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1.
Dev Biol ; 516: 207-220, 2024 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-39181419

RESUMEN

Larvacean tunicates feature a spectacular innovation not seen in other animals - the trunk oikoplastic epithelium (OE). This epithelium produces a house, a large and complex extracellular structure used for filtering and concentrating food particles. Previously we identified several homeobox transcription factor genes expressed during early OE patterning. Among these are two Pax3/7 copies that we named pax37A and pax37B. The vertebrate homologs, PAX3 and PAX7 are involved in developmental processes related to neural crest and muscles. In the ascidian tunicate Ciona intestinalis, Pax3/7 plays a role in the development of cells deriving from the neural plate border, including trunk epidermal sensory neurons and tail nerve cord neurons, as well as in the neural tube closure. Here we have investigated the roles of Oikopleura dioica pax37A and pax37B in the development of the OE, by using CRISPR-Cas9 mutant lines and analyzing scRNA-seq data from wild-type animals. We found that pax37B but not pax37A is essential for the differentiation of cell fields that produce the food concentrating filter of the house: the anterior Fol, giant Fol and Nasse cells. Trajectory analysis supported a neuroepithelial-like or a preplacodal ectoderm transcriptional signature in these cells. We propose that the highly specialized secretory epithelial cells of the Fol region either maintained or evolved neuroepithelial features. This is supported by a fragmented gene regulatory network involved in their development that also operates in ascidian epidermal neurons.


Asunto(s)
Factor de Transcripción PAX3 , Factor de Transcripción PAX7 , Urocordados , Animales , Urocordados/embriología , Urocordados/genética , Factor de Transcripción PAX7/genética , Factor de Transcripción PAX7/metabolismo , Factor de Transcripción PAX3/genética , Factor de Transcripción PAX3/metabolismo , Regulación del Desarrollo de la Expresión Génica/genética , Epitelio/metabolismo , Ciona intestinalis/genética , Ciona intestinalis/embriología , Diferenciación Celular/genética , Cresta Neural/metabolismo , Cresta Neural/embriología
2.
Front Zool ; 19(1): 26, 2022 Oct 28.
Artículo en Inglés | MEDLINE | ID: mdl-36307829

RESUMEN

A fascinating variety of adult body plans can be found in the Tunicates, the closest existing relatives of vertebrates. A distinctive feature of the larvacean class of pelagic tunicates is the presence of a highly specialized surface epithelium that produces a cellulose test, the "larvacean house". While substantial differences exist between the anatomy of larvacean families, most of the ontogeny is derived from the observations of a single genus, Oikopleura. We present the first study of Fritillaria development based on the observation of individuals reproduced in the laboratory. Like the other small epipelagic species Oikopleura dioica, the larvae of Fritillaria borealis grow rapidly in the laboratory, and they acquire the adult form within a day. We could show that major morphological differences exhibited by Fritillaria and Oikopleura adults originate from a key developmental stage during larval organogenesis. Here, the surface epithelium progressively retracts from the posterior digestive organs of Fritillaria larvae, and it establishes house-producing territories around the pharynx. Our results show that the divergence between larvacean genera was associated with a profound rearrangement of the mechanisms controlling the differentiation of the larval ectoderm.

3.
Dev Biol ; 443(2): 117-126, 2018 11 15.
Artículo en Inglés | MEDLINE | ID: mdl-30217597

RESUMEN

The mechanisms driving innovations that distinguish large taxons are poorly known and essentially accessible via a candidate gene approach. A spectacular acquisition by tunicate larvaceans is the house, a complex extracellular filtration device. Its components are secreted by the oikoplastic epithelium which covers the animal trunk. Here we describe the development of this epithelium in larvae through the formation of specific cellular territories known to produce distinct sets of house proteins (Oikosins). It involves cell divisions and morphological differentiation but very limited cell migration. A diverse set of homeobox genes, most often duplicated in the genome, are transiently and site-specifically expressed in the trunk epithelium at early larval stages. Using RNA interference, we show that two prop duplicates are involved in the differentiation of a region on and around the dorsal midline, regulating morphology and the production of a specific oikosin. Our observations favor a scenario in which multiple homeobox genes and most likely other developmental transcription factors were recruited for this innovation. Their frequent duplications probably predated, but were not required for the emergence of the house.


