This section includes a list of the latest IPNA scientific articles published in journals included in the Science Citation Index (SCI).
In DIGITAL.CSIC, institutional repository of the CSIC, you can find the complete list of scientific articles since 1962, as well as other collections of interest such as congresses, theses, books, informative material, etc. of the centre. The aim of DIGITAL.CSIC is to organize, preserve and disseminate in open access the results of our research.
In the institutional repository of the CSIC, you can find the complete list of scientific articles, as well as other collections of interest such as congresses, theses, books, informative material, etc.
Analysis of the IPNA 2014-2019 Scientific Production: bibliometric analysis from data collected in Scopus and Web of Science.
Bioinformatic Analysis of Genome-Predicted Bat Cathelicidins
Bats are unique in their potential to serve as reservoir hosts for intracellular pathogens. Recently, the impact of COVID-19 has relegated bats from biomedical darkness to the frontline of public health as bats are the natural reservoir of many viruses, including SARS-Cov-2. Many bat genomes have been sequenced recently, and sequences coding for antimicrobial peptides are available in the public databases. Here we provide a structural analysis of genome-predicted bat cathelicidins as components of their innate immunity. A total of 32 unique protein sequences were retrieved from the NCBI database. Interestingly, some bat species contained more than one cathelicidin. We examined the conserved cysteines within the cathelin-like domain and the peptide portion of each sequence and revealed phylogenetic relationships and structural dissimilarities. The antibacterial, antifungal, and antiviral activity of peptides was examined using bioinformatic tools. The peptides were modeled and subjected to docking analysis with the region binding domain (RBD) region of the SARS-CoV-2 Spike protein. The appearance of multiple forms of cathelicidins verifies the complex microbial challenges encountered by these species. Learning more about antiviral defenses of bats and how they drive virus evolution will help scientists to investigate the function of antimicrobial peptides in these species.
Pérez de Lastra, José Manuel; Asensio-Calavia, Patricia; González-Acosta, Sergio; Baca-González, Victoria; Morales-de la Nuez, Antonio
The Essentials of Marine Biotechnology
Coastal countries have traditionally relied on the existing marine resources (e.g., fishing, food, transport, recreation, and tourism) as well as tried to support new economic endeavors (ocean energy, desalination for water supply, and seabed mining). Modern societies and lifestyle resulted in an increased demand for dietary diversity, better health and well-being, new biomedicines, natural cosmeceuticals, environmental conservation, and sustainable energy sources. These societal needs stimulated the interest of researchers on the diverse and underexplored marine environments as promising and sustainable sources of biomolecules and biomass, and they are addressed by the emerging field of marine (blue) biotechnology. Blue biotechnology provides opportunities for a wide range of initiatives of commercial interest for the pharmaceutical, biomedical, cosmetic, nutraceutical, food, feed, agricultural, and related industries. This article synthesizes the essence, opportunities, responsibilities, and challenges encountered in marine biotechnology and outlines the attainment and valorization of directly derived or bio-inspired products from marine organisms. First, the concept of bioeconomy is introduced. Then, the diversity of marine bioresources including an overview of the most prominent marine organisms and their potential for biotechnological uses are described. This is followed by introducing methodologies for exploration of these resources and the main use case scenarios in energy, food and feed, agronomy, bioremediation and climate change, cosmeceuticals, bio-inspired materials, healthcare, and well-being sectors. The key aspects in the fields of legislation and funding are provided, with the emphasis on the importance of communication and stakeholder engagement at all levels of biotechnology development. Finally, vital overarching concepts, such as the quadruple helix and Responsible Research and Innovation principle are highlighted as important to follow within the marine biotechnology field. The authors of this review are collaborating under the European Commission-funded Cooperation in Science and Technology (COST) Action Ocean4Biotech – European transdisciplinary networking platform for marine biotechnology and focus the study on the European state of affairs.
