REGULOMICS: Biodiversity to address animal origins: the origin of animal genomic regulation

Marta Álvarez Presas has a degree in Biology from the University of Barcelona (UB). She did her doctoral thesis on the phylogeny and phylogeography of terrestrial planarians in the Brazilian Atlantic Forest and Europe.

In 2015, she completed her first postdoc at the UB with a grant from the Generalitat de Catalunya, delving into the use of new generation techniques (NGS). In 2018 she did a stay at the Center for Genomic Regulation of Barcelona (CRG) to improve her skills in bioinformatics. In 2019 she was an associate researcher at the Instituto de Biología Evolutiva (IBE, CSIC) in Barcelona, beginning a study on the origin of Bilateral animals. Between 2019 and 2022 she got a contract with the University of Bristol (United Kingdom), studying the evolution of parasitism using comparative genomics.

In April 2023 she returns to the IBE as a ComFuturo fellow, where she will study, with her project REGULOMICS, the origin of multicellularity through the analysis of gene regulation in different groups of unicellular organisms, relatives of animals.

La complejidad de los animales nos asombra a todos, y con razón. Los animales son increíbles en muchos sentidos, desde el punto de vista conductual, morfológico y genético. Pero sigue siendo un misterio el saber cómo evolucionaron los animales multicelulares a partir de sus antepasados unicelulares. El proyecto REGULOMICS propone utilizar herramientas genéticas para estudiar cómo se regulan, activan y desactivan los genes de las células en aquellos organismos unicelulares, para comprender su evolución hacia formas multicelulares más complejas. Los resultados obtenidos supondrán una importante contribución a la Biología y a otras disciplinas relacionadas, como la Genómica, la Biología Evolutiva, la Microbiología y la Biología Celular. Pero, además, este conocimiento sobre el origen de las redes de regulación genética, arrojará pistas importantes sobre las causas de enfermedades humanas, como el cáncer, directamente relacionadas con la pluricelularidad.

The complexity of animals astounds us all, and rightly so. Animals are amazing in many ways, behaviourally, morphologically and genetically. But how multicellular animals evolved from their unicellular ancestors remains a mystery. The REGULOMICS project proposes to use genetic tools to study how cell genes are regulated, turned on and off in those single-celled organisms, in order to understand their evolution into more complex multicellular forms. The results obtained will make an important contribution to biology and other related disciplines, such as genomics, evolutionary biology, microbiology and cell biology. In addition, this knowledge of the origin of gene regulatory networks will provide important clues to the causes of human diseases, such as cancer, which are directly related to multicellularity.

Extended project summary:

The complexity of animals amazes us, and with good reason. Animals are marvellous in so many ways, behaviourally, morphologically, and genetically. However, how multicellular animals evolved from their single-celled ancestors remains a mystery. In the last decade, we have come a long way in understanding the origins of animals, from identifying the closest unicellular relatives of animals (choanoflagellates, phylastereans, ichthyosporeans, corallochytreans) to studying their biology and sequencing their genomes. Thanks to these efforts, we now know what the unicellular ancestor of animals was like: a more complex creature than expected and already presenting genes (and molecular mechanisms) that in animals are involved in functions related to multicellularity.

What differentiates animals from their single-celled relatives? What specific regulatory features were key for animals to evolve? We now have both the knowledge and the genetic tools necessary to answer these questions. Therefore, REGULOMICS propose the use of these tools to study how genes are regulated, activated and deactivated in cells in the unicellular relatives of animals. It involves understanding the mechanisms that control gene expression, or how information from genes is used to make proteins that perform various functions in cells. The data generated will undoubtedly bring us closer to solving the mystery of animal origins, by unveiling the origin of animal genomic regulation. Furthermore, taking advantage of the numerous available genomes of unicellular relatives of animals, we will study the evolution of regulation and metabolism genes in these groups. The data obtained will also be relevant to many other disciplines, from evolution to genomics, development and cell biology.

