Arthropoda Research Articles

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes.

BackgroundAmbitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. To guide forthcoming genome generation efforts and promote efficient prioritization of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data.FindingsHere we present an automated analysis workflow that surveys genome assemblies from the United States NCBI, assesses their completeness using the relevant BUSCO datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, examine how key assembly metrics relate to gene content completeness, and compare results from using different BUSCO lineage datasets.ConclusionsThese results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritizations for ongoing and future sampling, sequencing, and genome generation initiatives.

Complete mitochondrial genomes of three fairy shrimps from snowmelt pools in Japan

BackgroundFairy shrimps belong to order Anostraca, class Branchiopoda, subphylum Crustacea, and phylum Arthropoda. Three fairy shrimp species (Eubranchipus uchidai, E. asanumai, and E. hatanakai) that inhabit snowmelt pools are currently known in Japan. Whole mitochondrial genomes are useful genetic information for conducting phylogenetic analyses. Mitochondrial genome sequences for Branchiopoda members are gradually being collated.ResultsSix whole mitochondrial genomes from the three Eubranchipus species are presented here. Eubranchipus species share the anostracan pattern of gene arrangement in their mitochondrial genomes. The mitochondrial genomes of the Eubranchipus species have a higher GC content than those of other anostracans. Accelerated substitution rates in the lineage of Eubranchipus species were observed.ConclusionThis study is the first to obtain whole mitochondrial genomes for Far Eastern Eubranchipus species. We show that the nucleotide sequences of cytochrome oxidase subunit I and the 16S ribosomal RNA of E. asanumai presented in a previous study were nuclear mitochondrial DNA segments. Higher GC contents and accelerated substitution rates are specific characteristics of the mitochondrial genomes of Far Eastern Eubranchipus. The results will be useful for further investigations of the evolution of Anostraca as well as Branchiopoda.

Marine biofouling organisms on beached, buoyant and benthic plastic debris in the Catalan Sea

Plastic debris provides long-lasting substrates for benthic organisms, thus acting as a potential vector for their dispersion. Its interaction with these colonizers is, however, still poorly known. This study examines fouling communities on beached, buoyant and benthic plastic debris in the Catalan Sea (NW Mediterranean), and characterizes the plastic type. We found 14 specimens belonging to two phyla (Annelida and Foraminifera) on microplastics, and more than 400 specimens belonging to 26 species in 10 phyla (Annelida, Arthropoda, Brachiopoda, Bryozoa, Chordata, Cnidaria, Echinodermata, Mollusca, Porifera and Sipuncula) on macroplastics. With 15 species, bryozoans are the most diverse group on plastics. We also report 17 egg cases of the catshark Scyliorhinus sp., and highlight the implications for their dispersal. Our results suggest that plastic polymers may be relevant for distinct fouling communities, likely due to their chemical structure and/or surface properties. Our study provides evidence that biofouling may play a role in the sinking of plastic debris, as the most abundant fouled plastics had lower densities than seawater, and all bryozoan species were characteristic of shallower depths than those sampled. More studies at low taxonomic level are needed in order to detect new species introduction and potential invasive species associated with plastic debris.

The Diversity Of Macrozoobenthos River Aek Buru District Labuhan Batu Utara

Benthos are organisms that live in the bottom of the waters, either animal or plant, living on the surface and in the bottom of the waters. This study aims to determine the diversity of Macrozoobenthos in the River Aek Hurry. The study began in November 2021 to January 2021. Sampling of macrozoobenthos done using a Surber net. based on differences in the substrate at the base of the river. Macrozoobenthos found in the Aek Buru consists of two Phyla, namely the Arthropods and Mollusks. Phylum Arthropoda are found is of the class of Insects belonging to the genus Hydropsyche, Polycentropus, psephenus, Dryops, Anthopotamu, Acroneuria and Triops. The phylum of Mollusks that are found are from a class of Bilvavia included in the Genus Corbicula and of the class of Gastropods of the Genera Melanoides and Melanatria. The abundance of macrozoobenthos of the highest on each of the stations is Polycentropus (66,67 ind/L) and Potadoma (266,67 ind/L). The abundance of macrozoobenthos of the highest found is Melanatria by 622,2 ind/L. Based on the value of the Index of Diversity (H) (0,367 – 0,602) the index of dominance (C) (0,132 – 0,386) and the evenness (E) (0,367 – 0,602) River Aek Buru in the category good condition with high species diversity. Physical and chemical factors of the water body capable of supporting life macrozoobenthos.

