André M Machado

André M Machado
University of Porto | UP · Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR)

Bioinformatician, CIIMAR – University of Porto

About

56
Publications
7,491
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288
Citations
Introduction
André Machado currently works at the CIIMAR - Interdisciplinary Center for Marine and Environmental Research, University of Porto . André does research in Transcriptomics, Genomics and general Bioinformatics.
Education
September 2013 - July 2016
Technical University of Lisbon
Field of study
  • Biotecnology
September 2008 - July 2012
University of Lisbon
Field of study
  • Biology

Publications

Publications (56)
Article
Elongation of very long-chain fatty acids (Elovl) proteins are critical players in the regulation of the length of a fatty acid. At present, eight members of the Elovl family (Elovl1–8), displaying a characteristic fatty acid substrate specificity, have been identified in vertebrates, including teleost fish. In general, Elovl1, Elovl3, Elovl6 and E...
Article
The common octopus, Octopus vulgaris, is a promising mollusc species for marine aquaculture diversification due to its high growth rates and commercial value. Yet, the elevated mortalities mainly related to lipid-linked nutritional deficiencies during the planktonic stage (paralarvae), hinder the development of efficient protocols for a complete re...
Article
The Atlantic chub mackerel, Scomber colias (Gmelin, 1789), is a medium-sized pelagic fish with substantial importance in the fisheries of the Atlantic Ocean and the Mediterranean Sea. Over the past decade, this species has gained special relevance, being one of the main targets of pelagic fisheries in the NE Atlantic. Here, we sequenced and annotat...
Article
Full-text available
Chondrichthyans (sharks, rays and chimeras) are a fascinating and highly vulnerable group of early branching gnathostomes. However, they remain comparatively poorly sampled from the point of view of molecular resources, with deep water taxa being particularly data deficient. The development of long-read sequencing technologies enables the analysis...
Article
Paracentrotus lividus is the most abundant, geographically distributed, and desirable echinoid species in Europe. Although economically important, this species has scarce genomic resources available. Here, we produced and comprehensively characterized the male and female gonad transcriptome of P. lividus. The P. lividus transcriptome assembly has 5...
Article
The primary focus of environmental toxicological studies is to address the direct effects of chemicals on exposed organisms (parental generation – F0), mostly overlooking effects on subsequent non-exposed generations (F1 and F2 – intergenerational and F3 transgenerational, respectively). Here, we addressed the effects of Simvastatin (SIM), one of t...
Article
Full-text available
Three peroxisome proliferator-activated receptor paralogues (PPARα, -β and -γ) are currently recognized in vertebrate genomes. PPARγ is known to modulate nutrition, adipogenesis and immunity in vertebrates. Natural ligands of PPARγ have been proposed; however, the receptor also binds synthetic ligands such as endocrine disruptors. Two paralogues of...
Preprint
Full-text available
The Atlantic chub mackerel, Scomber colias Gmelin, 1789, is a medium-size pelagic fish with substantial importance in the fisheries of the Atlantic Ocean and the Mediterranean Sea. Over the past decade, this species has gained special relevance being one of the main targets of pelagic fisheries in the NE Atlantic. Here, we sequenced and annotated t...
Article
Agriculture is facing major constraints with the increase of global warming, being drought, a major factor affecting productivity. Soybean (Glycine max) is among the most important food crops due to the high protein and lipid content of its seeds despite being considerably sensitive to drought. Previous knowledge has shown that drought induces a se...
Preprint
Full-text available
Paracentrotus lividus is the most abundant, distributed and desirable echinoid species in Europe. Although, economically important, this species has scarce genomic resources available. Here, we produced and comprehensively characterized the male and female gonad transcriptome of P. lividus. The P. lividus transcriptome assembly has 53,865 transcrip...
Article
Full-text available
Mammalian spermatozoa are a notable example of metabolic compartmentalization.¹ Energy in the form of ATP production, vital for motility, capacitation, and fertilization, is subcellularly separated in sperm cells. While glycolysis provides a local, rapid, and low-yielding input of ATP along the flagellum fibrous sheath, oxidative phosphorylation (O...
Article
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The difficulties involved in the study of deep-sea species imply the existence of a wide gap in knowledge of this ecosystem. Here, we have obtained the mitogenome of the Oven's halosaur, Halosaurus ovenii, for the first time using low coverage Illumina Paired-end (PE) sequencing. This species belongs to order Notacanthiformes, a poorly studied grou...
Article
