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Additional file 4. Review history.

Additional file 3. Supplementary Note 1.

Additional file 2: Figure S1. BraLan3 genome assembly and annotation quality comparison. Drer, Ggal, Mmus, Hsap, Bflo and Bbel correspond to the latest available genome assemblies for zebrafish, chicken, mouse, human, Florida amphioxus (B. floridae) and an Asian amphioxus (B. belcheri), respectively (see Methods). Blan2 corresponds to the latest genome reference for the European amphioxus previous to this publication [8] and Blan3 corresponds to BraLan3, the genome reference for the European amphioxus presented in this study. Percentage of the genome assembly sequence in scaffolds (sequences) of length greater than 1 million (M) nucleotides (size of chromosomal magnitude) versus the number of existing sequence gaps in these chromosomal-size sequences. Figure S2. A. Venn diagram representing the number of amphioxus specific orthologous groups (black) and amphioxus species-specific genes (gray). B. Percentage of small-scale gene duplications that are either multichromosomal, distant monochromosomal and tandem gene duplications in B. lanceolatum, chicken, mouse and human (Blan, Ggal, Mmus and Hsap respectively). Zebrafish is excluded from this comparison because of the effect that the 3R WGD in the teleost lineage could have had in the chromosomal localization of small-scale duplications. C. Similar to Fig. 5 for amphioxus inter-chromosomal, intra-chromosomal distant and tandemly duplicated small-scale duplicates that have single-copy orthologs in zebrafish. For B and C, Tandem gene duplications are defined as consecutive genes along the chromosomal sequence. Figure S3. Embryonic gene expression in single-copy and duplicated genes in B. lanceolatum. A. Box plots showing the distribution of the mean gene expression in transcripts per million (TPM) units across embryonic developmental stages for B. lanceolatum single-copy and small-scale duplicated genes. B. Same as A but dividing B. lanceolatum genes according to their vertebrate ortholog (single-copy, ohnolog, small-scale duplicate or B. lanceolatum specific). C-D. Box plots showing the distribution of developmental stage specificity of B. lanceolatum gene expression (Tau statistic) for the same gene groups as A and B. Tau values range from 0 (ubiquitous expression) to 1 (expression only in 1 tissue). Figure S4. Lower level of expression of duplicated genes compared to single copy genes within functional categories. Each point corresponds to a Gene Ontology (GO) term and its size refers to its number of human genes. A and B show molecular function categories, while C and D show biological processes categories. A and C show average expression in adult tissues, while B and D show average expression in embryonic stages. All points are filled with the same semi-transparent black color, thus opaque regions imply a high point density. Figure S5. Gene synteny comparison of B. lanceolatum and B. floridae with B. belcheri. One-to-one orthologs' synteny conservation between B. lanceolatum, B. floridae and B. belcheri. Black lines across plots correspond to the fusion/fission points of chromosome 1 in B. lanceolatum and chromosome 3 in B. floridae. Different colors depict different B. lanceolatum chromosomes on the left plots and different B. floridae chromosomes on the right plot. Figure S6. B. lanceolatum gene synteny comparison with B. floridae and G. gallus. A. Duplicated genes (many-to-many, many-to-one and one-to-many orthologs) synteny conservation between B. lanceolatum and B. floridae. B. B. lanceolatum within species duplicated genes (many-to-many, many-to-one and one-to-many orthologs) synteny conservation. C. One-to-one orthologs synteny conservation between B. lanceolatum and chicken (G. gallus). D. Same as in A for B. lanceolatum and chicken (G. gallus). In all cases (A-C) every gene is represented by its mid-point coordinates in the genome. Different colors depict different B. lanceolatum chromosomes.

Trabajo presentado en el EMBO Workshop The evolution of animal genomes, celebrado en modalidad virtual del 13 al 17 de septiembre de 2021.

Trabajo presentado en el EMBO Workshop The evolution of animal genomes, celebrado en modalidad virtual del 13 al 17 de septiembre de 2021.

Trabajo presentado en EMBO Workshop The evolution of animal genomes, celebrado en modalidad virtual del 13 al 17 de septiembre de 2021.