Fragmentation in mitochondrial genomes in relation to elevated sequence divergence and extreme rearrangements

BackgroundA single circular mitochondrial (mt) genome is a common feature across most metazoans. The mt-genome includes protein-coding genes involved in oxidative phosphorylation, as well as RNAs necessary for translation of mt-RNAs, whose order and number are highly conserved across animal clades, with few known exceptions of alternative mt-gene order or mt-genome architectures. One such exception consists of the fragmented mitochondrial genome, a type of genome architecture where mt-genes are split across two or more mt-chromosomes. However, the origins of mt-genome fragmentation and its effects on mt-genome evolution are unknown. Here, we investigate these origin and potential mechanisms underlying mt-genome fragmentation, focusing on a genus of booklice, Liposcelis, which exhibits elevated sequence divergence, frequent rearrangement of mt-gene order, and fragmentation of the mt genome, and compare them to other Metazoan clades.ResultsWe found this genus Liposcelis exhibits very low conservation of mt-gene order across species, relative to other metazoans. Levels of gene order rearrangement were, however, unrelated to whether or not mt-genomes were fragmented or intact, suggesting mitochondrial genome fragmentation is not affecting mt-gene order directly. We further investigated possible mechanisms underpinning these patterns and revealed very high conservation of non-coding sequences at the edges of multiple recombination regions across populations of one particular Liposcelis species, supportive of a hypothesis that mt-fragmentation arises from recombination errors between mt-genome copies. We propose these errors may arise as a consequence of a heightened mutation rate in clades exhibiting mt-fragmentation. Consistent with this, we observed a striking pattern across three Metazoan phyla (Arthropoda, Nematoda, Cnidaria) characterised by members exhibiting high levels of mt-gene order rearrangement and cases of mt-fragmentation, whereby the mt-genomes of species more closely related to species with fragmented mt-genomes diverge more rapidly despite experiencing strong purifying selection.ConclusionsWe showed that contrary to expectations, mt-genome fragmentation is not correlated with the increase in mt-genome rearrangements. Furthermore, we present evidence that fragmentation of the mt-genome may be part of a general relaxation of a natural selection on the mt-genome, thus providing new insights into the origins of mt-genome fragmentation and evolution.

Organophosphate-based flame retardant (tris(1,3-dichloro-2-propyl) phosphate) reduces fecundity and impairs embryonic development in marine invertebrates

Context It is important to understand how marine invertebrates may be affected by tris(1,3-dichloro-2-propyl) phosphate (TDCIPP), as an organophosphorus flame retardant. Aim The present research verified the hypothesis that TDCIPP would adversely affect the growth, development and reproduction of Crepidula onyx (phylum Mollusca) and Tigriopus japonicus (phylum Arthropoda). Methods Effects of chronic exposure for the whole life cycle were examined at two concentrations of TDCIPP chosen on the basis of results from preliminary range-finding test. Key results Exposure to 1 and 10 μg L−1 of TDCIPP significantly reduced larval and juvenile survival rate and shell length in C. onyx. TDCIPP caused adverse reproductive effects, including abnormal embryonic development, which led to non-viable broods and the malformation of larvae. Exposure to TDCIPP resulted in a 100-fold increase in incidence rate of abnormal larva formation. In T. japonicus, exposure to TDCIPP (10 μg L−1) resulted in non-viable broods and a significant reduction in the number of eggs and number of nauplii. Conclusions Larval survival, larval growth, fecundity, and embryonic development were identified as the TDCIPP-affected ecological endpoints in the marine invertebrate C. onyx and T. japonicus. Implications From a management perspective, these results can help us assess the ecological risk posed by TDCIPP.