Asunto(s)
Genes Homeobox/genética , Urocordados/genética , Urocordados/metabolismo , Animales , Evolución Biológica , Células Epiteliales/metabolismo , Epitelio/embriología , Epitelio/crecimiento & desarrollo , Evolución Molecular , Regulación del Desarrollo de la Expresión Génica/genética , Larva/crecimiento & desarrollo , Interferencia de ARN , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
4.
BMC Dev Biol ; 18(1): 4, 2018 02 27.
Artículo en Inglés | MEDLINE | ID: mdl-29486709

RESUMEN

BACKGROUND: Germ cell formation has been investigated in sessile forms of tunicates. This process involves the release of a subset of maternal transcripts from the centrosome-attracting body (CAB) in the progenitor cells of the germ line. When germ-soma segregation is completed, CAB structures are missing from the newly formed primordial germ cells (PGCs). In free-swimming tunicates, knowledge about germ cell formation is lacking. In this investigation, comparative gene expression and electron microscopy studies were used to address germ cell formation in Oikopleura dioica (O. dioica). RESULTS: We found that the RNA localization pattern of pumilio (pum1) is similar to the pattern described for a subset of maternal transcripts marking the posterior end of ascidian embryos. Transcripts marking the posterior end are called postplasmic or posterior-end mark (PEM) transcripts. We found no localization of vasa (vas) transcripts to any sub-region within the germ-line precursor cells. Expression of vas4 was detected in the newly formed PGCs. Electron microscopy studies confirmed the presence of structures with similar morphology to CAB. In the same cytoplasmic compartment, we also identified pum1 transcripts and an epitope recognized by an antibody to histone H3 phosphorylated on serine 28. CONCLUSIONS: Our findings support that a CAB-like structure participates in the segregation of maternal pum1 transcripts during germ-soma separation in O. dioica.


Asunto(s)
Centrosoma/metabolismo , Embrión no Mamífero/metabolismo , Desarrollo Embrionario , Células Germinativas/metabolismo , Urocordados/embriología , Animales , Centrosoma/ultraestructura , Gastrulación/genética , Regulación del Desarrollo de la Expresión Génica , Células Germinativas/citología , Células Germinativas/ultraestructura , Mitosis/genética , Modelos Biológicos , ARN Mensajero/genética , ARN Mensajero/metabolismo , Transcripción Genética , Urocordados/citología , Cigoto/metabolismo
5.
Nucleic Acids Res ; 43(7): 3701-11, 2015 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-25779047

RESUMEN

Selective pressure to maintain small genome size implies control of transposable elements, and most old classes of retrotransposons are indeed absent from the very compact genome of the tunicate Oikopleura dioica. Nonetheless, two families of retrotransposons are present, including the Tor elements. The gene organization within Tor elements is similar to that of LTR retrotransposons and retroviruses. In addition to gag and pol, many Tor elements carry a third gene encoding viral envelope-like proteins (Env) that may mediate infection. We show that the Tor family contains distinct classes of elements. In some classes, env mRNA is transcribed from the 5'LTR as in retroviruses. In others, env is transcribed from an additional promoter located downstream of the 5'LTR. Tor Env proteins are membrane-associated glycoproteins which exhibit some features of viral membrane fusion proteins. Whereas some elements are expressed in the adult testis, many others are specifically expressed in embryonic somatic cells adjacent to primordial germ cells. Such embryonic expression depends on determinants present in the Tor elements and not on their surrounding genomic environment. Our study shows that unusual modes of transcription and expression close to the germline may contribute to the proliferation of Tor elements.


