Cristian Cañestro

University of Barcelona | UB · Department of Genetics

The impact of gene loss on the diversification of taxa and the emergence of evolutionary innovations remains poorly understood. Here, our investigation on the evolution of the Fibroblast Growth Factors (FGFs) in appendicularian tunicates as a case study reveals a scenario of “less, but more” characterized by massive losses of all Fgf gene subfamili...

The impact of gene loss on the divergence of taxa and the generation of evolutionary innovations is a fundamental aspect of Evolutionary Biology that remains unclear. Here, using the evolution of the Fibroblast Growth Factors (FGFs) in appendicularians as a case study, we investigate how gene losses have influenced the evolution of chordates, espec...

Genome structural variations within species are rare. How selective constraints preserve gene order and chromosome structure is a central question in evolutionary biology that remains unsolved. Our sequencing of several genomes of the appendicularian tunicate Oikopleura dioica around the globe reveals extreme genome scrambling caused by thousands o...

Microplastics pose risks to marine organisms through ingestion, entanglement, and as carriers of toxic additives and environmental pollutants. Plastic pre-production pellet leachates have been shown to affect the development of sea urchins and, to some extent, mussels. The extent of those developmental effects on other animal phyla remains unknown....

Genes are not randomly distributed throughout chromosomes. How gene order evolves and how selective constraints act to preserve or vary gene order, both at the macrosyntenic level of whole chromosomes or microsyntenic level of gene blocks, are central questions of evolutionary biology and genomics that remain largely unsolved. Here, after sequencin...

Appendicularian tunicates are some of the most abundant mesozooplankton organisms with key roles in marine trophic webs and global carbon flux. Like most appendicularians with cosmopolitan distributions, Oikopleura dioica Fol, 1872 is considered a single species worldwide based on morphological features that distinguish them from other appendicular...

Appendicularian tunicates are some of the most abundant mesozooplankton organisms with key roles in marine trophic webs and global carbon flux. Like most appendicularians with cosmopolitan distributions, Oikopleura dioica Fol, 1872 is considered a single species worldwide based on morphological features that distinguish them from other appendicular...

A central question in chordate evolution is the origin of sessility in adult ascidians, and whether the appendicularian complete free-living style represents a primitive or derived condition among tunicates1. According to the ‘a new heart for a new head’ hypothesis, the evolution of the cardiopharyngeal gene regulatory network appears as a pivotal...

Chordate Oikopleura dioica probably is the fastest evolving metazoan reported so far, and thereby, a suitable system in which to explore the limits of evolutionary processes. For this reason, and in order to gain new insights on the evolution of protein modularity, we have investigated the organization, function and evolution of multi-modular metal...

To investigate novel patterns and processes of protein evolution, we have focused in the metallothioneins (MTs), a singular group of metal-binding, cysteine-rich proteins that, due to their high degree of sequence diversity, still represents a black hole in Evolutionary Biology. We have identified and analyzed more than 160 new MTs in non-vertebrat...

Gene loss is a pervasive source of genetic variation that influences species evolvability, biodiversity and the innovation of evolutionary adaptations. To better understand the evolutionary patterns and impact of gene loss, here we investigate as a case study the evolution of the wingless (Wnt) family in the appendicularian tunicate Oikopleura dioi...

A key problem in understanding chordate evolution has been the origin of sessility of ascidians, and whether the appendicularian free-living style represents a primitive or derived condition of tunicates. To address this problem, we performed comprehensive developmental and genomic comparative analyses of the cardiopharyngeal gene regulatory networ...

The urochordate Oikopleura dioica is emerging as a nonclassical animal model in the field of evolutionary developmental biology (a.k.a. evo-devo) especially attractive for investigating the impact of gene loss on the evolution of mechanisms of development. This is because this organism fulfills the requirements of an animal model (i.e., has a simpl...

Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes a...

Elephants and fruit bats have evolved large brains even though they have lost a gene that is fundamental to the supply of energy to the brain when glucose is not available.

The increasing levels of heavy metals derived from human activity are poisoning marine environments, threating zooplankton and ocean food webs. To protect themselves from the harmful effects of heavy metals, living beings have different physiological mechanisms, one of which is based on metallothioneins (MTs), a group of small cysteine-rich protein...

Locomotion by tail beating powered by a system of bilateral paraxial muscle and notochord is likely one of the key evolutionary innovations that facilitated the origin and radiation of chordates. The innovation of paraxial muscle was accompanied by gene duplications in stem chordates that gave rise to muscular actins from cytoplasmic ancestral form...

