Microsyntenic Clusters Reveal Conservation of lncRNAs in Chordates Despite Absence of Sequence Conservation

Homologous long non-coding RNAs (lncRNAs) are elusive to identify by sequence similarity due to their fast-evolutionary rate. Here we develop LincOFinder, a pipeline that finds conserved intergenic lncRNAs (lincRNAs) between distant related species by means of microsynteny analyses. Using this tool, we have identified 16 bona fide homologous lincRNAs between the amphioxus and human genomes. We characterized and compared in amphioxus and Xenopus the expression domain of one of them, Hotairm1, located in the anterior part of the Hox cluster. In addition, we analyzed the function of this lincRNA in Xenopus, showing that its disruption produces a severe headless phenotype, most probably by interfering with the regulation of the Hox cluster. Our results strongly suggest that this lincRNA has probably been regulating the Hox cluster since the early origin of chordates. Our work pioneers the use of syntenic searches to identify non-coding genes over long evolutionary distances and helps to further understand lncRNA evolution

Amphioxus functional genomics and the origins of vertebrate gene regulation.

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 across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that-in vertebrates-over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations

Genoarquitectura del sistema nervioso durante el desarrollo embrionario del anfioxo: implicaciones evolutivas para el origen del cerebro de vertebrados

[spa] En esta tesis se ha estudiado en detalle la genoarquitectura de la placa neural del anfioxo en desarrollo. La expresión de varios genes había sido descrita en el primordio nerual del anfioxo, pero no existe ningún consenso sobre la significación morfológica de las partes distinguibles por patrones moleculares concretos descritos en el sistema nervioso central. En este estudio hemos analizado cerca de cincuenta genes de diferenciación y, sobretodo, factores de transcripción que se expresan en el análogo neural de las néurulas de anfioxo, corroborando y complementado estudios previos. En vertebrados, sus ortólogos delinean distintos territorios cerebrales, contribuyendo con el concepto de bauplan neural gracias al modelo prosomérico. Nuestro principal objetivo fue determinar si el anfioxo podría constituir una aproximación a ese modelo, y en ese caso, en qué medida se podría definir un bauplan neural para cordados. Nuestros resultados revelan varios patrones de expresión discretos que discriminan tanto entre regionalización antero posterior como dorso ventral. En el caso de la regionalización antero posterior, los territorios Otx- y Gbx-positivos son fácilmente identificables pronto en el desarrollo, de la misma forma que ocurre en vertebrados. Dentro del territorio Otx-positivo, en la región se delimitan dos subdivisiones: el primordio del hipotálamo (HyP) y el primordio del di-mesencéfalo (DiMeP), la el límite entre las dos es conicidente con la aposición de los dominios de Fesf y Irx. Y, conjuntamente con el primordio rombo- espinal (RhSp), que se define en el territorio Gbx-positivo, las tres subunidades principales quedan delimitadas por las mismas barreras topológicas que definen equivalentes dominios moleculares, tanto en cefalocordados como en vertebrados. Además los límites entre las tres subunidades principales son coincidentes con el posicionamiento y desarrollo de los organizadores secundarios en vertebrados. Ésta correspondecia topológica entre la región tálamo-pretecto-mesencefálica con el DiMeP, simple o simplificado de anfioxo, sugiere que estas tres regiones en vertebrados, que están delimitadas y especificadas por los organizadores secundarios compartan origen evolutivo. Extendiendo las correlaciones y extrapolaciones que surgen de este studio genoarquitectónico, en esta tesis se describe un bauplan neural para cordados y se discuten otros temas relacionados con el origen y la evolución del complejo sistema nervioso central de vertebrados.[eng] In this thesis we have studied thoroughly the genoarquitecture of the neural plate of amphioxus embryos. The expression of various genes have been studied variously in the neural primordium of Amphioxus but, there was no consensus about the morphological significance of the CNS regions that are distinguishable by characteristic molecular patterns. We have now analysed around fifty differentiation genes and transcription factors that are expressed in the neural anlage of amphioxus at the middle neurula stage, corroborating and complementing earlier reports. Homologs of the chosen markers delineate distinct brain territories in vertebrates, contributing to current concepts of the neural bauplan by means of the prosomeric model. Our main aim was to determine whether amphioxus in any way approximates that model, and whether if it can be defined a common neural bauplan for chordates. Our results revealed various discrete patterns discriminating along both the anteroposterior and dorsoventral dimensions (AP, DV). As regards AP expression patterns, Otx-positive versus Gbx-positive territories were early observable, as in vertebrates. The Otx-positive subregion is further partitioned by several markers in two major parts, which we named as primordial hypothalamus (HyP) and a primordial di-mesencephalon (DiMeP). And, along with the rhombospinal primordium (RhSP), that corresponds to the Gbx-positive territory, the three main subunits are delimited by the same topological boundaries, defining the same molecular limits, that define the secondary organizers in vertebrates. This topological correspondence between the thalamic-pretectal-mesencephalic region with the DiMeP in amphioxus suggests that this three regions in vertebrates, that are surrounded by the specifying effect of the secondary organizers, may share common ancestry. Extending the correlations that issue from this genoarquitectonic study, in this thesis, a neural bauplan for chordates is described, and other issues related with the origin and evolution of central nervous systems are debated