Asunto(s)
Retrovirus Endógenos/genética , Regulación del Desarrollo de la Expresión Génica , Células Germinativas , ARN/genética , Urocordados/genética , Secuencia de Aminoácidos , Animales , Células HEK293 , Humanos , Datos de Secuencia Molecular , Polimorfismo Genético , Regiones Promotoras Genéticas , Homología de Secuencia de Aminoácido , Proteínas del Envoltorio Viral/química
6.
Genesis ; 53(1): 183-93, 2015 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-25044679

RESUMEN

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 the world capable to indefinitely maintain Oikopleura dioica, one in the SARS institute (Bergen, Norway) and the other in the Osaka University (Japan). Here, we describe the setup of a new facility in the University of Barcelona (Spain) in which we have modified previously published husbandry protocols to optimize the weekly production of thousands of embryos and hundreds of mature animals using the minimum amount of space, human resources, and technical equipment. This optimization includes novel protocols of cryopreservation and solid cultures for long-term maintenance of microalgal stocks-Chaetoceros calcitrans, Isochrysis sp., Rhinomonas reticulate, and Synechococcus sp.-needed for Oikopleura dioica feeding. Our culture system maintains partially inbred lines healthy with similar characteristics to wild animals, and it is easily expandable to satisfy on demand the needs of any laboratory that may wish to use Oikopleura dioica as a model organism.


Asunto(s)
Modelos Animales , Urocordados/crecimiento & desarrollo , Animales , Criopreservación , Medios de Cultivo/química , Microalgas
7.
J Exp Zool B Mol Dev Evol ; 324(2): 114-27, 2015 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-25676192

RESUMEN

Using RNA interference, we have selectively perturbed neurotransmitter-related features of the larval swimming behavior of Oikopleura dioica, a tunicate with a central nervous system comprising about 130 neurons. We injected dsRNA into fertilized eggs to knockdown the expression of the genes, respectively, encoding ChAT (choline acetyltransferase) and GAD (glutamic acid decarboxylase), enzymes critical for the biosynthesis of acetylcholine and GABA. These two neurotransmitters have conserved roles during evolution, particularly within chordate motor systems, where they mediate respectively neuromuscular and central inhibitory signals. In Oikopleura, interference with ChAT expression prevented the normal bidirectional, propagating tail movement characteristic of swimming, permitting only repeated unilateral tail bends. Proper swimming was never observed, and the resting period between episodes of activity was lengthened. This phenotype is most likely caused by the reduction of transcription observed for both the targeted ChAT gene and the VAChT gene (Vesicular Acetylcholine Transporter), both genes being transcribed from the same operon. Interference with GAD expression led to an uncoordinated version of swimming with a spiral movement trajectory, but with episodes similar in duration and cycle frequency to those of normal swimming. Our results suggest locomotor functions for ChAT and GABA that are more subtle than previously proposed for tunicates and opens the way for a genetic dissection of Oikopleura neuronal circuits, which are likely to be among the most simplified in the chordate phylum.


Asunto(s)
Colina O-Acetiltransferasa/genética , Glutamato Descarboxilasa/genética , Urocordados/fisiología , Acetilcolina/metabolismo , Animales , Colina O-Acetiltransferasa/metabolismo , Regulación del Desarrollo de la Expresión Génica , Técnicas de Silenciamiento del Gen , Glutamato Descarboxilasa/metabolismo , Larva/crecimiento & desarrollo , Larva/fisiología , Interferencia de ARN , ARN Bicatenario/genética , Natación/fisiología , Urocordados/crecimiento & desarrollo , Cigoto , Ácido gamma-Aminobutírico/metabolismo
8.
Nucleic Acids Res ; 41(Database issue): D845-53, 2013 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-23185044

RESUMEN

We report the development of OikoBase (http://oikoarrays.biology.uiowa.edu/Oiko/), a tiling array-based genome browser resource for Oikopleura dioica, a metazoan belonging to the urochordates, the closest extant group to vertebrates. OikoBase facilitates retrieval and mining of a variety of useful genomics information. First, it includes a genome browser which interrogates 1260 genomic sequence scaffolds and features gene, transcript and CDS annotation tracks. Second, we annotated gene models with gene ontology (GO) terms and InterPro domains which are directly accessible in the browser with links to their entries in the GO (http://www.geneontology.org/) and InterPro (http://www.ebi.ac.uk/interpro/) databases, and we provide transcript and peptide links for sequence downloads. Third, we introduce the transcriptomics of a comprehensive set of developmental stages of O. dioica at high resolution and provide downloadable gene expression data for all developmental stages. Fourth, we incorporate a BLAST tool to identify homologs of genes and proteins. Finally, we include a tutorial that describes how to use OikoBase as well as a link to detailed methods, explaining the data generation and analysis pipeline. OikoBase will provide a valuable resource for research in chordate development, genome evolution and plasticity and the molecular ecology of this important marine planktonic organism.


