Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome

Multiple alignment of Ty1-copia RT paralog sequences identified in teff cv Enantite and Tsedey. (MSF 51 kb

RetrOryza: a database of the rice LTR-retrotransposons

Long terminal repeat (LTR)-retrotransposons comprise a significant portion of the rice genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. In addition, because LTR-retrotransposons can influence the expression of neighboring genes, the complete identification of these elements in the rice genome is essential in order to study their putative functional interactions with the plant genes. The aims of the database are to (i) Assemble a comprehensive dataset of LTR-retrotransposons that includes not only abundant elements, but also low copy number elements. (ii) Provide an interface to efficiently access the resources stored in the database. This interface should also allow the community to annotate these elements. (iii) Provide a means for identifying LTR-retrotransposons inserted near genes. Here we present the results, where 242 complete LTR-retrotransposons have been structurally and functionally annotated. A web interface to the database has been made available (), through which the user can annotate a sequence or search for LTR-retrotransposons in the neighborhood of a gene of interest

Genome-wide identification and characterisation of exapted transposable elements in the large genome of sunflower (Helianthus annuus L.)

Transposable elements (TEs) are an important source of genome variability, playing many roles in the evolution of eukaryotic species. Besides well-known phenomena, TEs may undergo the exaptation process and generate the so-called exapted transposable element genes (ETEs). Here we present a genome-wide survey of ETEs in the large genome of sunflower (Helianthus annuus L.), in which the massive amount of TEs, provides a significant source for exaptation. A library of sunflower TEs was used to build TE-specific Hidden Markov Model profiles, to search for all available sunflower gene products. In doing so, 20,016 putative ETEs were identified and further investigated for the characteristics that distinguish TEs from genes, leading to the validation of 3,530 ETEs. The analysis of ETEs transcription patterns under different stress conditions showed a differential regulation triggered by treatments mimicking biotic and abiotic stress; furthermore, the distribution of functional domains of differentially regulated ETEs revealed a relevant presence of domains involved in many aspects of cellular functions. A comparative genomic investigation was performed including species representative of Asterids and appropriate outgroups: the bulk of ETEs resulted specific to the sunflower, while few ETEs presented orthologues in the genome of all analysed species, making the hypothesis of a conserved function. This study highlights the crucial role played by exaptation, actively contributing to species evolution

Transposable element distribution, abundance and role in genome size variation in the genus Oryza

<p>Abstract</p> <p>Background</p> <p>The genus <it>Oryza </it>is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop – rice (<it>Oryza sativa </it>[AA]). Genome size variation in the <it>Oryza </it>is more than 3-fold and ranges from 357 Mbp in <it>Oryza glaberrima </it>[AA] to 1283 Mbp in the polyploid <it>Oryza ridleyi </it>[HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative <it>Oryza </it>species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation.</p> <p>Results</p> <p>We identified the elements primarily responsible for the most strikingly genome size variation in <it>Oryza</it>. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the <it>Oryza </it>and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species <it>Oryza coarctata </it>[HHKK] whose placement in the <it>Oryza </it>genus is controversial.</p> <p>Conclusion</p> <p>Long Terminal Repeat retrotransposons are the major component of the <it>Oryza </it>genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the <it>Oryza </it>genus. Two families of Ty3-<it>gypsy </it>elements (<it>RIRE2 </it>and <it>Atlantys</it>) account for a significant portion of the genome size variations present in the <it>Oryza </it>genus.</p

Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera

Background: Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5'UTR, ORF and 3'UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera). Results: Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera. Conclusions: Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species

The Amborella genome: an evolutionary reference for plant biology

The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics

Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey

BACKGROUND: Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. AIMS: In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) library for the nurse shark, Ginglymostoma cirratum. RESULTS: The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 × 10(10 )bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6–28 primary positive clones per probe of which 50–90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. CONCLUSION: We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome

Neuroblastoma en niños menores de 18 meses. Experiencia de 10 años en el Centro Hematooncológico Pediátrico del Centro Hospitalario Pereira Rossell

ResumenIntroducciónEl neuroblastoma es el tumor maligno más frecuente en los lactantes. Su curso clínico es variable, desde la regresión espontánea a la progresión maligna, y los factores pronósticos son múltiples, como la edad, el estadio, la amplificación de N-myc y la ploidía tumoral. Se describen las características de todos los pacientes con neuroblastoma menores de 18 meses asistidos en CHOP.Pacientes y métodosEstudio observacional, descriptivo y retrospectivo en el período entre el 31 de enero de 2000 y el 31 de enero de 2011. El diagnóstico se realizó por histología y aspirado de médula ósea. Los pacientes se estadificaron por INSS; el tratamiento se decidió según el estadio y el riesgo.ResultadosSe incluyeron 22 pacientes menores de 18 meses (52% de todos los neuroblastomas), con una media de edad de 9,6 meses. Once pacientes se encontraban en estadio 4. La localización más frecuente fue suprarrenal; presentaban metástasis 13 pacientes. Quince niños recibieron poliquimioterapia y 20 fueron tratados quirúrgicamente. La amplificación del gen N-myc se demostró en 3 pacientes. La sobrevida global fue del 77% y la sobrevida libre de enfermedad fue del 77%.Discusión y conclusionesLa mayor parte de los casos fueron diagnosticados en niños menores de 9 meses. Fueron más frecuentes los estadios 4 y 1. No se pudo demostrar asociación entre N-myc y el estadio de enfermedad. La sobrevida fue excelente.AbstractIntroductionNeuroblastoma is the most common malignant tumor in infants. Its clinical behavior is variable, from spontaneous regression to malignant progression; prognostic factors are multiple, such as age, stage, N-myc amplification and tumor ploidy. We describe the characteristic of all patients with neuroblastoma less than 18 months of age assisted in CHOP.Patients and methodsRetrospective, observational and descriptive study in the period between 31/1/00 y 31/01/11. Diagnose was made from histology and bone marrow aspirate. Patients were classified by INSS stage; treatment was decided according to stage and risk.ResultsTwenty two patients were included (52% of allneuroblastomas), with a mean age of 9,6 months.Eleven patients were classified in stage 4. The most frequent localization was adrenal; 14 patientspresented methastasis. Fifteen patients received chemotherapy and 20 were surgically intervened. N-myc amplification was detected in 3 patients. Overall survival was 77% and event-free survival was 77%.Discussion and conclusionsThe majority of cases were diagnosed in children younger than 9 months.Stages 4 and 1 were the most frequent. No association between N-myc and stage could be determined.Overall and event-free survival were excellent