Crustacean and protozoan parasites of some cyprinid fish living in the Murat River (Bingöl-Türkiye), with new host records

Some Cyprinid fish species: Cyprinion macrostomum (Heckel, 1843), Capoeta umbla (Heckel, 1843), Chondrostoma regium (Heckel, 1843), and Squalius cephalus (Linnaeus, 1758) living naturally in the Murat River, were investigated for Protozoan and Crustacean parasite fauna and their distribution. Fish samples were collected from different stations between July 2017 - June 2019, examined in the Bingöl University Zoology Research Laboratory, and the data were explained with various variables. The normality test revealed that the data were not normally distributed (p< 0.05), as with large samples, so non-parametric tests explained the data. A total of 365 fish were examined, and 100 fish (27.4%) were infected with at least one Protozoan or Crustacean parasite. Four different parasite species were recorded on the examined fish, namely Ichthyophthirius multifiliis and Trichodina sp. belonging to the phylum Ciliophora (Protozoan), Ergasilus sieboldi, and Lamproglena pulchella belonging to the phylum Arthropoda (Crustacean). As a result of this study, for the first time, Protozoan and Crustacean parasites of different cyprinid fish were examined according to the host species, seasonal distribution, host size, and new host records were reported for three parasites.

Role of Invertebrate Diversity with Special Reference to Insects in Agro- biodiversity and Ecological Services – Indian Efforts

Invertebrates occupy larger proportion in the animal species diversity in almost all habitats and are important components of all ecosystems. The importance of the ecological role played by these invertebrates are not given due consideration and the diversity is under-sampled and understudied. Insects belonging to phylum Arthropoda form a major component that renders several ecological functions and ecosystem services. In this chapter, the importance of the insect services are highlighted and the role of ICAR-National Bureau of Agricultural Insect Resources, Bengaluru in documentation of the insect diversity, its utilization and conservation is emphasized, which are in line with the mandate of the Bureau and Delhi declaration on Agrobiodiversity management.

Status of Derailing Taxonomy and List of Indian Taxonomists Working on Various Taxa of Phylum Arthropoda

This review article is a brief introduction to taxonomy. How taxonomy play important role in conservation plans and why this field is important from the perspective of rich diversified India has been mentioned. This article is a tribute to all the eminent Indian taxonomists who have paved the sector of arthropod’s taxonomy and taxonomists who are working on it, making many unknown species documented and familiar to us. This article tries to acknowledge all the traditional taxonomists from the Indian subcontinent. Along with it much-needed measures have also been mentioned for conserving taxonomy and skilled taxonomists.

Overview of protein posttranslational modifications in Arthropoda venoms.

Accidents with venomous animals are a public health issue worldwide. Among the species involved in these accidents are scorpions, spiders, bees, wasps, and other members of the phylum Arthropoda. The knowledge of the function of proteins present in these venoms is important to guide diagnosis, therapeutics, besides being a source of a large variety of biotechnological active molecules. Although our understanding about the characteristics and function of arthropod venoms has been evolving in the last decades, a major aspect crucial for the function of these proteins remains poorly studied, the posttranslational modifications (PTMs). Comprehension of such modifications can contribute to better understanding the basis of envenomation, leading to improvements in the specificities of potential therapeutic toxins. Therefore, in this review, we bring to light protein/toxin PTMs in arthropod venoms by accessing the information present in the UniProtKB/Swiss-Prot database, including experimental and putative inferences. Then, we concentrate our discussion on the current knowledge on protein phosphorylation and glycosylation, highlighting the potential functionality of these modifications in arthropod venom. We also briefly describe general approaches to study “PTM-functional-venomics”, herein referred to the integration of PTM-venomics with a functional investigation of PTM impact on venom biology. Furthermore, we discuss the bottlenecks in toxinology studies covering PTM investigation. In conclusion, through the mining of PTMs in arthropod venoms, we observed a large gap in this field that limits our understanding on the biology of these venoms, affecting the diagnosis and therapeutics development. Hence, we encourage community efforts to draw attention to a better understanding of PTM in arthropod venom toxins.