Asunto(s)
Bases de Datos Genéticas , Genómica , Transcriptoma , Urocordados/genética , Animales , Minería de Datos , Perfilación de la Expresión Génica , Internet , Anotación de Secuencia Molecular , Análisis de Secuencia por Matrices de Oligonucleótidos , Urocordados/embriología , Urocordados/crecimiento & desarrollo
9.
BMC Genomics ; 13: 55, 2012 Feb 02.
Artículo en Inglés | MEDLINE | ID: mdl-22300585

RESUMEN

BACKGROUND: Animals have developed extensive mechanisms of response to xenobiotic chemical attacks. Although recent genome surveys have suggested a broad conservation of the chemical defensome across metazoans, global gene expression responses to xenobiotics have not been well investigated in most invertebrates. Here, we performed genome survey for key defensome genes in Oikopleura dioica genome, and explored genome-wide gene expression using high density tiling arrays with over 2 million probes, in response to two model xenobiotic chemicals - the carcinogenic polycyclic aromatic hydrocarbon benzo[a]pyrene (BaP) the pharmaceutical compound Clofibrate (Clo). RESULTS: Oikopleura genome surveys for key genes of the chemical defensome suggested a reduced repertoire. Not more than 23 cytochrome P450 (CYP) genes could be identified, and neither CYP1 family genes nor their transcriptional activator AhR was detected. These two genes were present in deuterostome ancestors. As in vertebrates, the genotoxic compound BaP induced xenobiotic biotransformation and oxidative stress responsive genes. Notable exceptions were genes of the aryl hydrocarbon receptor (AhR) signaling pathway. Clo also affected the expression of many biotransformation genes and markedly repressed genes involved in energy metabolism and muscle contraction pathways. CONCLUSIONS: Oikopleura has the smallest number of CYP genes among sequenced animal genomes and lacks the AhR signaling pathway. However it appears to have basic xenobiotic inducible biotransformation genes such as a conserved genotoxic stress response gene set. Our genome survey and expression study does not support a role of AhR signaling pathway in the chemical defense of metazoans prior to the emergence of vertebrates.


Asunto(s)
Benzo(a)pireno/farmacología , Clofibrato/farmacología , Regulación de la Expresión Génica/efectos de los fármacos , Genoma , Inactivación Metabólica/genética , Urocordados , Xenobióticos/farmacología , Animales , Sistema Enzimático del Citocromo P-450/clasificación , Sistema Enzimático del Citocromo P-450/genética , Sistema Enzimático del Citocromo P-450/metabolismo , Bases de Datos Genéticas , Redes Reguladoras de Genes , Urocordados/efectos de los fármacos , Urocordados/genética , Urocordados/metabolismo
10.
Nature ; 439(7079): 965-8, 2006 Feb 23.
Artículo en Inglés | MEDLINE | ID: mdl-16495997

RESUMEN

Tunicates or urochordates (appendicularians, salps and sea squirts), cephalochordates (lancelets) and vertebrates (including lamprey and hagfish) constitute the three extant groups of chordate animals. Traditionally, cephalochordates are considered as the closest living relatives of vertebrates, with tunicates representing the earliest chordate lineage. This view is mainly justified by overall morphological similarities and an apparently increased complexity in cephalochordates and vertebrates relative to tunicates. Despite their critical importance for understanding the origins of vertebrates, phylogenetic studies of chordate relationships have provided equivocal results. Taking advantage of the genome sequencing of the appendicularian Oikopleura dioica, we assembled a phylogenomic data set of 146 nuclear genes (33,800 unambiguously aligned amino acids) from 14 deuterostomes and 24 other slowly evolving species as an outgroup. Here we show that phylogenetic analyses of this data set provide compelling evidence that tunicates, and not cephalochordates, represent the closest living relatives of vertebrates. Chordate monophyly remains uncertain because cephalochordates, albeit with a non-significant statistical support, surprisingly grouped with echinoderms, a hypothesis that needs to be tested with additional data. This new phylogenetic scheme prompts a reappraisal of both morphological and palaeontological data and has important implications for the interpretation of developmental and genomic studies in which tunicates and cephalochordates are used as model animals.