Full-text available
We focus on the stalked goose barnacle L. anatifera adhesive system, an opportunistic less selective species for the substrate, found attached to a variety of floating objects at seas. Adhesion is an adaptative character in barnacles, ensuring adequate positioning in the habitat for feeding and reproduction. The protein composition of the cement mu...
Article
Full-text available
Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially...
Preprint
Whole genome sequence data is an ideal tool for characterizing processes in ecology and evolution. Despite the lowering in sequencing costs, it can be challenging to produce a genome and high-coverage resequencing data for a non-model species. New population genomics data analysis pipelines based on genotype likelihoods allow for a significant redu...
Article
Full-text available
Skates, Chondrichthyes fishes from order Rajiformes, are the most species-rich group of all Batoidea. However, their phylogenetic relationships and systematics is still a highly discussed and controversial subject. The use of complete mitogenome has shown to be a promising tool to fill this gap of knowledge. Here, the complete mitogenome of the Ibe...
Preprint
Full-text available
Mammalia spermatozoa are a notable example of energetic compartmentalization. While mitochondrial oxidative phosphorylation is restricted to the midpiece, sperm-specific glycolysis operates in the flagellum. Consequently, these highly specialized cells exhibit a clear adaptability to fuel substrates. This plasticity is essential to ensure sperm mot...
Article
Full-text available
Cartilaginous fish are fascinating taxa, present in the folklore and art of many different cultures. Moreover, they display several unique anatomical, physiological, molecular, and behavioral characteristics making them extremely interesting from a biological perspective. Nevertheless, some crucial knowledge gaps remain, including phylogenetic rela...
Preprint
Full-text available
Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially...
Article
Full-text available
The skin is a multi-layered organ, often displaying associated structures, that establishes a protective interface between the organism and the surrounding environment. In mammals, the skin provides a physical and immune barrier, while contributing to thermoregulation and water balance. Within cetaceans, the archetypal mammalian skin was drasticall...
Article
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The hypothesis that exposure to certain environmental chemicals during early life stages may disrupt reproduction across multiple non-exposed generations has significant implications for understanding disease etiology and adverse outcomes. We demonstrate here reproductive multi and transgenerational effects, at environmentally relevant levels, of o...
Article
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Marine biofouling remains an unsolved problem with a serious economic impact on several marine associated industries and constitutes a major vector for the spread of non-indigenous species (NIS). The implementation of biofouling monitoring programs allows for better fouling management and also for the early identification of NIS. However, few monit...
Article
Full-text available
The use of transcriptomics data brings new insights and works as a powerful tool to explore the molecular mode of action (MoA) of transgenerational inheritance effects of contaminants of emerging concern. Therefore, in this dataset, we present the transcriptomic data of the transgenerational effects of environmentally relevant simvastatin levels, o...
Article
Full-text available
The generation of omic resources is central to develop adequate management strategies for species with economic value. Here, we provide high-coverage RNA-seq datasets of liver tissue (containing between 80,2 and 88,4 million of paired-end reads) from four wildtype teleost species with high commercial value: Trachurus trachurus (TTR; Atlantic horse...
Article
Nuclear receptors (NRs) are key transcription factors that originated in the common ancestor of metazoans. The vast majority of NRs are triggered by binding to either endogenous (e.g. retinoic acid) or exogenous (e.g. xenobiotics) ligands, and their evolution and expansion is tightly linked to the function of endocrine systems. Importantly, they re...
Article
Full-text available
Adhesive secretion has a fundamental role in barnacles’ survival, keeping them in an adequate position on the substrate under a variety of hydrologic regimes. It arouses special interest for industrial applications, such as antifouling strategies, underwater industrial and surgical glues, and dental composites. This study was focused on the goose b...
Article
Full-text available
Deep-sea fish taxa are elusive, difficult to study, and in multiple cases, represent taxonomic conundrums. Here, we sequenced the complete mitogenome of the shortfin spiny eel, Notacanthus bonaparte, for the first time using low coverage Illumina Paired-end (PE) sequencing. The shortfin spiny eel belongs to the order Notacanthiformes, a relatively...
Article
Full-text available