Testing the Presence of an Opportunistic Pathogen Nosema ceranae (Microsporidia) in Housefly (Musca domestica) using Polymerase Chain Reaction

Houseflies, being vector of serious human disease, have been extensively used in the laboratory to research on aging and sex determination. It also plays an important role in breaking down the organic matter and thus makes its contribution in food cycle. Houseflies belong to the phylum Arthropoda and serves as vector for many pathogens transmiting disease from lower to higher vertebrates. Microsporidiosis (also known as nosemosis) is a disorder of honeybee and various other pollinators belonging to the class Insecta that are affecting nation’s economy up to a great extent. Microsporidian spores have reportedly infected insects, fishes, crustaceous, human and thus causing huge threat to society. In order to establish a clear understanding for its role in the transmission of microsporidiosis, the present study was designed to detect and identify a microsporidian parasite- Nosema ceranae by amplifying 16sRNA (Small Subunit rRNA) gene using molecules technique Polymerase Chain Reaction (PCR). Results of the present study suggested no existence of Nosema ceranae spores as, in spite of performing gradient PCR, no amplification of gene occurred. The research work paves a way for other researchers to investigate the possible reasons behind the absence of Nosema ceranae infection in housefly and also on why the infection is not prevalent in this model organism.

Three-dimensional modeling as a methodological innovation for teaching zoology and as a strategy for environmental education

The great diversity of animals and the relationship between their morphological characteristics, adaptations and life strategies are approached in the teaching of zoology. The use of innovative and alternative methodologies, such as zoological modeling, are tools that can contribute to a high interest in the study of zoology and it is use in an environmental education strategy. In this study, the zoological modeling intermediated the teaching-learning process in undergraduate students of the Biological Sciences course and the connection of teaching practices with environmental extension activities. Twenty-two animal models were built with representatives of the Phylum Arthropoda, Mollusca, Cnidaria and Echinodermata, approaching aspects of external, internal morphology and life cycle. The process of perception, viability and assimilation of the construction of the zoological modeling was analyzed through interviews with 40 undergraduates and 100 children and teenagers, the target audience of the workshops. The results showed that the three-dimensional modeling stimulates environmental students in the teaching-learning process and it is use in education activities were efficient, awakening curiosity, enabling the demystification of animals and the dissemination of their essential ecosystem services for the conservation of biodiversity.

Impacts of Anthropogenic Stressors on Hydrochemistry, Benthic Macroinvertebrates and Sediment Characteristics of the Lagos Lagoon, Nigeria

The anthropogenic impact on the water, benthic macroinvertebrates and sediment grain size of Lagos lagoon was investigated between July and October, 2019. Ten sampling stations were selected based on their importance as likely sources of different forms of anthropogenic stressor to the lagoon. Water temperatures, pH and salinity were measured in situ. Water and benthic samples were collected monthly and analysed using standard methods. Nutrient levels were determined using a spectrophotometer. The hydrochemistry of the stations differed significantly (p<0.05) with the exception of temperature and pH. The sediment grains across the study stations consists basically of sand and mud, with sand dominating the grain type. A total of 502 individuals comprising 3 phyla, 4 classes, 10 families and 11 species was recorded. The phylum mollusca which contributed 92% to the total number of individuals was represented by two Classes; Gastropoda and Bivalvia, with the gastropod Tympanotonus fuscatus having the highest number of individuals (321). Thephylum Annelida represented by one Class, Polychaeta and two Species Nereis sp. and Capitella capitata contributed 6% to the total number of individuals. The class Crustacea, representing the Phylum Arthropoda was the least sampled (7 individuals) constituting about 1.4% of the total population Result showed that different pollution sources have negatively impacted the water chemistry of the lagoon and reduced the diversity and abundance of its benthic macroinvertebrates community. The sedentary nature of this group of benthic fauna could be the major reason why they are most impacted.