Asunto(s)
Filogenia , Urocordados/clasificación , Vertebrados/clasificación , Animales , Evolución Molecular , Funciones de Verosimilitud , Urocordados/genética , Urocordados/fisiología , Vertebrados/genética
11.
Gen Comp Endocrinol ; 171(3): 332-40, 2011 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-21362424

RESUMEN

When mutated in mammals, paired-like homeobox Prop1 gene produces highly variable pituitary phenotypes with impaired regulation of Pit1 and eventually defective synthesis of Pit1-regulated pituitary hormones. Here we have identified fish prop1 orthologs, confirmed their pituitary-specific expression, and blocked the splicing of zebrafish prop1 transcripts using morpholino oligonucleotides. Very early steps of the gland formation seemed unaffected based on morphology and expression of early placodal marker pitx. Prop1 knock-down reduced the expression of pit1, prl (prolactin) and gh (growth hormone), as expected if the function of Prop1 is conserved throughout vertebrates. Less expectedly, lim3 was down regulated. This gene is expressed from early stages of vertebrate pituitary development but is not known to be Prop1-dependent. In situ hybridizations on prop1 morphants using probes for the pan pituitary gene pitx3 and for the hormone gene markers prl, gh and tshß, revealed abnormal shape, growth and cellular organization of the developed adenohypophysis. Strikingly, the effects of prop1 knock-down on adenohypophysis morphology and gene expression were gradually reversed during late development, despite persistent splice-blocking of transcripts. Therefore, prop1 function appears to be conserved between mammals and fish, at least for the mediation of hormonal cell type differentiation via pit1, but the existence of other fish-specific pathways downstream of prop1 are suggested by our observations.


Asunto(s)
Proteínas de Homeodominio/metabolismo , Hipófisis/metabolismo , Proteínas de Pez Cebra/metabolismo , Animales , Proteínas de Homeodominio/química , Proteínas de Homeodominio/clasificación , Proteínas de Homeodominio/genética , Hibridación in Situ , Filogenia , Reacción en Cadena de la Polimerasa , Salmón , Tirotropina de Subunidad beta/metabolismo , Factor de Transcripción Pit-1/química , Factor de Transcripción Pit-1/clasificación , Factor de Transcripción Pit-1/genética , Factor de Transcripción Pit-1/metabolismo , Pez Cebra , Proteínas de Pez Cebra/química , Proteínas de Pez Cebra/clasificación , Proteínas de Pez Cebra/genética
12.
Proc Natl Acad Sci U S A ; 105(20): 7229-34, 2008 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-18490654

RESUMEN

A key problem in understanding deuterostome evolution has been the origin of the chordate body plan. A biphasic life cycle with a sessile adult and a free-swimming larva is traditionally considered ancestral in chordates with subsequent neotenic loss of the sessile adult stage. Molecular phylogenies challenged this view, suggesting that the primitive life cycle in chordates was entirely free-living as in modern day larvaceans. Here, we report the precise cell lineage and fate map in the normal embryo of the larvacean Oikopleura dioica, using 4D microscopy technique and transmission electron microscopy. We document the extraordinary rapidity of cleavage and morphogenetic events until hatching and demonstrate that--compared with ascidians--fate restriction occurs considerably earlier in O. dioica and that clonal organization of the cell lineage is more tightly coupled to tissue fate. We show that epidermal cells in the trunk migrate through 90 degrees, reminiscent of events in ascidian metamorphosis and that the axis of bilateral symmetry in the tail rotates in relation to the trunk. We argue that part of the tail muscle cells are ectomesodermal, because they are more closely associated with prospective epidermis than with other tissues in the cell lineage. Cladistic comparison with other deuterostomes suggests that these traits are derived within tunicates strengthening the hypothesis that the last common ancestor of tunicates had a sessile adult and thus support traditional morphology-derived scenarios. Our results allow hypothesizing that molecular developmental mechanisms known from ascidian models are restricted to fewer, yet identifiable, cells in O. dioica.