Rotter, Ana; Barbier, Michéle; Bertoni, Franceso; Bones, Atle M.; Cancela, M. Leonor; Carlsson, Jens; Carvalho, Maria F.; Cegłowska, Marta; Chirivella-Martorell, Jerónimo; Conk Dalay, Meltem; Cueto, Mercedes; Dailianis, Thanos; Deniz, Irem; Díaz-Marrero, Ana R.; Drakulovic, Dragana; Dubnika, Arita; Edwards, Christine; Einarsson, Hjörleifur; Erdogan, Aysegül; Eroldogan, Orhan Tufan; Ezra, David; Fazi, Stefano; FitzGerald, Richard J.; Gargan, Laura M.; Gaudêncio, Susana P.; Gligora Udovic, Marija; Ivoševic DeNardis, Nadica; Jónsdóttir, Rósa; Kataržyte, Marija; Klun, Katja; Kotta, Jonne; Ktari, Leila; Ljubešic, Zrinka; Lukic Bilela, Lada; Mandalakis, Manolis; Massa-Gallucci, Alexia; Matijošyte, Inga; Mazur-Marzec, Hanna; Mehiri, Mohamed; Laurentius Nielsen, Søren; Novoveská, Lucie; Overlingé, Donata; Perale, Guiseppe; Ramasamy, Praveen; Rebours, Céline; Reinsch, Thorsten; Reyes, Fernando; Rinkevich, Baruch; Robbens, Johan; Röttinger, Eric; Rudovica, Vita; Sabotic, Jerica; Safarik, Ivo; Talve, Siret; Tasdemir, Deniz; Theodotou Schneider, Xenia; Thomas, Olivier P.; Torunska-Sitarz, Anna; Varese, Giovanna Cristina; Vasquez, Marlen I.
Impact of Zinc, Glutathione, and Polyphenols as Antioxidants in the Immune Response against SARS-CoV-2
SARS-CoV-2, the coronavirus triggering the disease COVID-19, has a catastrophic health and socioeconomic impact at a global scale. Three key factors contribute to the pathogenesis of COVID-19: excessive inflammation, immune system depression/inhibition, and a set of proinflammatory cytokines. Common to these factors, a central function of oxidative stress has been highlighted. A diversity of clinical trials focused predominantly on antioxidants are being implemented as potential therapies for COVID-19. In this study, we look at the role of zinc, glutathione, and polyphenols, as key antioxidants of possible medicinal or nutritional significance, and examine their role in the antiviral immune response induced by SARS-Cov-2. An unresolved question is why some people experience chronic COVID and others do not. Understanding the relationship between SARS-CoV-2 and the immune system, as well as the role of defective immune responses to disease development, would be essential to recognize the pathogenesis of COVID-19, the risk factors that affect the harmful consequences of the disease, and the rational design of successful therapies and vaccinations. We expect that our research will provide a novel perspective that contributes to the design of clinical or nutritional targets for the prevention of this pandemic.
Pérez de Lastra, José Manuel; Andrés-Juan, Celia; Plou Gasca, Francisco José; Pérez-Lebeña, Eduardo
Three new subterranean species of Baezia (Curculionidae, Molytinae) for the Canary Islands
The genus Baezia Alonso-Zarazaga & García, 1999 is endemic to the Canary Islands, where four species were known to date. Based on morphological evidence, three new species of Baezia are described in this study: Baezia aranfaybo García & López, sp. nov. from El Hierro island, and Baezia madai García & Oromí sp. nov. and Baezia tizziri García & Andújar, sp. nov. from La Palma island. Notes on their biology, habitat, and distribution are presented. The number of taxa in this endemic Canarian genus increases to seven eyeless species. One species has been reported from the soil (endogean environment), with the other six associated with caves and the mesovoid shallow substratum (hypogean or subterranean environment). Frequent association with the presence of roots suggests that species of Baezia may inhabit the continuum represented by the endogean and hypogean environments. Identification key to the seven species are provided.
