Biology subjects

Pires da Silva, A.

Publications and source records attributed to Pires da Silva, A..

10 recordsLinked to original sources

bioRxiv2026

Massive programmed DNA elimination during embryogenesis in the trioecious nematode Auanema rhodense

In animals, the germline is usually set aside early in development and its genome is protected to ensure faithful transmission of genetic information to future generations. Genetic alterations in somatic cells are not inherited by progeny, and the somatic genome does not have to be protected from change in the same way. In some species, programmed DNA elimination (PDE) results in the directed loss of genetic material from somatic cells. Here, we report extreme PDE in Auanema rhodense, a free-living nematode with a remarkable, trioecious life history and unusual patterns of sex chromosome inheritance. We find that nearly two thirds of the A. rhodense germline genome is eliminated from somatic cells, with DNA lost from chromosome ends as well as within chromosomes, resulting in fragmentation of the seven germline chromosomes into fourteen somatic chromosomes. Most eliminated DNA comprises multi-megabase tandem repeat blocks. Eliminated DNA on the X chromosome harbours germline-restricted repeats that are distinct from those on the autosomes. The eliminated DNA includes many highly-repeated non-coding RNA loci but few protein-coding genes. Elimination sites are strongly associated with a palindromic sequence motif that likely directs DNA breakage and new telomere repeat array addition. Cytologically, PDE begins at the 12-cell stage of embryogenesis, is synchronous across all chromosomes, and is characterised by the formation of transient micronucleus-like bodies. Together, these findings reveal unusually extensive PDE in a free-living nematode and raise the possibility that germline-restricted repeat architecture may contribute to the atypical sex chromosome inheritance observed in Auanema.

genomics↗

bioRxiv2023

A QTL influences sex ratios by controlling asymmetric organelle positioning during male spermatogenesis in Auanema freiburgense

Auanema freiburgense is a trioecious nematode with co-existing males, females, and selfing hermaphrodites. Crosses of XO males with XX females result in a low percentage of XO sons due to the elimination of the nullo-X spermatids by the fathers. This process yields most viable sperm containing an X chromosome, leading to a higher transmission probability of the X chromosome compared to expected transmission via random segregation. The mechanism underlying this process involves the asymmetric distribution of essential cellular organelles during sperm formation, which likely depends on the X chromosome. Specifically, sperm components segregate with the X chromosome daughter cell, while other components are discarded in the nullo-X daughter cell. Here we found that intercrossing two strains of A. freiburgense results in lines in which males produce viable nullo-X sperm. Thus, crosses of those hybrid males with females result in a high percentage of sons. To uncover the genetic basis of nullo-spermatid elimination and X-chromosome drive, we generated a genome assembly for A. freiburgense and genotyped the intercrossed lines. We identified a QTL encompassing several genes on the X chromosome that are associated with its non-Mendelian inheritance observed in A. freiburgense. This finding provides valuable clues to the underlying factors involved in asymmetric organelle partitioning during male meiotic division and thus non-Mendelian transmission of the X chromosome and sex ratios.

developmental biology↗

bioRxiv2022

The X chromosome is a potential polarising signal for asymmetric cell divisions in meiotic cells of a nematode

The unequal partition of molecules and organelles during cell division results in daughter cells with different fates. Asymmetric cell divisions have been best characterised in systems in which extrinsic signals polarise the mother cell during cell division. However, the mechanisms of asymmetric cell division mediated by intrinsic signals, and the nature of these signals, are mostly unknown. Here we report an asymmetric cell division in the nematode Auanema rhodensis that may be cued by the X chromosome. In the wildtype XO male, the spermatocyte divides asymmetrically to generate X-bearing spermatids that inherit components necessary for sperm viability, and nullo-spermatids that inherits components to be discarded. We found that in XX mutant pseudomales, sperm components co-segregate with the X chromosome, supporting the hypothesis that the X chromosome is employed as a polarising signal for partitioning essential cytoplasmic components for sperm function.

developmental biology↗

bioRxiv2021

Sexual morph specialisation in a trioecious nematode balances opposing selective forces.