The tridimensional (3D) organization of the genome is just beginning to be understood and, despite the tremendous progress witnessed in the recent years, many essential questions remain unanswered. Major methodological and conceptual challenges need to be overcome to reach a comprehensive view of the physiological impact of 3D genome architecture in health and disease. CSIC is in a privileged position to undertake these challenges

Publicado en Madrid, 185 p. ; 17 cm., How life appeared on Earth and how then it diversified into the different and currently existing forms of life are the unanswered questions that will be discussed this volume. These questions delve into the deep past of our planet, where biology intermingles with geology and chemistry, to explore the origin of life and understand its evolution, since “nothing makes sense in biology except in the light of evolution” (Dobzhansky, 1964). The eight challenges that compose this volume summarize our current knowledge and future research directions touching different aspects of the study of evolution, which can be considered a fundamental discipline of Life Science. The volume discusses recent theories on how the first molecules arouse, became organized and acquired their structure, enabling the first forms of life. It also attempts to explain how this life has changed over time, giving rise, from very similar molecular bases, to an immense biological diversity, and to understand what is the hylogenetic relationship among all the different life forms. The volume further analyzes human evolution, its relationship with the environment and its implications on human health and society. Closing the circle, the volume discusses the possibility of designing new biological machines, thus creating a cell prototype from its components and whether this knowledge can be applied to improve our ecosystem. With an effective coordination among its three main areas of knowledge, the CSIC can become an international benchmark for research in this field.

Resumen del trabajo presentado al VII Biennial Congress of the Spanish Society for Evolutionary Biology (Sociedad Española de Biología Evolutiva), celebrado en Sevilla del 5 al 7 de febrero de 2020.

The Spanish Society for Developmental Biology (SEBD) organized its 17th meeting in November 2020 (herein referred to as SEBD2020). This meeting, originally programmed to take place in the city of Bilbao, was forced onto an online format due to the SARS-CoV2, COVID-19 pandemic. Although, we missed the live personal interactions and missed out on the Bilbao social scene, we were able to meet online to present our work and discuss our latest results. An overview of the activities that took place around the meeting, the different scientific sessions and the speakers involved are presented here. The pros and cons of virtual meetings are discussed.

Trabajo presentado en el 17th Spanish Society for Developmental Biology meeting, celebrado en modalidad virtual del 18 al 20 de noviembre de 2020.

Some of the mayor known unknowns of modern science deal with how lifeappeared on Earth and how from there it diversified into the different life forms present today. These questions delve into the deep past of our planet, where biology intermingles with geology and chemistry, to explore the origin of life. In addition, by learning how biological systems change over time, we can design novel biological machines based on this knowledge to fulfil unmet tasks.The main overarching theme addressed in this topic is evolution. Not because of much repeated is Theodosius Dobzhansky 1964’s statement less true: Nothing makes sense in biology except in the light of evolution. Understanding evolution will provide us with clues about the origin of life, and on the precise molecular mechanisms that operate in living beings and how they change in time. We will then be ready to attempt putting together these mechanisms in novel ways, paving the way for synthetic biology. Evolution is the single most overarching and one of the few, if not only, general principles in Biology.In this topic, we explore and discuss several aspects related to the study of evolution, as a fundamental and core discipline in Life Sciences, which must permeate different research areas in the coming years.

Resumen del trabajo presentado al VII Biennial Congress of the Spanish Society for Evolutionary Biology (Sociedad Española de Biología Evolutiva), celebrado en Sevilla del 5 al 7 de febrero de 2020., Biological entities, whether proteins, blue whales, sensory organs or cis-regulatory elements are continuously interacting with other structures, establishing complex networks through which biological information is exchanged. These interaction networks are assembled and maintained during the course of evolution. But, what happens when new elements are incorporated for the first time into these systems? We have expressed highly divergent mammalian-specific homeodomain transcription factors (TFs), such as LEUTX and ARGFX, in the completely foreign chromatin environment of zebrafish embryos. We show that LEUTX mRNA injection disrupts early zebrafish development and embryos are arrested during early gastrulation. In the case of ARGFX, ChIP-seq experiments of injected zebrafish embryos show that the ectopic binding sites in zebrafish are preferentially found in chromatin regions that are open and accessible during zebrafish development, some of them are found in the zebrafish orthologues of ARGFX endogenous target genes in mammals. Our results suggest that biological molecular structures, such as TFs, have inherent capacities to interpret and read the information contained in other biological systems, even when these systems have not co-evolved with and are foreign to these biological structures.

Resumen del trabajo presentado al VII Biennial Congress of the Spanish Society for Evolutionary Biology (Sociedad Española de Biología Evolutiva), celebrado en Sevilla del 5 al 7 de febrero de 2020.