García, Rafael; Andújar, Carmelo; Oromí, Pedro; Emerson, Brent C.; López, Heriberto
Sharing and Reporting Benefits from Biodiversity Research
The most remarkable feature of our planet is the diversity of its life forms, ranging from viruses and nanobacteria to blue whales and giant sequoias to satanic leaf‐tailed geckos and leafy seadragons (look them up!). Life is found in essentially all environments on earth, and the number of species living on our planet is many times greater than we could have imagined a century ago. A well‐regarded estimate pegs the number of eukaryotic species on earth at 8.7 million (±1.3 million), of which fewer than 15% are currently described (Mora et al., 2011). The diversity of prokaryotes is less clear (and highly controversial), but an analysis of 1.6 billion 16S ribosomal RNA sequences estimated that 0.8–1.6 million prokaryotic operational taxonomic units exist globally (Louca et al., 2019). While we do not know how many species are currently extant, or have existed in the past, we do know that this biodiversity is valuable, providing food, fibre and medicine, furnishing ecosystem services such as water and air purification, nutrient cycling, pollination and carbon uptake, and contributing to technological innovations ranging from biotechnology to robotics to material science. Moreover, biodiversity underlies the cultural identity of human populations and is important to human health and well‐being. Geographically, species richness increases from the Polar Regions to the tropics in terrestrial and surface marine ecosystems. Thus, some countries, especially those in tropical and subtropical regions, are endowed with much greater biodiversity than others. Unfortunately, benefits arising from the access and utilization of this biodiversity have been unequally shared, with (paradoxically) biodiversity‐poor countries often accruing the lion's share of economic gains. There can be imbalances within countries as well, wherein some segments of the population obtain greater economic benefits from biodiversity and associated traditional knowledge than indigenous peoples. The “Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization,” which came into force in 2014, is an international agreement designed to ensure that the benefits arising from biodiversity are shared equitably (https://www.cbd.int/abs/). However, few scientific journals require compliance with the Nagoya Protocol or the reporting of benefits from biodiversity research. In this editorial, we (the editors of Molecular Ecology and Molecular Ecology Resources) express support for the Nagoya Protocol and the principle of benefit sharing. We believe that scientific journals publishing research on biodiversity can play an important role in implementing the Nagoya Protocol and in reporting on benefits generated from such research. Below, we provide background on the Nagoya Protocol, discuss the kinds of benefits that may arise from biodiversity research, describe the rationale for reporting on these benefits and introduce changes to the journals’ Data Accessibility Statements to incorporate the requirements and goals of the Nagoya Protocol.
Marden, Emily; Abbott, Richard J.; Austerlitz, Frédéric; Ortiz Barrientos, Daniel; Baucom, Regina S.; Bongaerts, Pim; Bonin, Aurélie; Bonneaud, Camille; Browne, Luke; Buerkle, C. Alex; Caicedo, Ana L.; Coltman, David W.; Cruzan, Mitchell B.; Davison, Angus; DeWoody, J. Andrew; Dumbrell, Alex J.; Emerson, Brent C.; Fountain-Jones, Nicholas M.; Gillespie, Rosemary; Giraud, Tatiana; Hansen, Michael M.; Hodgins, Kathryn A.; Heuertz, Myriam; Hirase, Shotaro; Hooper, Rebecca; Hohenlohe, Paul; Kane, Nolan C.; Kelley, Joanna L.; Kinziger, Andrew P.; McKenzie, Valerie J.; Moreau, Corrie S.; Nazareno, Alison G.; Pelletier, Tara A.; Pemberton, Josephine M.; Qu, Yanhua; Renaut, Sébastien; Riginos, Cynthia; Rodríguez-Ezpeleta, Naiara; Rogers, Sean M.; Russell, Jacob A.; Schoville, Sean D.; Shi, Suhua; Smith, Megan; Sork, Victoria L.; Stone, Graham N.; Taberlet, Pierre; Videvall, Elin; Waits, Lisette; Warschefsky, Emily; Wayne, Robert K.; Whibley, Annabel; Willoughby, Janna; Yoder, Jeremy B.; Zinger, Lucie; Sibbett, Benjamin; Narum, Shawn; Rieseberg, Loren H.
Trophic ecology of an introduced top predator (Felis catus) on a small African oceanic islet (Santa Luzia, Cabo Verde Islands)
Studies on feral cat diet offer important ecological information and are the first step towards determining their impact upon endangered species. However, in comparing seasonal changes in diet with seasonal prey availability, the scarce amount of research into oceanic islands worldwide must be considered when deciding if a specific population is actually affected by cat predation. Cat diet was analysed on Santa Luzia (Cabo Verde Islands) since this invasive predator is considered one of the main threats to native endangered species that require conservation measures. These previous studies were carried out in different seasons, providing contrasting results, skinks being more preyed upon in the rainy season and mice in the driest periods. To check these different results, we focussed on how cat diet varied seasonally in response to changes in prey abundance. Saurians were the most important prey group, followed by mice, invertebrates and birds. No seasonal differences were, however, observed in the different prey groups consumed, saurians being the main prey in both seasons. All cases reflected their respective abundances. Results corroborate the generalist and opportunistic trophic ecology of feral cats, providing important information to assess their impact on prey populations and design future eradication programmes.