The evolutionary origins of chordate hematopoeisis and vertebrate endothelia

AbstractThe vertebrate circulatory system is the most complex vascular system among those of metazoans, with key innovations including a multi-chambered heart and highly specialized blood cells. Invertebrate vessels, on the other hand, consist of hemal spaces between the basal laminae of epithelia. How the evolutionary transition from an invertebrate-type system to the complex vertebrate one occurred is, however, poorly understood. We investigate here the development of the cardiovascular system of the cephalochordate amphioxus Branchiostoma lanceolatum in order to gain insight into the origin of the vertebrate cardiovascular system. The cardiac markers Hand, Csx (Nkx2-5) and Tbx4/5 reveal a broad cardiac-like domain in amphioxus; such a decentralized organization during development parallels that seen in the adult anatomy. Our data therefore support the hypothesis that amphioxus never possessed a proper heart, even transiently during development. We also define a putative hematopoietic domain, supported by the expression of the hematopoietic markers Scl and Pdvegfr. We show that this area is closed to the dorsal aorta anlages, partially linked to excretory tissues, and that its development is regulated by retinoic acid, thus recalling the aorta-gonads-mesonephros (AGM) area of vertebrates. This region probably produces Pdvegfr+ hemal cells, with an important role in amphioxus vessel formation, since treatments with an inhibitor of PDGFR/VEGFR lead to a decrease of Laminin in the basal laminae of developing vessels. Our results point to a chordate origin of hematopoiesis in an AGM-like area from where hemal Pdvegfr+ cells are produced. These Pdvegfr+ cells probably resemble the ancestral chordate blood cells from which the vertebrate endothelium later originated

Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain.

All vertebrate brains develop following a common Bauplan defined by anteroposterior (AP) and dorsoventral (DV) subdivisions, characterized by largely conserved differential expression of gene markers. However, it is still unclear how this Bauplan originated during evolution. We studied the relative expression of 48 genes with key roles in vertebrate neural patterning in a representative amphioxus embryonic stage. Unlike nonchordates, amphioxus develops its central nervous system (CNS) from a neural plate that is homologous to that of vertebrates, allowing direct topological comparisons. The resulting genoarchitectonic model revealed that the amphioxus incipient neural tube is unexpectedly complex, consisting of several AP and DV molecular partitions. Strikingly, comparison with vertebrates indicates that the vertebrate thalamus, pretectum, and midbrain domains jointly correspond to a single amphioxus region, which we termed Di-Mesencephalic primordium (DiMes). This suggests that these domains have a common developmental and evolutionary origin, as supported by functional experiments manipulating secondary organizers in zebrafish and mice

Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain

All vertebrate brains develop following a common Bauplan defined by anteroposterior (AP) and dorsoventral (DV) subdivisions, characterized by largely conserved differential expression of gene markers. However, it is still unclear how this Bauplan originated during evolution. We studied the relative expression of 48 genes with key roles in vertebrate neural patterning in a representative amphioxus embryonic stage. Unlike nonchordates, amphioxus develops its central nervous system (CNS) from a neural plate that is homologous to that of vertebrates, allowing direct topological comparisons. The resulting genoarchitectonic model revealed that the amphioxus incipient neural tube is unexpectedly complex, consisting of several AP and DV molecular partitions. Strikingly, comparison with vertebrates indicates that the vertebrate thalamus, pretectum, and midbrain domains jointly correspond to a single amphioxus region, which we termed Di-Mesencephalic primordium (DiMes). This suggests that these domains have a common developmental and evolutionary origin, as supported by functional experiments manipulating secondary organizers in zebrafish and mice.Spanish Ministry of Economy and Competitiveness and European FEDER funds (grant number BFU2014-57516-P). To Luis Puelles and Jose Luis Ferran. European Research Council (grant number ERC-StG-LS2-637591). To Manuel Irimia. Spanish Ministry of Economy and Competitiveness (grant number SEV-2012-0208).Centro de Excelencia Severo Ochoa (to CRG, Manuel Irimia). Spanish Ministry of Economy and Competitiveness (grant number BFU2014-58908-P). To Jordi Garcia-Fernadez. Seneca Foundation, Comunidad de Murcia (grant number 19904/GERM/15). To Luis Puelles. Generalitat de Catalunya (grant number). ICREA Academia Prize to Jordi Garcia-Fernandez. Spanish Ministry of Economy and Competitiveness (grant number BFU2013-43213-P). To Paola Bovolenta. Spanish Ministry of Economy and Competitiveness (grant number BFU2014-55076-P). To Manuel Irimia. Including an FPI PhD fellowship to Laura Lopez-Blanch. Marine Alliance for Science and Technology Scotland (MASTS) (grant number). To Ildiko Somorjai

Genoarchitectonic signatures of the Rhombencephalo-Spinal primordium (RhSp).