Ecological interactions between invasive and native fouling species in the reservoir of a hydroelectric plant

In this study, we investigate the main ecological interactions between fouling aquatic organisms (both invasive and native) present in the reservoir of the Governador José Richa hydroelectric plant, located in southern Brazil, and to identify the most suitable period for the interruption of machinery operation for cleaning and maintenance of the hydraulic systems of this plant. A total of 32 experimental plates were fixed to a metallic structure positioned close to the plant's water intake. Three species of invasive fouling were identified in our samples (Limnoperna fortunei [Mollusca], Cordylophora sp., and Hydra sp. [Cnidaria]) and six native taxa belonging to the phyla Protozoa, Ciliophora, Amoebozoa, and Arthropoda. Spring and summer were the seasons with the highest fouling rates, as well as densities of fouling organisms. The highest levels of diversity were recorded during the colder seasons. Several interactions between the organisms were identified, such as mutualism, commensalism, competition, epibiosis, cannibalism, and predation. The data obtained suggest that, from the biological point of view, the most suitable period for machine shutdown destined for the removal of biological fouling in the hydraulic systems of the studied plant is between the end of spring and the beginning of summer.

Species That Fly at a Higher Game: Patterns of Deep–Water Emergence Along the Chilean Coast, Including a Global Review of the Phenomenon

Deep-water emergence (DWE) is the phenomenon where marine species normally found at great depths (i.e., below 200 m), can be found locally occurring in significantly shallower depths (i.e., euphotic zone, usually shallower than 50 m). Although this phenomenon has been previously mentioned and deep-water emergent species have been described from the fjord regions of North America, Scandinavia, and New Zealand, local or global hypotheses to explain this phenomenon have rarely been tested. This publication includes the first literature review on DWE. Our knowledge of distribution patterns of Chilean marine invertebrates is still very scarce, especially from habitats below SCUBA diving depth. In our databases, we have been gathering occurrence data of more than 1000 invertebrate species along the Chilean coast, both from our research and from the literature. We also distributed a list of 50 common and easily in situ-identifiable species among biologically experienced sport divers along the Chilean coast and recorded their sighting reports. Among other findings, the analysis of the data revealed patterns from 28 species and six genera with similar longitudinal and bathymetric distribution along the entire Chilean coast: along the Chilean coast these species are typically restricted to deep water (>200 m) but only in some parts of Chilean Patagonia (>39°S–56°S), the same species are also common to locally abundant at diving depths (<30 m). We found 28 of these ‘deep’ species present in shallow-water of North Patagonia, 32 in Central Patagonia and 12 in South Patagonia. The species belong to the phyla Cnidaria (six species), Mollusca (four species), Arthropoda (two species) and Echinodermata (16 species). We ran several analyses comparing depth distribution between biogeographic regions (two-way ANOVA) and comparing abiotic parameters of shallow and deep sites to search for correlations of distribution with environmental variables (Generalized Linear Models). For the analyses, we used a total of 3328 presence points and 10635 absence points. The results of the statistical analysis of the parameters used, however, did not reveal conclusive results. We summarize cases from other fjord regions and discuss hypotheses of DWE from the literature for Chilean Patagonia.