Medina, Félix M.; Melo, Tommy; Oliveira, Paulo; Nogales, Manuel; Geraldes, Pedro
Demographic consequences of dispersal‐related trait shift in two recently diverged taxa of montane grasshoppers
Although the pervasiveness of intraspecific wing‐size polymorphism and transitions to flightlessness have long captivated biologists, the demographic outcomes of shifts in dispersal ability are not yet well understood and have been seldom studied at early stages of diversification. Here, we use genomic data to infer the consequences of dispersal‐related trait variation in the taxonomically controversial short‐winged (Chorthippus corsicus corsicus) and long‐winged (Chorthippus corsicus pascuorum) Corsican grasshoppers. Our analyses revealed lack of contemporary hybridization between sympatric long‐ and short‐winged forms and phylogenomic reconstructions supported their taxonomic distinctiveness, rejecting the hypothesis of intraspecific wing polymorphism. Statistical evaluation of alternative models of speciation strongly supported a scenario of Pleistocene divergence (<1.5 Ma) with ancestral gene flow. According to neutral expectations from differences in dispersal capacity, historical effective migration rates from the long‐ to the short‐winged taxon were threefold higher than in the opposite direction. Although populations of the two taxa present a marked genetic structure and have experienced parallel demographic histories, our coalescent‐based analyses suggest that reduced dispersal has fueled diversification in the short‐winged C. c. corsicus. Collectively, our study illustrates how dispersal reduction can speed up geographical diversification and increase the opportunity for allopatric speciation in topographically complex landscapes.
Ortego, Joaquín; Gutiérrez-Rodríguez, Jorge; Noguerales, Víctor
Tidal Influence on Seismic Activity During the 2011–2013 El Hierro Volcanic Unrest
The El Hierro volcanic unrest started in July 2011, with an increase in observed seismicity rates and surface deformation. After the initial onset, hypocenters migrated southward through September 2011, culminating in a submarine eruption beginning on October 10, 2011 and finishing in February 2012. The seismic activity continued, with remarkable periods of unrest through 2012 and 2013. The most significant episodes of seismic activity during this unrest are related to magma migration at depth. In this work, we compute tidal stress for each earthquake, at its hypocenter depth, and assign them a tidal stress phase angle. We have found statistically significant correlations between the occurrence of earthquakes and tidal stress phase angles, corresponding mainly to increasing tidal stress change rates. We found primarily that the magnitude of vertical and E‐W horizontal tidal stress values and their changing rates with time were correlated with earthquake occurrence times. We also found that there is no correlation between tides and seismicity at times with no observed surface displacements, suggesting that tidal modulation might be related to overpressure during migration of magma. Tidal modulation changes with depth and the influence of ocean‐loading tides is stronger than the influence of solid Earth tides. Our results support the hypothesis that tidal stress may modulate the seismicity during volcanic unrest, particularly during shallow depth magma migration.
Miguelsanz, Luis; González, Pablo J.; Tiampo, Kristy F.; Fernández Torres, José
A Beginner’s Guide to Osmoprotection by Biostimulants
Water is indispensable for the life of any organism on Earth. Consequently, osmotic stress due to salinity and drought is the greatest threat to crop productivity. Ongoing climate change includes rising temperatures and less precipitation over large areas of the planet. This is leading to increased vulnerability to the drought conditions that habitually threaten food security in many countries. Such a scenario poses a daunting challenge for scientists: the search for innovative solutions to save water and cultivate under water deficit. A search for formulations including biostimulants capable of improving tolerance to this stress is a promising specific approach. This review updates the most recent state of the art in the field.
Jiménez-Arias, David; García-Machado, Francisco J.; Morales-Sierra, Sarai; García-García, Ana L.; Herrera, Antonio J.; Valdés, Francisco; Luis, Juan C.; Borges, Andrés A.
Structural Diversity using Hyp “Customizable Units”: Proof‐of‐Concept Synthesis of Sansalvamide‐Related Antitumoral Peptides
The potential of “customizable units” to generate structural diversity for biological screenings is highlighted in this proof‐of‐concept synthesis of new peptides related to the potent antitumoral Sansalvamide A. Using L‐4‐hydroxyproline (Hyp) as a customizable unit in a linear parent peptide, an improved procedure for selective peptide modification was developed. A divergent Hyp scission‐reductive amination process was carried out, affording five linear peptides with cationic residues, and notably, an N‐alkyl moiety that affected the conformation of the peptide. After two steps (saponification and macrocyclization), sixteen differently N1‐substituted linear and cyclic peptides were obtained. For the first time, the activity of the linear and cyclic compounds was compared. Not only some linear analogs but also cyclic compounds with scarcely studied cationic residues were active against MCF7 breast cancer line. Thus, the structural diversity generated from customizable units can be valuable in drug discovery.