The coexistence of different mating strategies, whereby a species can reproduce both by selfing and outcrossing, is an evolutionary enigma that has long intrigued biologists (Darwin, 1877). Theory predicts only two stable mating states : outcrossing with strong inbreeding depression or selfing with weak inbreeding depression. As these two mating strategies are subject to opposing selective forces, mixed breeding systems are thought to be a rare transitory state, yet they have been found to persist even after multiple speciation events. We hypothesise that if each mating strategy plays a distinctive role during the species life history, opposing selective pressures could be balanced, permitting the stable co-existence of selfing and outcrossing sexual morphs. In this scenario, we would expect each sexual morph to be specialised in their respective roles. Here we show, using a combination of behavioural, physiological and gene expression studies, that the selfing (hermaphrodite) and outcrossing (female) sexual morphs of the trioecious nematode Auanema freiburgensis have distinct adaptations optimised for their different roles during the life cycle. A. freiburgensis hermaphrodites are produced under stressful conditions, are specialised for dispersal to new habitat patches and exhibit metabolic and intestinal changes that enable them to meet the energetic cost of dispersal and reproduction. In contrast, A. freiburgensis females are produced in favourable conditions, facilitate rapid population growth and compensate for the lack of reproductive assurance by reallocating resources from intestinal development to robust mate-finding behaviour. The specialisation of each mating system for their role in the life cycle could balance opposing selective forces allowing the stable maintenance of both outcrossing and selfing mating systems in A. freiburgensis.

evolutionary biology↗

bioRxiv2020

Chromatin-associated effectors of energy-sensing pathways mediate intergenerational effects

Environmental stimuli experienced by the parental generation influence the phenotype of subsequent generations. The effects of these stimuli on the parental generation may be passed through the germline, but the mechanisms of this non-Mendelian type of inheritance are poorly known. Here we show that modulation of nutrient-sensing pathways in the parental generation of a nematode (Auanema freiburgensis) regulates phenotypic plasticity of its offspring. In response to pheromones, AMP-activated protein kinase (AMPK), mechanistic target of rapamycin complex 1 (mTORC1) and insulin signaling regulate stress resistance and sex determination across a generation. The effectors of these pathways are closely associated with the chromatin and their regulation affects the acetylation chromatin status in the germline. These results suggest that highly conserved metabolic sensors regulate phenotypic plasticity by changing the epigenetic status of the germline.

developmental biology↗

bioRxiv2020

Towards genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles.

Plant-parasitic nematodes are a continuing threat to food security, causing an estimated 100 billion USD in crop losses each year. The most problematic are the obligate sedentary endoparasites (primarily root knot nematodes and cyst nematodes). Progress in understanding their biology is held back by a lack of tools for functional genetics: forward genetics is largely restricted to studies of natural variation in populations, and reverse genetics is entirely reliant on RNA interference. There is an expectation that the development of functional genetic tools would accelerate the progress of research on plant-parasitic nematodes, and hence the development of novel control solutions. Here, we develop some of the foundational biology required to deliver a functional genetic tool kit in plant-parasitic nematodes. We characterise the gonads of male Heterodera schachtii and Meloidogyne hapla in the context of spermatogenesis. We test and optimise various methods for the delivery, expression, and/or detection of exogenous nucleic acids in plant-parasitic nematodes. We demonstrate that delivery of macromolecules to cyst and root knot nematode male germlines is difficult, but possible. Similarly, we demonstrate the delivery of oligonucleotides to root knot nematode gametes. Finally, we develop a transient expression system in plant-parasitic nematodes by demonstrating the delivery and expression of exogenous mRNA encoding various reporter genes throughout the body of H. schachtii juveniles using lipofectamine-based transfection. We anticipate these developments to be independently useful, will expedite the development of genetic modification tools for plant-parasitic nematodes, and ultimately catalyze research on a group of nematodes that threaten global food security.