Investigating environmental hazards than could affect appendicularians is of prime ecological interest because they are among the most abundant components of the mesozooplankton. This work shows that embryo development of the appendicularian Oikopleura dioica is compromised by diatom bloom-derived biotoxins, even at concentrations in the same range...

Background: What impact gene loss has on the evolution of developmental processes, and how function shuffling has affected retained genes driving essential biological processes, remain open questions in the fields of genome evolution and EvoDevo. To investigate these problems, we have analyzed the evolution of the Wnt ligand repertoire in the chor...

Reporter analyses of Hox1 and Brachyury (Bra) genes have revealed examples of redundant enhancers that provide regulatory robustness. Retinoic acid (RA) activates through an RA-response element the transcription of Hox1 in the nerve cord of the ascidian Ciona intestinalis. We also found a weak RA-independent neural enhancer within the second intron...

The parathyroid hormone (PTH) family is a group of structurally-related secreted peptides involved in bone mineral homeostasis and multitude of developmental processes in vertebrates. These peptides mediate actions through PTH receptors (PTHRs), which belong to the transmembrane G protein-coupled receptor group. To date, genes encoding for PTH and...

Regulation of bone development, growth, and remodeling traditionally has been thought to depend on endocrine and autocrine/paracrine modulators. Recently, however, brain-derived signals have emerged as key regulators of bone metabolism, although their mechanisms of action have been poorly understood. We reveal the existence of an ancient parathyroi...

The bloom of Genomics is revealing gene loss as a pervasive evolutionary force generating genetic diversity that shapes the evolution of species. Outside bacteria and yeast, however, the understanding of the process of gene loss remains elusive, especially in the evolution of animal species. Here, using the dismantling of the retinoic acid metaboli...

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons (vol 48, pg 427, 2016)

The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essentia...

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by...

The genome sequencing and the development of RNAi knockdown technologies in the urochordate Oikopleura dioica are making this organism an attractive emergent model in the field of EvoDevo. To succeed as a new animal model, however, an organism needs to be easily and affordably cultured in the laboratory. Nowadays, there are only two facilities in t...

To help understand the elusive mechanisms of zebrafish sex determination, we studied the genetic machinery regulating production and breakdown of retinoic acid (RA) during the onset of meiosis in gonadogenesis. Results uncovered unexpected mechanistic differences between zebrafish and mammals. Conserved synteny and expression analyses revealed that...

The study of the evolutionary origin of vertebrates has been linked to the study of genome duplications since Susumo Ohno suggested that the successful diversification of vertebrate innovations was facilitated by two rounds of whole-genome duplication (2R-WGD) in the stem vertebrate. Since then, studies on the functional evolution of many genes dup...

The origin and evolution of the vertebrates have been linked to the study of genome duplications since Susumo Ohno ventured the 2R-hypothesis, suggesting that the successful diversification of complex vertebrates was facilitated by polyploidization in the stem vertebrate ancestor due to two rounds of whole-genome duplication (2R-WGD). This chapter...

In vertebrates, DNA methylation is an epigenetic mechanism that modulates gene transcription, and plays crucial roles during development, cell fate maintenance, germ cell pluripotency and inheritable genome imprinting. DNA methylation might also play a role as a genome defense mechanism against the mutational activity derived from transposon mobili...

Transposable elements (TEs) are main components of eukaryote genomes—up to 50% in some vertebrates—which can replicate and jump to new locations. TEs contribute to shape genome evolution, actively by creating new genes (or exons) or altering gene expression as consequence of transposition, and passively by serving as illegitimate recombinational ho...

Analysis of zebrafish BRC repeats. (A) Alignment of the eight mammalian BRC repeats to the corresponding repeats in zebrafish and stickleback. Sequence identity between homologous zebrafish and human BRC repeats varied from 16% (BRC1) to 50% (BRC7) (mean = 38%). (B) Alignment of zebrafish BRC repeats identified four more (w,x,y,z) than are found in...

Expression of female-specific, male-specific, and meiotic recombination markers in adjacent sections of 47dpf wild-type and brca2 mutant gonads revealed male development in brca2 immature mutant testis. Oocytes in wild-type ovaries strongly expressed vasa (A) and weakly expressed amh in granulosa cells (B). Somatic cells of the ovary expressed cyp1...

Sequence of Brca2 inferred from the well-assembled sequenced genome of the stickleback, Gasterosteus aculeatus. The stickleback sequence was used as a comparator to infer the structure of the zebrafish brca2 gene. Ensembl (http://www.ensembl.org/Gasterosteus_aculeatus/blastview) was searched using as query brca2 exons conserved between zebrafish an...