<p><b>(A-C′′)</b>. <i>Hox1</i>, <i>Hox3</i>, and <i>Hox6</i> were expressed in the alar and basal plates of some caudal domains of the RhSp region in a sequential rostro-caudal order. (<b>D-D′′)</b> <i>Nkx6</i> was detected at different degrees of expression mainly at the floor plate of the Di-Mesencephalic primordium (DiMes) and RhSp domains and a localized bilateral spot at the equivalent position of the fifth somite. (<b>E-E´´)</b> <i>FoxB</i> mRNA was observed extending caudally from the DiMes/RhSp border into the basal plate of the entire RhSp region. <b>(F-G´´)</b> <i>Pax2/5/8</i> and <i>Msx</i> mRNAs were detected in some patches in the alar plate of the RhSp region. Expression patterns correspond to lateral <b>(A-G)</b> or dorsal views <b>(A′-G′)</b> at the 21 h post fertilization (hpf) embryonic stage, and are represented in schematics dorsal views <b>(A′′-G′′)</b>. Somites (dotted lines) were used as main landmarks to localize the position of the patterns analyzed in the late neural plate. Scale bar: 50 μm.</p

Three major molecular anteroposterior (AP) regions are observed in the incipient amphioxus neural tube.

<p><b>(A)</b> Whole-mount in situ hybridization of chicken <i>Otx2</i> at Hamburger–Hamilton 5 (HH5) stage. (<b>B,C</b>) Expression of amphioxus <i>Otx</i> at 21 h post fertilization (hpf) in dorsal <b>(B)</b> and lateral <b>(C)</b> views. (<b>D)</b> Whole-mount in situ hybridization of chicken <i>Gbx2</i> at HH5 stage. (<b>E,F</b>) Expression of amphioxus <i>Gbx</i> at 21 hpf in dorsal <b>(E)</b> and lateral <b>(F)</b> views. <b>G)</b> Whole-mount in situ hybridization of chicken <i>Fezf2</i> at HH5 stage. (<b>H,I</b>) Expression of amphioxus <i>Otx</i> at 21 hpf in dorsal <b>(H)</b> and lateral <b>(I)</b> views. (<b>J)</b> Schematic representation of HH5 chicken neural plate with the archencephalic prototagma (ARCH) and deuteroencephalic prototagma (DEU) domains depicted. The boundary between ARCH and DEU correspond to the border between <i>Otx2</i> and <i>Gbx2</i> expression patterns <b>(A,D)</b>. (<b>K,L)</b> Double chromogenic in situ hybridization combining amphioxus <i>Fezf</i> and <i>Gbx</i> probes in dorsal <b>(K)</b> and lateral <b>(L)</b> views, showing two subdivisions in the amphioxus ARCH territory: a rostral hypothalamo-prethalamic primordium (HyPTh) domain (<i>Fezf</i> and <i>Otx</i> positive) and a caudal Di-Mesencephalic primordium (DiMes) domain (<i>Fezf negative</i> and <i>Otx</i> positive) <b>(L′)</b>. (<b>M</b>) Schematic representation of the three major AP subdivisions in the amphioxus central nervous system (CNS) at the 21 hpf stage and the relative expression of their key markers. (<b>N,O</b>) Single chromogenic in situ hybridization with an amphioxus <i>IrxB</i> probe in dorsal <b>(N)</b> an lateral <b>(O)</b> views. Insets in B, E, H, K, and N depict the neural components of the corresponding gene expression patterns. Arrowheads mark the ARCH–DEU boundary, and asterisks mark the corresponding limit at the notochord level, based on <i>Gbx</i> expression. Abbreviations: n, notochord. Scale bar: 50 μm.</p

Schematic representation of informative markers used in this study.

<p><b>(A)</b> Main tagmata and Hypothalamo-Prethalamic (HyPTh), Di-Mesencephalic (DiMes), and Rhombencephalo-Spinal (RhSp) primordia. <b>(B)</b> HyPTh internal subdivisions. (<b>C)</b> RhSp internal subdivisions.</p