Asunto(s)
Biología Evolutiva , Regulación del Desarrollo de la Expresión Génica , Urocordados/embriología , Urocordados/fisiología , Animales , División Celular , Linaje de la Célula , Núcleo Celular/metabolismo , Células Epidérmicas , Epidermis/metabolismo , Epidermis/patología , Evolución Molecular , Gástrula/fisiología , Metamorfosis Biológica , Microscopía/métodos , Modelos Biológicos , Filogenia , Factores de Tiempo
13.
Nat Ecol Evol ; 5(2): 231-242, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33199869

RESUMEN

The causes and consequences of genome reduction in animals are unclear because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact 73.8-megabase genome of Dimorphilus gyrociliatus, a meiobenthic segmented worm. The D. gyrociliatus genome retains traits classically associated with larger and slower-evolving genomes, such as an ordered, intact Hox cluster, a generally conserved developmental toolkit and traces of ancestral bilaterian linkage. Unlike some other animals with small genomes, the analysis of the D. gyrociliatus epigenome revealed canonical features of genome regulation, excluding the presence of operons and trans-splicing. Instead, the gene-dense D. gyrociliatus genome presents a divergent Myc pathway, a key physiological regulator of growth, proliferation and genome stability in animals. Altogether, our results uncover a conservative route to genome compaction in annelids, reminiscent of that observed in the vertebrate Takifugu rubripes.


Asunto(s)
Anélidos , Evolución Molecular , Animales , Anélidos/genética , Ligamiento Genético , Genoma , Takifugu/genética
14.
Nature ; 431(7004): 67-71, 2004 Sep 02.
Artículo en Inglés | MEDLINE | ID: mdl-15343333

RESUMEN

Tunicate embryos and larvae have small cell numbers and simple anatomical features in comparison with other chordates, including vertebrates. Although they branch near the base of chordate phylogenetic trees, their degree of divergence from the common chordate ancestor remains difficult to evaluate. Here we show that the tunicate Oikopleura dioica has a complement of nine Hox genes in which all central genes are lacking but a full vertebrate-like set of posterior genes is present. In contrast to all bilaterians studied so far, Hox genes are not clustered in the Oikopleura genome. Their expression occurs mostly in the tail, with some tissue preference, and a strong partition of expression domains in the nerve cord, in the notochord and in the muscle. In each tissue of the tail, the anteroposterior order of Hox gene expression evokes spatial collinearity, with several alterations. We propose a relationship between the Hox cluster breakdown, the separation of Hox expression domains, and a transition to a determinative mode of development.


Asunto(s)
Tipificación del Cuerpo/genética , Evolución Molecular , Regulación del Desarrollo de la Expresión Génica , Genes Homeobox/genética , Familia de Multigenes/genética , Urocordados/embriología , Urocordados/genética , Animales , Fertilización , Orden Génico/genética , Genómica , Hibridación in Situ , Datos de Secuencia Molecular , ARN Mensajero/genética , ARN Mensajero/metabolismo , Urocordados/anatomía & histología
15.
Mol Biol Evol ; 25(7): 1333-43, 2008 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-18424774

RESUMEN

Hox cluster organization represents a valuable marker to study the effects of recent genome duplication in salmonid fish (25-100 Mya). Using polymerase chain reaction amplification of cDNAs, BAC library screening, and genome walking, we reconstructed 13 Hox clusters in the Atlantic salmon containing 118 Hox genes including 8 pseudogenes. Hox paralogs resulting from the genome duplication preceding the radiation of ray-finned fish have been much better preserved in salmon than in other model teleosts. The last genome duplication in the salmon lineage has been followed by the loss of 1 of the 4 HoxA clusters. Four rounds of genome duplication after the vertebrate ancestor salmon Hox clusters display the main organizational features of vertebrate Hox clusters, with Hox genes exclusively that are densely packed in the same orientation. Recently, duplicated Hox clusters have engaged a process of divergence, with several cases of pseudogenization or asymmetrical evolution of Hox gene duplicates, and a marked erosion of identity in noncoding sequences. Strikingly, the level of divergence attained strongly depends on the Hox cluster pairs rather than on the Hox genes within each cluster. It is particularly high between both HoxBb clusters and both HoxDa clusters, whereas both HoxBa clusters remained virtually identical. Positive selection on the Hox protein-coding sequences could not be detected.