Expression of brca2 during zebrafish development. (A) Expression of brca2 during zebrafish development assayed by RT-PCR. Total RNA was extracted using TRI REAGENT according to manufacturer's instructions (Molecular Research Center Inc., TR-118) from pools of 40 to 50 embryos for each developmental stage. First strand cDNA was generated from 2 µg o...

Primers for brca2(fancd1) RACE-PCR, PCR, genotyping, and cDNA analysis. Numbers correspond to the position of the most 3′ base on the Danio cDNA sequence (Accession number NM_001110394.1). Primers F1-F4 and R1-R4 correspond to those in Figure 3. (0.06 MB DOC)

Sequence of the DNA binding domain (DBD) of Brca2 in four vertebrates, zebrafish, human chicken, and mouse. Abbreviations: HD, helical domain; OB, oligo nucleotide binding motifs. (1.22 MB TIF)

brca2 mutant embryos exhibited normal hematopoietic development. Human Fanconi anemia patients develop profound anemia of several lineages. To investigate hematopoietic development in zebrafish brca2(fancd1) mutants, we studied gene expression patterns. Results showed that 16-somite stage wild-type embryos (A) and mutant (B) embryos had the same ex...

Brca2 function is not essential to localize brca2, pou5f1, or vasa transcripts in zebrafish oocytes. (A–F) In situ hybridizations on serial sections of wild-type (A–C) and brca2;tp53 double mutant females (D–F). In wild-type ovaries transcripts of the brca2 (A) and pou5f1 (B) genes localized to the same small cortical region of stage III oocytes wh...

Mild mutations in BRCA2 (FANCD1) cause Fanconi anemia (FA) when homozygous, while severe mutations cause common cancers including breast, ovarian, and prostate cancers when heterozygous. Here we report a zebrafish brca2 insertional mutant that shares phenotypes with human patients and identifies a novel brca2 function in oogenesis. Experiments show...

Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retain...

The molecular genetic mechanisms of sex determination are not known for most vertebrates, including zebrafish. We identified a mutation in the zebrafish fancl gene that causes homozygous mutants to develop as fertile males due to female-to-male sex reversal. Fancl is a member of the Fanconi Anemia/BRCA DNA repair pathway. Experiments showed that ze...

Enzymes that synthesize retinoic acid (RA) constitute the first level of regulation of RA action. In vertebrates, enzymes of the medium-chain alcohol dehydrogenase (MDR-Adh) family catalyze the first step of the RA synthetic pathway by oxidizing retinol. Among MDR-Adh enzymes, Adh3 is the only member present in non-vertebrates, and whether Adh3 is...

Fibroblast growth factors (Fgfs) encode small signaling proteins that help regulate embryo patterning. Fgfs fall into seven families, including FgfD. Nonvertebrate chordates have a single FgfD gene; mammals have three (Fgf8, Fgf17, and Fgf18); and teleosts have six (fgf8a, fgf8b, fgf17, fgf18a, fgf18b, and fgf24). What are the evolutionary processe...

Fanconi anemia (FA) is a genetic disease resulting in bone marrow failure, high cancer risks, and infertility, and developmental anomalies including microphthalmia, microcephaly, hypoplastic radius and thumb. Here we present cDNA sequences, genetic mapping, and genomic analyses for the four previously undescribed zebrafish FA genes (fanci, fancj, f...

Genome duplications increase genetic diversity and may facilitate the evolution of gene subfunctions. Little attention, however, has focused on the evolutionary impact of lineage-specific gene loss. Here, we show that identifying lineage-specific gene loss after genome duplication is important for understanding the evolution of gene subfunctions in...

High-resolution images of the clusters of the Synteny Database. (0.17 MB PDF)

Supplementary information for dot-plot on Figure 3A. (0.05 MB PDF)

Phylogenetic trees of the vertebrate Aldh1A gene family, inferred by maximum-likelihood, neighbor-joining, maximum-parsimony, and Bayesian methods. (4.46 MB PDF)

Supplementary information for dot-plot on Figure 2A. (0.58 MB PDF)

Supplementary information for dot-plots on Figure 4A–C. (0.16 MB PDF)

In vertebrates, retinoic acid (RA) is an important morphogenetic signal that controls embryonic development, as well as organ homeostasis in adults. RA action depends on the function of the RA-genetic machinery, which includes a metabolic module and a signaling module. The metabolic module regulates the spatiotemporal distribution of RA by the comb...