Cartilaginous fishes are a highly vulnerable vertebrate group but remain poorly studied, especially those occupying deep-water ecological niches. Here, we describe the complete mitogenome of the deep-water chimaeriform Hydrolagus affinis (de Brito Capello, 1868) (Holocephali: Chimaeridae). The mitogenome has 19,437 nucleotides and the same overall...
Article
Long-chain (C20–24) polyunsaturated fatty acids (LC-PUFA) are physiologically important nutrients for vertebrates including fish. Previous studies have addressed the metabolism of LC-PUFA in the Amazonian teleost tambaqui (Colossoma macropomum), an emerging species in Brazilian aquaculture, showing that all the desaturase and elongase activities re...
Article
Full-text available
Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending ev...
Article
Full-text available
To appraise how evolutionary processes, such as gene duplication and loss, influence an organism’s xenobiotic sensitivity is a critical question in toxicology. Of particular importance are gene families involved in the mediation of detoxification responses, such as members of the nuclear receptor subfamily 1 group I (NR1I), the pregnane X receptor...
Article
Full-text available
The appearance of mammalian-specific skin features was a key evolutionary event contributing for the elaboration of physiological processes such as thermoregulation, adequate hydration, locomotion, and inflammation. Skin inflammatory and autoimmune processes engage a population of skin-infiltrating T cells expressing a specific C-C chemokine recept...
Article
Full-text available
Genomes are dynamic biological units, with processes of gene duplication and loss triggering evolutionary novelty. The mammalian skin provides a remarkable case study on the occurrence of adaptive morphological innovations. Skin sebaceous glands, for instance, emerged in the ancestor of mammals serving pivotal roles, such as lubrication, waterproof...
Article
Full-text available
The teleost fish tambaqui, Colossoma macropomum, is a valuable resource for the Brazillian aquaculture sector, representing more than one-quarter of the total production. In this context, the development of molecular tools is paramount to address and improve productivity, nutrition, and genetic breeding programs. In this study, we applied RNA-seq t...
Article
Full-text available
: Melatonin, the hormone of darkness, is a peculiar molecule found in most living organisms. Emerging as a potent broad-spectrum antioxidant, melatonin was repurposed into extra roles such as the modulation of circadian and seasonal rhythmicity, affecting numerous aspects of physiology and behaviour, including sleep entrainment and locomotor activi...
Preprint
Full-text available
The appearance of mammalian-specific skin features was a key evolutionary event contributing for the elaboration of physiological processes such as thermoregulation, adequate hydration, locomotion and inflammation. Skin inflammatory and autoimmune processes engage a population of skin-infiltrating T cells expressing a specific C-C chemokine recepto...
Article
Full-text available
Nucleobase-Ascorbate Transporter (NAT) family includes ascorbic acid, nucleobases, and uric acid transporters: With broad evolutionary distribution. In vertebrates, four members have been previously recognized, the ascorbate transporters Slc23a1 and Slc3a2, the nucleobase transporter Slc23a4 and an orphan transporter Slc23a3. Using phylogenetic and...
Preprint
Full-text available
Melatonin, the hormone of darkness, is a peculiar molecule found in most living organisms. Emerging as a potent broad-spectrum antioxidant, melatonin was repurposed into extra roles such as the modulation of circadian and seasonal rhythmicity: affecting numerous aspects of physiology and behaviour, including sleep entrainment and locomotor activity...
Article
Barnacles are sessile organisms globally distributed in marine and estuarine environments. The production of protein-based adhesives by cement glands is crucial for these organisms and plays a vital role in substrate attachment, thus inspiring biotechnological applications. Moreover, barnacles belong to bio-fouling communities, whose fixation onto...
Article
Full-text available
Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research...
Article
In vertebrates, the essential fatty acids (FA) that satisfy the dietary requirements for a given species depend upon its desaturation and elongation capabilities to convert the C18 polyunsaturated fatty acids (PUFA), namely linoleic acid (LA, 18:2n-6) and α-linolenic acid (ALA, 18:3n-3), into the biologically active long-chain (C20-24) polyunsatura...
Preprint
Full-text available
Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research...
Article
The Cetacea infraorder comprises a very unique group within the mammalian lineage. While sharing common ancestors with terrestrial mammals, their exclusive dependence on aquatic environments makes them attractive models to explore the landscape of molecular shifts in radical habitat transitions. Among their diverse anatomical and physiological solu...
Article
