 (4) ◽  
pp. 327 ◽  
Author(s):  
Saskia Grootemaat ◽  
Ian J. Wright ◽  
Peter M. van Bodegom ◽  
Johannes H. C. Cornelissen ◽  
Veronica Shaw
Keyword(s):  
Forest Tree ◽  
Remarkable Feature ◽  
Interspecific Differences ◽  
Eucalypt Plantations ◽  
Physical Traits ◽  
Key Driver ◽  
Multiple Species ◽  
Species Specific ◽  
First Time ◽  
Different Tissues

Bark shedding is a remarkable feature of Australian trees, yet relatively little is known about interspecific differences in bark decomposability and flammability, or what chemical or physical traits drive variation in these properties. We measured the decomposition rate and flammability (ignitibility, sustainability and combustibility) of bark from 10 common forest tree species, and quantified correlations with potentially important traits. We compared our findings to those for leaf litter, asking whether the same traits drive flammability and decomposition in different tissues, and whether process rates are correlated across tissue types. Considerable variation in bark decomposability and flammability was found both within and across species. Bark decomposed more slowly than leaves, but in both tissues lignin concentration was a key driver. Bark took longer to ignite than leaves, and had longer mass-specific flame durations. Variation in flammability parameters was driven by different traits in the different tissues. Decomposability and flammability were each unrelated, when comparing between the different tissue types. For example, species with fast-decomposing leaves did not necessarily have fast-decomposing bark. For the first time, we show how patterns of variation in decomposability and flammability of bark diverge across multiple species. By taking species-specific bark traits into consideration there is potential to make better estimates of wildfire risks and carbon loss dynamics. This can lead to better informed management decisions for Australian forests, and eucalypt plantations, worldwide.

Genetic and morphological diversity of the cosmopolitan chaetognath Pseudosagitta maxima (Conant, 1896) in the Atlantic Ocean and its relationship with the congeneric species

2017 ◽  
Vol 74 (7) ◽  
pp. 1875-1884 ◽  
Author(s):  
Dmitry N. Kulagin ◽  
Tatiana V. Neretina
Keyword(s):  
Atlantic Ocean ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Morphological Diversity ◽  
Maturity Stage ◽  
Congeneric Species ◽  
Morphological Examination ◽  
Posterior Teeth ◽  
Biogeographic Patterns ◽  
True Diversity

Abstract Until recently many oceanic zooplankton species have been considered as cosmopolitan organisms. At present it became evident that some of them comprise many distinct molecular operational taxonomic units (MOTUs) that often are regarded as cryptic species. As they can significantly change our perceptions of large-scale biogeographic patterns, it is important to characterize the true diversity within common and ecologically important groups. We have analysed the molecular and morphological diversity of the cosmopolitan mesopelagic chaetognath Pseudosagitta maxima throughout the Atlantic Ocean from 60° S to 85° N and its position within the genus Pseudosagitta. Three distinct mitochondrial clades within P. maxima were revealed with phylogenetic analyses (Maximum Likelihood, Bayesian Inference) and were geographically separated. The subsequent analyses of nuclear markers (H3, ITS1) have shown that P. maxima most likely comprises two distinct MOTUs, tropical and bipolar, that also have some morphological differences. The latter MOTU consists of two genetically slightly divergent populations: southern and northern. The morphological examination allowed the determination of a character (type of hook coloration) that accurately distinguishes juveniles of the P. maxima complex from the other congeneric species. Molecular data have shown that evolutionary P. lyra and P. gazellae are more closely related to each other than to P. maxima. Number of hooks, number of anterior and posterior teeth and the arrangement of ova in the ovary were proposed to be the most useful morphological characters to distinguish between tropical and bipolar MOTUs within the P. maxima complex. The first three characters should be determined for each maturity stage separately.

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