Phylogenetic relationships among chordate Pax2/5/8 proteins. The data provided illustrates the independent gene family expansions that permitted parallel histories of subfunction partitioning among vertebrate paralogs (Pax2, Pax5 and Pax8) and among urochordate paralogs (Pax2/5/8a and Pax2/5/8b).

The thyroid in vertebrates and its homolog, the endostyle in nonvertebrate chordates, share a molecular code for dorsoventral patterning. Little is yet known, however, about mechanisms that pattern the endostyle's anterior-posterior (AP) axis. To extend our understanding of thyroid development and evolution, we studied Oikopleura dioica, a larvacea...

Gene duplication provides opportunities for lineage diversification and evolution of developmental novelties. Duplicated genes generally either disappear by accumulation of mutations (nonfunctionalization), or are preserved either by the origin of positively selected functions in one or both duplicates (neofunctionalization), or by the partitioning...

Reciprocal questions often frame studies of the evolution of developmental mechanisms. How can species share similar developmental genetic toolkits but still generate diverse life forms? Conversely, how can similar forms develop from different toolkits? Genomics bridges the gap between evolutionary and developmental biology, and can help answer the...

Developmental signaling by retinoic acid (RA) is thought to be an innovation essential for the origin of the chordate body plan. The larvacean urochordate Oikopleura dioica maintains a chordate body plan throughout life, and yet its genome appears to lack genes for RA synthesis, degradation, and reception. This suggests the hypothesis that the RA-m...

Development of many chordate features depends on retinoic acid (RA). Because the action of RA during development seems to be restricted to chordates, it had been previously proposed that the "invention" of RA genetic machinery, including RA-binding nuclear hormone receptors (Rars), and the RA-synthesizing and RA-degrading enzymes Aldh1a (Raldh) and...

In non-vertebrate chordates, central nervous system (CNS) development has been studied in only two taxa, the Cephalochordata and a single Class (Ascidiacea) of the morphologically diverse Urochordata. To understand development and molecular regionalization of the brain in a different deeply diverging chordate clade, we isolated and determined the e...

The role of Anti-Müllerian hormone (Amh) during gonad development has been studied extensively in mammals, but is less well understood in other vertebrates. In male mammalian embryos, Sox9 activates expression of Amh, which initiates the regression of the Mullerian ducts and inhibits the expression of aromatase (Cyp19a1), the enzyme that converts a...

We report the first class II transposon in cephalochordates, which we have named Amphioxus Transposable Element 1 (ATE-1). ATE-1 members have been identified in the genome of Branchiostoma lanceolatum (BlATE-1) and B. floridae (BfATE-1). Structural analysis revealed that ATE-1 elements consist of a central region (CR) with no homology with any codi...

BfCR1 is the first non-long terminal repeat retrotransposon to be characterised in the amphio- xus genome. Sequence alignment of the predicted translation product reveals that BfCR1 belongs to the CR1-like retroposon class, a family widely distributed in vertebrate and invertebrate lineages. Structural analysis shows conservation of the specific mo...

Gene and genome duplications in the vertebrate lineage explain the complexity of extant gene families. Among these, the medium-chain alcohol dehydrogenase (ADH), which expanded by tandem duplications after the cephalochordate-vertebrate split, is a good model with which to analyze the evolution of gene function. Although the ancestral member of thi...

A draft sequence of the compact genome of the sea squirt Ciona intestinalis, a non-vertebrate chordate that diverged very early from other chordates, including vertebrates, illuminates how chordates originated and how vertebrate developmental innovations evolved.

Amphioxus (subphylum Cephalochordata) is the closest living relative to vertebrates and widely used for phylogenetic analyses of vertebrate gene evolution. Amphioxus genes are highly polymorphic, but the origin and nature of this variability is unknown. We have analyzed the alcohol dehydrogenase locus (Adh3) in two amphioxus species (Branchiostoma...

The alcohol dehydrogenase (ADH) family has evolved into at least eight ADH classes during vertebrate evolution. We have characterized three prevertebrate forms of the parent enzyme of this family, including one from an urochordate (Ciona intestinalis) and two from cephalochordates (Branchiostoma floridae and Branchiostoma lanceolatum). An evolution...

Molecular studies on the pathology of Alzheimer's disease (AD) have revealed that mutations in presenilin genes (PS) account for some familial cases. Although the contribution of these genes to the etiology is clear, their biological function remains obscure. Approaches using model organisms have been hampered by the fact that rodents contain two P...