Asunto(s)
Evolución Molecular , Genes Homeobox , Familia de Multigenes , Salmo salar/genética , Animales , Secuencia de Bases , Duplicación de Gen , Datos de Secuencia Molecular , Filogenia , Alineación de Secuencia , Homología de Secuencia de Ácido Nucleico
16.
Curr Biol ; 29(19): 3193-3199.e4, 2019 10 07.
Artículo en Inglés | MEDLINE | ID: mdl-31543449

RESUMEN

An overwhelming majority of eukaryotic introns have GT/AG ends, whose identities play a critical role for their recognition and removal by the U2 spliceosome, a well-conserved complex of protein and RNAs. Introns with other splice sites exist at very low frequencies in various genomes, and some of them are processed by the U12 spliceosome. Here, we show that, in the chordate Fritillaria borealis, the majority of old introns have been lost and replaced by introns with highly divergent splice sites. The new introns of F. borealis are exceptionally diverse, though more frequently AG/AC or AG/AT, and features of thousands of them support an origin from transposons. They cannot be processed in human cells, but their splicing is rescued by mutating terminal dinucleotides to GT/AG. With lariat sequencing and splicing inhibitor assays, we show that F. borealis introns are spliced by the U2 spliceosome, which thus evolved to a different selectivity, with neither novel U1 small nuclear RNA (snRNA) types nor major remodeling of its protein and snRNA complements. This genome-wide recolonization by non-canonical introns emphasizes the importance of transposons as a resource of novel introns in a context of massive intron loss. An evolution of the spliceosome may also permit to neutralize harmful transposons through their conversion into introns.


Asunto(s)
Evolución Molecular , Intrones/genética , Empalmosomas/fisiología , Urocordados/genética , Animales
17.
Curr Biol ; 29(7): 1161-1168.e6, 2019 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-30880010

RESUMEN

In eukaryotes, genome size correlates little with the number of coding genes or the level of organismal complexity (C-value paradox). The underlying causes of variations in genome size, whether adaptive or neutral, remain unclear, although several biological traits often covary with it [1-5]. Rapid increases in genome size occur mainly through whole-genome duplications or bursts in the activity of transposable elements (TEs) [6]. The very small and compact genome of Oikopleura dioica, a tunicate of the larvacean class, lacks elements of most ancient families of animal retrotransposons [7, 8]. Here, we sequenced the genomes of six other larvaceans, all of which are larger than that of Oikopleura (up to 12 times) and which increase in size with greater body length. Although no evidence was found for whole-genome duplications within the group of species, the global amount of TEs strongly correlated with genome size. Compared to other metazoans, however, the TE diversity was reduced in all species, as observed previously in O. dioica, suggesting a common ancestor with a compacted genome. Strikingly, non-autonomous elements, particularly short interspersed nuclear elements (SINEs), massively contributed to genome size variation through species-specific independent amplifications, ranging from 3% in the smallest genome up to 49% in the largest. Variations in SINE abundance explain as much as 83% of interspecific genome size variation. These data support an indirect influence of autonomous TEs on genome size via their ability to mobilize non-autonomous elements.