Review: Manfaat Feromon Sek Pada Ordo Lepidoptera Untuk Pengendalian Hama Lepidoptera

Lepidoptera is one of the orders of the phylum Arthropoda Insecta class consist of butterflies that are active during the day and moths at night. Both of them belong to the order Lepidoptera and have an important role in the ecosystem. Beneficial role for plants as pollinating insects and disadvantaged role as pests of cultivated plants. An example is the fall armyworm Spodoptera sp attacking rice plants, Pteroma sp attacks sengon plants, and Helicoverpa armigera attacks red chili plants. One of the efforts to control pests is the use of sex pheromones. Several types of sex pheromones were identified, for example the sex pheromone of the cabbage leaf caterpillar Pluttela xylostella was )-11-hexadecenal, (Z)-11-hexadecenol, and (Z)-11-hexadecenyl acetate with ratio 8:18:100 and 10:1:90. Potato tuber borer (Phthorimaea operculella Zell.) sex pheromones is (E,Z)- 4,7-13 Ac (trans-4, cis-7-tridecadienyl acetate) and (E,Z,Z)-4,7,10-13 Ac (trans-4, cis-7, cis-10-tridecatrienyl acetate) with ratio 1 : 2,5. Using pheromones sex on agricultural land can significantly suppress Lepidoptera pest populations.

Komunitas makrozoobentos dan kaitannya dengan kualitas air aliran sungai Senggarang, Kota Tanjungpinang

Senggarang is one of the coastal villages in Tanjungpinang City which has a river that flows from the upstream downstream into the sea. The flow of the Senggarang river has distinctive characteristics that are commonly found in small island waters, namely having a relatively short upstream to downstream distance, and the downstream part is influenced by tidal conditions. Various activities along the Senggarang river flow would cause changes in water quality which would impact the presence of macrozoobenthic. The objective of this study was to determine the relationship between the macrozoobenthic community and the water quality of the Senggarang river. Macrozoobenthic sampling, and environmental parameters were carried out using random sampling methods. The results of this study were obtained 27 species from 6 phylum, namely phylum Arthropoda 13 species, phylum Ciliophora 3 species, phylum Echinodermata 1 species, phylum Mollusca 4 species, phylum Nematoda 5 species, and phylum Tardigrada 1 species. The average macrozoobenthic density is 172 ind./ m3 for freshwater and 704 ind./ m3 for brackish waters. The average diversity value for freshwater is 1.29 and 2.16 waters with medium salinity, the average uniformity value of 0.85 freshwater and 0.94 of high in brackish waters, the average dominance value of 0.32 freshwater and 0.13 of low in brackish waters. The relationship of macrozoobenthos with the quality of freshwater based on PCA analyses related to temperature and dissolved oxygen, in brackish waters to temperature, dissolved oxygen, and current.Keywords: Macrozoobenthic community, PCA, River flow, Water quality

Dead, fossil or alive: Bioapatite diagenesis and fossilization

Calcium carbonate, silica and calcium phosphate have been selectively used by organisms in the production of mineralized hard parts throughout the Phanerozoic. Among these materials, bioapatite has enabled fundamental acquisitions in the evolution of life. Despite the remarkable biological success, the crystallography of bioapatite and the eventual modification of its lattice parameters over geological time have in contrast been scarcely investigated.In our study, we analyzed living, dead and fossil remains of both vertebrate and invertebrate organisms that biomineralized apatite, ranging from the Cambrian to the Recent, a time interval spanning over 500 million years. We detected in this way the bioapatite crystal features of the major phosphatic phyla (Brachiopoda, Arthropoda, Bryozoa, and Chordata: the latter including conodonts, cartilaginous and bony fishes, amphibians, reptiles, birds and mammals). Groups were investigated using either fossil or recent material (dead and/or alive, the former indicating organisms who died in recent times, the latter referring to material extracted from living organisms). The experimental results revealed that phosphatic materials from living, dead, and fossilized organisms have a distinct crystallographic signature. In fact, bioapatite in fossils is characterized by lower values of the crystal lattice cell parameter a (9.320–9.439 Å compared to 9.355–9.466 Å in dead and alive organisms), whereas the cell parameter c is less variable (6.857–6.911 Å for fossils and 6.861–6.902 Å for recent bioapatite); Student t-tests, applied to the means of these ranges of values (a¯=9.369 Å, c¯=6.887 Å, volume¯=523.6 Å3 for fossil values, a¯=9.415 Å, c¯=6.878 Å, volume¯=528.0 Å3 for recent values), highlighted significant differences between fossils and recent samples at a level p < 0.01 for the three cell parameters. These changes, which begin at the death of the organism and only stabilize in the ultimate stages of fossilization, mirror the isomorphic chemical substitutions within the crystal lattice and drive to a general decrease of the cell volume (i.e., the volume of the bioapatite hexagonal crystalline cell frame) over time, with an average reduction of 4.4 Å3 (0.8%) from alive to fossil organisms.