genetics↗

bioRxiv2018

Chromosome-wide evolution and sex determination in a nematode with three sexes

The free-living nematode Auanema rhodensis is a rare example of a species with three sexes, in which males, females and hermaphrodites coexist. A. rhodensis males have only one X chromosome (XO), whereas females and hermaphrodites have two (XX). The A. rhodensis X chromosome is unusual: it does not recombine in hermaphrodites and is transmitted from father to son. The mechanism that controls the production of females versus hermaphrodites is unknown but is dependent on maternal and larval environmental factors. Here we report the genome sequence and genetic map of A. rhodensis, placing over 95% of the sequence in seven linkage groups. Comparison of the seven A. rhodensis chromosomes to chromosomal assemblies of Caenorhabditis elegans and three other rhabditine nematodes identified deeply conserved linkage groups we call Nigon units, some of which have been maintained in all species analysed. Others have undergone breakage and fusion, and the A. rhodensis karyotype is the product of a unique set of rearrangements involving three Nigon units. The A. rhodensis X chromosome is much smaller than the autosomes, is less gene dense and is 3 to 4 times more polymorphic, reflecting its unique transmission history. Differential expression analyses comparing females and hermaphrodites, identified several candidate genes, including orthologues of C. elegans gld-1, tra-1 and dmd-10/11, that are potentially involved in the female-hermaphrodite sexual decision.

genetics↗

bioRxiv2018

Liposome-based transfection enhances RNAi and CRISPR-mediated mutagenesis in non-model nematode systems

Nematodes belong to one of the most diverse animal phyla. However, functional genomic studies in nematodes, other than in a few species, have often been limited in their reliability and success. Here we report that by combining liposome-based technology with microinjection, we were able to establish a wide range of genomic techniques in the newly described nematode genus Auanema. The method also allowed heritable changes in dauer larvae of Auanema, despite the immaturity of the gonad at the time of the microinjection. As proof of concept for potential functional studies in other nematode species, we also induced RNAi in the free-living nematode Pristionchus pacificus and targeted the human parasite Strongyloides stercoralis.

developmental biology↗

bioRxiv2018

Sensory neurons control heritable adaptation to stress through germline reprogramming

Maternal neuronal signaling has been reported to program adaptive changes in offspring physiology in diverse organisms [1, 2]. However, the mechanisms for the inheritance of adaptive maternal effects through the germline are largely unknown. In the nematode Auanema freiburgensis, stress-resistance and sex of the offspring depend on environmental cues experienced by the mother. Maternal sensing of high population densities results in the production of stress-resistant larvae (dauers) that develop into hermaphrodites. Ablation of the maternal ASH chemosensory neurons results only in non-dauer offspring that develop into males or females. High population densities correlate with changes in the methylation status of H3K4 and H3K9 in the maternal germline. Inhibition of JMJD histone demethylases prevents mothers from producing dauers and hermaphrodite offspring in high-density conditions. Our results demonstrate a case of soma-to-germline transmission of environmental information that influences the phenotype of the following generation through changes in histone modifications of the maternal germline.\n\nHighlightsO_LIHigh population density leads to the production of hermaphrodite offspring.\nC_LIO_LIThe ASH neuron in the hermaphrodite mother senses population density.\nC_LIO_LIHistone modifications in the maternal germline correlate with the sex of offspring.\nC_LIO_LIInhibition of histone demethylases results in female offspring in all conditions.\nC_LI

developmental biology↗

bioRxiv2017

Gender- and gamete-specific patterns of X chromosome segregation in a three-gendered nematode

Meiosis is at the core of sexual reproduction and alterations to its program can have dramatic effects. In this study, we investigate the segregation pattern of the X chromosome in Auanema rhodensis, a three-gendered nematode. This species has an atypical pattern of X chromosome segregation during male spermatogenesis that results in the exclusive production of haplo-X sperm. Here we use a combination of genetic and cytological approaches to show that while XX females undergo conventional meiosis to produce mostly haplo-X oocytes, hermaphrodites undergo atypical meiosis to produce nullo-X oocytes and mostly diplo-X sperm. Gender- and gamete-specific alterations of the normal meiotic program include non-pairing of the X homologs and precocious separation of X chromatids. Given these intra-species, intra-individual and intra-gametogenesis variations in meiotic program of A. rhodensis, we argue that it is an ideal model to study the plasticity of meiosis and how it can be modulated.\n\nHighlights- Matings between A. rhodensis hermaphrodites and males generate only male crossprogeny.\n- Hermaphrodites generate mostly nullo-X oocytes and diplo-X sperm.\n- Following normal Mendelian genetics, XX females produce haplo-X oocytes.\n- In cross-progeny, sons always inherit the X chromosome from the father.

genetics↗