Asunto(s)
Elementos Transponibles de ADN/genética , Tamaño del Genoma , Urocordados/genética , Animales , Elementos de Nucleótido Esparcido Corto/genética , Especificidad de la Especie
18.
Curr Biol ; 15(1): R12-3, 2005 Jan 11.
Artículo en Inglés | MEDLINE | ID: mdl-15649342

RESUMEN

Homeodomain transcription factors are involved in many developmental processes and have been intensely studied in a few model organisms, such as mouse, Drosophila and Caenorhabditis elegans. Homeobox genes fall into 10 classes (ANTP, PRD, POU, LIM, TALE, SIX, Cut, ZFH, HNF1, Prox) and 89 different families/groups, all of which are present in vertebrates. Additional groups may be uncovered by further genome annotation, particularly of complex vertebrate genomes. Eight of these groups have been found only in vertebrates, but not in the genome of the tunicate Ciona intestinalis. The other 81 groups of homeobox gene that have been detected in vertebrates so far probably appeared during the early evolution of bilaterians or earlier, as they are also present outside the chordates. How the homeobox genes evolved during and after the main radiation of the bilaterians remains poorly understood, as only a few animal genomes have been sequenced completely. However, drastic changes have occurred at least in the lineage of C. elegans , such as loss of several Hox genes and Hox cluster fragmentation . Here we report considerable alterations of the homeobox gene complement in the tunicate lineage.


Asunto(s)
Evolución Molecular , Genes Homeobox/genética , Genoma , Filogenia , Factores de Transcripción/genética , Urocordados/genética , Animales , Secuencia de Bases , Análisis por Conglomerados , Etiquetas de Secuencia Expresada , Datos de Secuencia Molecular , Análisis de Secuencia de ADN
19.
Gene ; 417(1-2): 19-26, 2008 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-18486365

RESUMEN

Several transcription regulators play key roles during pituitary morphogenesis. Well known intrinsic signals of the adenohypophysis such as the K(50)paired-like homeodomain proteins regulate commitment, proliferation, differential specification and maintenance of adenohypophyseal cells. We have cloned and successively characterized the mRNA localization of three pitx gene-pairs and three of their splice variants in salmon, pitx1alpha, pitx1beta; pitx2alpha, pitx2beta; pitx3alpha, pitx3beta; pitx1alphash, pitx1betash and pitx2alphaA. The high level of conservation between the pitx paralog-pairs indicates that they likely arose from lineage-specific genome duplication. We also report the isolation of a pitx1 gene in zebrafish. Comparative ISH studies of zebrafish, salmon and mouse pitx genes indicate both conservation and divergence of spatial expression domains in vertebrates. Significant differences were observed between the expressions of pitx orthologs during pituitary development. We suggest that the ancestral pituitary expression at early and late events of morphogenesis is preserved in different species through complementary shuffling of expression between the distinct pitx members of the family. Moreover, ISH analysis of the pitx salmon repertoire shows rapid evolution in this lineage, differences in spatio-temporal expression are observed between gene duplicates.


Asunto(s)
Evolución Biológica , Peces/genética , Hipófisis/embriología , Animales , Peces/embriología , Duplicación de Gen , Expresión Génica , Morfogénesis , Filogenia , Hipófisis/metabolismo , Salmón , Factores de Transcripción/genética , Pez Cebra , Proteínas de Pez Cebra/genética
20.
Gene Expr Patterns ; 8(7-8): 508-14, 2008 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-18620079

RESUMEN

Hox genes encode transcription factors that play important roles in patterning the anterior-posterior (A-P) body axis. In vertebrates, up to 14 Hox genes are physically linked in 4-13 chromosomal clusters. Their expression patterns obey spatial and temporal collinearity. Genes located at the 3' end of the clusters are expressed earlier and more anteriorly than those at the 5' end. To investigate how the expression of Hox genes has evolved after very recent ( approximately 25-100 Mya) and relatively recent ( approximately 320-350 Mya) genome duplications, we focused on three paralogous groups of salmon anterior Hox genes, in which gene duplicates have been retained. RNA-RNA whole mount in situ hybridization with gene-specific probes at early development stages showed essentially conserved expression patterns for most genes when compared to mouse and zebrafish orthologs. However, changes in spatial expression were observed for the ancient fish gene duplicate HoxB3b, while recently duplicated genes showed divergence in their expression levels.


Asunto(s)
Genes Homeobox , Salmo salar/genética , Animales , Duplicación de Gen , Expresión Génica , Filogenia , Factores de Tiempo
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