Click here to see reportage interview with Marta Álvarez at Innovaspain

Scientific output derived from the ComFuturo REGULOMICS Project

Scientific articles

D.A. Salamanca-Díaz; H.R Horkan; H. García-Castro; H. Emili; M. Salinas-Saavedra; A. Pérez-Posada; M.E. Rossi; M. Álvarez-Presas. The Hydractinia cell atlas reveals cellular and molecular principles of cnidarian coloniality. NATURE COMMUNICATIONS. DOI:10.1038/s41467- 025-57168-z

Works presented at congresses

J. Lorente-Sorolla; A. Verdes; I. de Sosa; C. Díez-Vives; E. Rossi; M. Conejero; M. Turón; M. Álvarez-Presas; et al. Diverse systems and ancient origins of sex determination genes in sponges. World Sponge Conference. Oral communication. Vila do Conde, Portugal. 9/09/2025-13/09/2025

M. Álvarez-Presas; M. Antó; I. Ruiz-Trillo; E. Casacuberta. Unicellular regulatory landscapes and the origins of animal multicellularity. Congress of the European Society for Evolutionary Biology (ESEB). Oral communication. Barcelona, Spain. 17/08/2025-22/08/2025

A. Mas; M. Álvarez-Presas. Refining the genome annotation of Abeoforma whisleri: Improving gene prediction for downstream comparative analysis. Jornades de Biologia Evolutiva. Oral communication. Barcelona, Spain. 27/06/2025

D. Montiel; M. Álvarez-Presas. Bioinformatic analysis on the evolution of gene families key to animal multicellularity. Jornades de Biologia Evolutiva. Oral communication. Barcelona, Spain. 27/06/2025

J. Paps, M. Álvarez-Presas; I. Ruiz-Trillo. Novel genomic approaches support Xenacoelomorpha as sister to all Bilateria. Origin of metazoans conference. Oral communication. Roscoff, France. 06/2025

M. Álvarez-Presas; M. Antó; I. Ruiz-Trillo; E. Casacuberta. Gene regulation in Ichthyosporeans: a comparative evolutionary perspective. Choannos&Friends 2025 meeting. Poster. Paris, France. 20/05/2025-22/05/2025

F. J. Bascón; M. Álvarez-Presas; M.M. Legger; C. Scazzocchio; I. Ruiz-Trillo; E. Casacuberta. Unravelling the nuclear and cytoplasmic division regulation in unicellular Holozoa. Choannos&Friends 2025 meeting. Poster. Paris, France. 20/05/2025-22/05/2025

M. Álvarez-Presas; B. Crespo; E. Casacuberta; I. Ruiz-Trillo. Gene regulation and animal origins: Lessons from early Holozoans. EuroEvoDevo 2024 conference. Poster. Helsinki, Finland. 25/06/2024-29/06/2024

F.J. Bascón; M.M. Leger; M. Álvarez-Presas; R. Müksch; S. Willems; P.S. Ara; C. Scazzocchio; I. Ruiz-Trillo; E. Casacuberta. Unraveling the nuclear and cytoplasmic division regulation in unicelular Holozoa. EuroEvoDevo 2024 conference. Poster. Helsinki, Finland. 25/06/2024- 29/06/2024

B. Crespo; M. Álvarez-Presas. Gene families and the origins of complexity: A comparative genomics approach to better understand multicellularity. Jornadas de Biologia Evolutiva. Oral presentation. Barcelona, Spain. 22/06/2024

M. Álvarez-Presas; I. Ruiz-Trillo; J. Paps. Assessing the origin of Bilateria with new geno genomic methods. SMBE conference 2023. Oral presentation. Ferrara, Italy. 23/07/2023-27/07/2023

Presentations at scientific seminars

M. Álvarez-Presas. “Transposable elements in the animal unicellular relatives”. Seminario impartido en el Institut de Biologia Evolutiva (IBE, UPF-CSIC) para Multicellgenome lab. Barcelona, Spain. 29/01/2025

M. Álvarez-Presas. “EvoSearch: a new pipeline to solve an old problem”. Seminario impartido en el Institut de Biologia Evolutiva (IBE, UPF-CSIC) para Multicellgenome lab. Barcelona, Spain. 14/11/2024

M. Álvarez-Presas. “Ancestral Sequence Reconstruction of the aspartyl aminopeptidase protein (DNPEP) at the origin of vertebrates and at the origin of animals”. Seminario impartido en el Institut de Biologia Evolutiva (IBE, UPF-CSIC) para Multicellgenome lab. Barcelona, Spain. 9/05/2024

M. Álvarez-Presas. “The origin of animal genomic regulation through the lens of NGS”. Seminario impartido en el Institut de Biologia Evolutiva (IBE, UPF-CSIC) para Multicellgenome lab. Barcelona, Spain. 14/03/2024.

M. Álvarez-Presas. “Animal genomic regulation from an evolutionary perspective”. Seminario impartido en la University of Bristol, online. 13/03/2024.

M. Álvarez-Presas. “A new genomic approach to shed light on the mystery of the evolution of Bilateria”. Seminario impartido en el Institut de Biologia Evolutiva (IBE, UPF-CSIC). Barcelona, Spain. 26/04/2023.