Fatty acids (FAs) constitute a considerable fraction of all lipid molecules with a fundamental role in numerous physiological processes. In animals, the majority of complex lipid molecules are derived from the transformation of FAs through several biochemical pathways. Yet, for FAs to enroll in these pathways they require an activation step. FA act...
Preprint
A bstract Fatty acids (FAs) constitute a considerable fraction of all lipid molecules with a fundamental role in numerous physiological processes. In animals, the majority of complex lipid molecules are derived from the transformation of FAs through several biochemical pathways. Yet, for FAs to enroll in these pathways they require an activation st...
Preprint
Full-text available
Nucleobase-Ascorbate Transporter (NAT) family includes ascorbic acid, nucleobases and uric acid transporters, with a broad evolutionary distribution. In vertebrates, four members have been previously recognized, the ascorbate transporters Slc23a1 and Slc3a2, the nucleobase transporter Slc23a4 and an orphan transporter SLC23A3. Here we identify a fi...
Article
Full-text available
Mackerels represent a valuable fishery worldwide. Their ample geographic distribution and capture levels make them an insightful model to address stock management strategies in the context of global changes. Yet, and despite recent impressive genome and transcriptome sequencing efforts from teleost species, available resources from the Scombridae f...
Article
Cartilaginous fishes (sharks, rays and chimaeras) comprise a highly diversified group of basal vertebrates occupying a plethora of ecological aquatic niches. They represent critical components of marine ecosystems and food webs, although numerous species are threatened and almost half are poorly known. Genomic resources emerging from this basal jaw...
Thesis
Full-text available
The Saccharomyces cerevisiae 12-spanner drug: H+ antiporters (DHA1) and 14- spanner drug: H+ antiporters (DHA2) of the Major Facilitator Superfamily (MFS) are involved in Multidrug/Multixenobiotic resistance (MDR/MXR) phenomenon. The aim of the present work is to reconstruct and characterize the evolution of the DHA1 genes encoded in 33 hemiascomyc...
Poster
Drought induces changes in lipid composition of plant leaves, compromising growth and productivity. In general there is a decrease in membrane versus neutral lipids ratio. However, these mechanisms are still poorly understood, namely regarding the identity of the lipolytic enzymes involved in membrane lipid catabolism. We have previously identified...
Poster
Full-text available
Soybean is an important source of protein and oil for food and industrial applications. There is an important increase in global demand for this legume, but environmental stresses, such as drought, are responsible for significant decreases in yield. The recent sequencing of the soybean genome is a valuable tool for fundamental studies and for crop...
Poster
Drought is one of the major stresses affecting plant growth and productivity. One of the effects of this stress is the loss of compartmentalization, linked to the degradation of membrane lipids. Some lipolytic enzymes playing pivotal roles in membrane remodeling and signaling during drought have been identified in the past few years. Although there...
Poster
Full-text available
Phospholipase A (PLA) is a superfamily of enzymes releasing fatty acids from membrane lipids. They have several functions during development and in response to stress which includes signaling, massive lipid degradation or membrane repair, by selectively removing oxidatively modified fatty acids. In plants, PLA belongs to three major groups: DAD-lik...

Projects

Projects (2)
Project
During the last ten years, in a series of funded projects, the team has filled the gap of knowledge of FMs´ evolutionary histories and biological features. Now, the present project will use an innovative multidisciplinary approach to test the adaptive genetic variation related to environmental variation in natural populations of FM. The aims of this project are to 1) assess genomic changes and responses associated with climatic adaptations 2) evaluate if adaptation is the factor that can mitigate the impact of climate regime variation 3) expand our understanding of neutral vs. adaptive genes. As we aim to identify the molecular kernel and functional pathways potentially involved in environmental stress response, three target FM species were selected based on their close evolutionary relationships, similarities in life-history traits, and with both drought (U. delphinus and U. mancus) and cold (U. pictorum) tolerances.
Project
To study how marine fishes adapt to deep waters by NGS DNA and RNA analyses. By comparative analyses in two different marine fish taxa (genus Gaidropsarus and order Notacanthiformes), identify functional modifications in key gene groups related to adaptation to deep sea, evolutionary convergence events, and newly developed adaptations compared with phylogenetic inheritance. The new data obtained will be useful to estimate the potential adaptation to marine fish species to deeper waters, helping to stablish proper conservation and management politicies.