Marine invertebrates associated with rhodoliths/maërl beds from northeast Brazil (State of Paraíba).

BackgroundThis study investigates the marine macroinvertebrate fauna of rhodolith beds (non-geniculated red corallinaceaous algae) in northeast Brazilian. A total of 57 species were identified, belonging to six phyla (Platyhelminthes, Annelida, Sipuncula, Mollusca, Arthropoda and Echinodermata), of which 50 are considered here as new records for the Paraíba State. Annelids (Class Polychaeta) were the most representative taxa in Miramar and Seixas Beaches, while molluscs were dominant in Maceió Beach.New informationThis is the first study that includes an identification key, diagnostic features and distribution patterns worldwide and local (including new records) of the marine invertebrate fauna associated with rhodolith beds in northeast Brazil (State of Paraíba). Sampling events were performed in 2018, at low tide in the intertidal to shallow subtidal zones (1.5 and 4.0 m depth), in Miramar, Seixas and Maceió Beaches. A total of 17 species were found for the first time on Seixas Beach, as well as all identified species for Miramar and Maceió. This study tries to contribute to the knowledge of marine invertebrates in northeast Brazilian shallow habitats, providing a baseline for future environmental studies.

The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research

Simple SummaryHigh-quality genome assemblies are essential tools for modern biological research. In the past, creating genome assemblies was prohibitively expensive and time-consuming for most non-model insect species due to, in part, the technical challenge of isolating the necessary quantity and quality of DNA from many species. Sequencing methods have now improved such that many insect genomes can be sequenced and assembled at scale. We created the Ag100Pest Initiative to propel agricultural research forward by assembling reference-quality genomes of important arthropod pest species. Here, we describe the Ag100Pest Initiative’s processes and experimental procedures. We show that the Ag100Pest Initiative will greatly expand the diversity of publicly available arthropod genome assemblies. We also demonstrate the high quality of preliminary contig assemblies. We share arthropod-specific technical details and insights that we have gained during the project. The methods and preliminary results presented herein should help other researchers attain similarly high-quality assemblies, effectively changing the landscape of insect genomics.The phylum Arthropoda includes species crucial for ecosystem stability, soil health, crop production, and others that present obstacles to crop and animal agriculture. The United States Department of Agriculture’s Agricultural Research Service initiated the Ag100Pest Initiative to generate reference genome assemblies of arthropods that are (or may become) pests to agricultural production and global food security. We describe the project goals, process, status, and future. The first three years of the project were focused on species selection, specimen collection, and the construction of lab and bioinformatics pipelines for the efficient production of assemblies at scale. Contig-level assemblies of 47 species are presented, all of which were generated from single specimens. Lessons learned and optimizations leading to the current pipeline are discussed. The project name implies a target of 100 species, but the efficiencies gained during the project have supported an expansion of the original goal and a total of 158 species are currently in the pipeline. We anticipate that the processes described in the paper will help other arthropod research groups or other consortia considering genome assembly at scale.