Cuevas, Fernando; Saavedra, Carlos J.; Romero-Estudillo, Iván; Boto, Alicia; Ordóñez, Mario; Vergara, Irene
Impact of Desert Dust Events on the Cardiovascular Disease: A Systematic Review and Meta-Analysis
Background: Whether or not inhalation of airborne desert dust has adverse health effects is unknown. The present study, based on a systematic review and meta-analysis, was carried out to assess the influence desert dust on cardiovascular mortality, acute coronary syndrome, and heart failure. Methods: A systematic search was made in PubMed and Embase databases for studies published before March 2020. Studies based on daily measurements of desert dust were identified. The meta-analysis evaluated the impact of desert dust on cardiovascular events the same day (lag 0) of the exposure and during several days after the exposure (lags 1 to 5). The combined impact of several days of exposure was also evaluated. The incidence rate ratio (IRR) with 95% confidence intervals (CI) was calculated using the inverse variance random effects method. Results: Of the 589 identified titles, a total of 15 studies were selected. The impact of desert dust on the incidence of cardiovascular mortality was statistically significant (IRR = 1.018 (95%CI 1.008–1.027); p < 0.001) in lag 0 of the dust episode, in the following day (lag 1) (IRR = 1.005 (95%CI 1.001–1.009); p = 0.022), and during both days combined (lag 0–1) (IRR = 1.015 (95%CI 1.003–1.028); p = 0.014). Conclusions: The inhalation to desert dust results in a 2% increase (for every 10 µg/m3) in cardiovascular mortality risk.
Domínguez-Rodríguez, Alberto; Báez-Ferrer, Néstor; Abreu-González, Pedro; Rodríguez, Sergio; Díaz, Rocío; Avanzas, Pablo; Hernández-Vaquero, Daniel
Ovary Signals for Pollen Tube Guidance in Chalazogamous Mangifera indica L.
Most flowering plants show porogamy in which the pollen tubes reach the egg apparatus through the micropyle. However, several species show chalazogamy, an unusual pollen tube growth, in which the pollen tubes reach the embryo sac through the chalaza. While ovary signals for pollen tube growth and guidance have been extensively studied in porogamous species, few studies have addressed the process in chalazogamous species such as mango (Mangifera indica L.), one of the five most important fruit crops worldwide in terms of production. In this study, we characterize pollen–pistil interaction in mango, paying special attention to three key players known to be involved in the directional pollen tube growth of porogamous species such as starch, arabinogalactan proteins (AGPs), and γ-aminobutyric acid (GABA). Starch grains were observed in the style and in the ponticulus at anthesis, but their number decreased 1 day after anthesis. AGPs, revealed by JIM8 and JIM13 antibodies, were homogenously observed in the style and ovary, but were more conspicuous in the nucellus around the egg apparatus. GABA, revealed by anti-GABA antibodies, was specifically observed in the transmitting tissue, including the ponticulus. Moreover, GABA was shown to stimulate in vitro mango pollen tube elongation. The results support the heterotrophic growth of mango pollen tubes in the style at the expense of starch, similarly to the observations in porogamous species. However, unlike porogamous species, the micropyle of mango does not show high levels of GABA and starch, although they were observed in the ponticulus and could play a role in supporting the unusual pollen tube growth in chalazogamous species.
Lora Cabrera, Jorge; Pérez Méndez, Verónica; Herrero Romero, María; Hormaza Urroz, José Ignacio
Bioactive Metabolites from the Endophytic Fungus Aspergillus sp. SPH2
In the current study, an ethyl acetate extract from the endophytic fungus Aspergillus sp. SPH2 isolated from the stem parts of the endemic plant Bethencourtia palmensis was screened for its biocontrol properties against plant pathogens (Fusarium moniliforme, Alternaria alternata, and Botrytis cinerea), insect pests (Spodoptera littoralis, Myzus persicae, Rhopalosiphum padi), plant parasites (Meloidogyne javanica), and ticks (Hyalomma lusitanicum). SPH2 gave extracts with strong fungicidal and ixodicidal effects at different fermentation times. The bioguided isolation of these extracts gave compounds 1–3. Mellein (1) showed strong ixodicidal effects and was also fungicidal. This is the first report on the ixodicidal effects of 1. Neoaspergillic acid (2) showed potent antifungal effects. Compound 2 appeared during the exponential phase of the fungal growth while neohydroxyaspergillic acid (3) appeared during the stationary phase, suggesting that 2 is the biosynthetic precursor of 3. The mycotoxin ochratoxin A was not detected under the fermentation conditions used in this work. Therefore, SPH2 could be a potential biotechnological tool for the production of ixodicidal extracts rich in mellein.
Morales-Sánchez, Viridiana; Díaz, Carmen E.; Trujillo, Elena; Olmeda, Sonia A.; Valcarcel, Félix; Muñoz, Rubén; Andrés, María Fe; González-Coloma, Azucena
Long‐term cloud forest response to climate warming revealed by insect speciation history
Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridizing at lower elevations. Our results suggest that genomic data are a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change.
Salces-Castellano, Antonia; Stankowski, Sean; Arribas, Paula; Patiño, Jairo; Karger, Dirk N.; Butlin, Roger; Emerson, Brent C.
Anthropogenic Perturbations to the Atmospheric Molybdenum Cycle
Molybdenum (Mo) is a key cofactor in enzymes used for nitrogen (N) fixation and nitrate reduction, and the low availability of Mo can constrain N inputs, affecting ecosystem productivity. Natural atmospheric Mo aerosolization and deposition from sources such as desert dust, sea‐salt spray, and volcanoes can affect ecosystem function across long timescales, but anthropogenic activities such as combustion, motor vehicles, and agricultural dust have accelerated the natural Mo cycle. Here we combined a synthesis of global atmospheric concentration observations and modeling to identify and estimate anthropogenic sources of atmospheric Mo. To project the impact of atmospheric Mo on terrestrial ecosystems, we synthesized soil Mo data and estimated the global distribution of soil Mo using two approaches to calculate turnover times. We estimated global emissions of atmospheric Mo in aerosols (<10 μm in diameter) to be 23 Gg Mo yr‐1, with 40 to 75% from anthropogenic sources. We approximated that for the top meter of soil, Mo turnover times range between 1,000 to 1,000,000 years. In some industrialized regions, anthropogenic inputs have enhanced Mo deposition 100‐fold, lowering the soil Mo turnover time considerably. Our synthesis of global observational data, modeling, and a mass balance comparison with riverine Mo exports suggest that anthropogenic activity has greatly accelerated the Mo cycle, with potential to influence N‐limited ecosystems.
Wong, Michelle Y.; Rathod, Sagar D.; Marino, Roxanne; Li, Longlei; Howarth, Robert W.; Alastuey, Andres; Alaimo, Maria Grazia; Barraza, Francisco; Carneiro, Manuel Castro; Chellam, Shankararaman; Chen Yu-Cheng; Cohen, David D.; Connelly, David; Dongarra, Gaetano; Gomez, Dario; Hand, Jenny; Harrison, R.M.; Hopke, Philip K.; Hueglin, Christoph; Kuang, Yuan-wen; Lambert, Fabrice; Liang, James; Losno, Remi; Maenhaut, Willy; Milando, Chad; Couto Monteiro, Maria Inês; Morera-Gómez, Yasser; Querol, Xavier; Rodríguez, Sergio; Smichowski, Patricia; Varrica, Daniela; Xiao, Yi-hua; Xu, Yangjunjie; Mahowald, Natalie M.
Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully account for the complex nature of concomitant sequences and the highly variable DNA contribution of specimens in a metabarcoding sample. We propose, as a complement to denoising, the metabarcoding Multidimensional Abundance Threshold Evaluation (metaMATE) framework, a novel approach that allows comprehensive examination of multiple dimensions of abundance filtering and the evaluation of the prevalence of unwanted concomitant sequences in denoised metabarcoding datasets. metaMATE requires a denoised set of ASVs as input, and designates a subset of ASVs as being either authentic (mitochondrial DNA haplotypes) or nonauthentic ASVs (NUMTs and erroneous sequences) by comparison to external reference data and by analysing nucleotide substitution patterns. metaMATE (i) facilitates the application of read abundance filtering strategies, which are structured with regard to sequence library and phylogeny and applied for a range of increasing abundance threshold values, and (ii) evaluates their performance by quantifying the prevalence of nonauthentic ASVs and the collateral effects on the removal of authentic ASVs. The output from metaMATE facilitates decision-making about required filtering stringency and can be used to improve the reliability of intraspecific genetic information derived from metabarcode data. The framework is implemented in the metaMATE software (available at https://github.com/tjcreedy/metamate).
Andújar, Carmelo; Creedy, Thomas J.; Arribas, Paula; López, Heriberto; Salces-Castellano, Antonia; Pérez‐Delgado, Antonio José; Vogler, Alfried P.; Emerson, Brent C.