Genomic organization of eukaryotic tRNAs

BACKGROUND: Surprisingly little is known about the organization and distribution of tRNA genes and tRNA-related sequences on a genome-wide scale. While tRNA gene complements are usually reported in passing as part of genome annotation efforts, and peculiar features such as the tandem arrangements of tRNA gene in Entamoeba histolytica have been described in some detail, systematic comparative studies are rare and mostly restricted to bacteria. We therefore set out to survey the genomic arrangement of tRNA genes and pseudogenes in a wide range of eukaryotes to identify common patterns and taxon-specific peculiarities. RESULTS: In line with previous reports, we find that tRNA complements evolve rapidly and tRNA gene and pseudogene locations are subject to rapid turnover. At phylum level, the distributions of the number of tRNA genes and pseudogenes numbers are very broad, with standard deviations on the order of the mean. Even among closely related species we observe dramatic changes in local organization. For instance, 65% and 87% of the tRNA genes and pseudogenes are located in genomic clusters in zebrafish and stickleback, resp., while such arrangements are relatively rare in the other three sequenced teleost fish genomes. Among basal metazoa, Trichoplax adherens has hardly any duplicated tRNA gene, while the sea anemone Nematostella vectensis boasts more than 17000 tRNA genes and pseudogenes. Dramatic variations are observed even within the eutherian mammals. Higher primates, for instance, have 616 +/- 120 tRNA genes and pseudogenes of which 17% to 36% are arranged in clusters, while the genome of the bushbaby Otolemur garnetti has 45225 tRNA genes and pseudogenes of which only 5.6% appear in clusters. In contrast, the distribution is surprisingly uniform across plant genomes. Consistent with this variability, syntenic conservation of tRNA genes and pseudogenes is also poor in general, with turn-over rates comparable to those of unconstrained sequence elements. Despite this large variation in abundance in Eukarya we observe a significant correlation between the number of tRNA genes, tRNA pseudogenes, and genome size. CONCLUSIONS: The genomic organization of tRNA genes and pseudogenes shows complex lineage-specific patterns characterized by an extensive variability that is in striking contrast to the extreme levels of sequence-conservation of the tRNAs themselves. The comprehensive analysis of the genomic organization of tRNA genes and pseudogenes in Eukarya provides a basis for further studies into the interplay of tRNA gene arrangements and genome organization in general

Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum

<p>Abstract</p> <p>Background</p> <p>Schistosomes are trematode parasites of the phylum Platyhelminthes. They are considered the most important of the human helminth parasites in terms of morbidity and mortality. Draft genome sequences are now available for <it>Schistosoma mansoni </it>and <it>Schistosoma japonicum</it>. Non-coding RNA (ncRNA) plays a crucial role in gene expression regulation, cellular function and defense, homeostasis, and pathogenesis. The genome-wide annotation of ncRNAs is a non-trivial task unless well-annotated genomes of closely related species are already available.</p> <p>Results</p> <p>A homology search for structured ncRNA in the genome of <it>S. mansoni </it>resulted in 23 types of ncRNAs with conserved primary and secondary structure. Among these, we identified rRNA, snRNA, SL RNA, SRP, tRNAs and RNase P, and also possibly MRP and 7SK RNAs. In addition, we confirmed five miRNAs that have recently been reported in <it>S. japonicum </it>and found two additional homologs of known miRNAs. The tRNA complement of <it>S. mansoni </it>is comparable to that of the free-living planarian <it>Schmidtea mediterranea</it>, although for some amino acids differences of more than a factor of two are observed: Leu, Ser, and His are overrepresented, while Cys, Meth, and Ile are underrepresented in <it>S. mansoni</it>. On the other hand, the number of tRNAs in the genome of <it>S. japonicum </it>is reduced by more than a factor of four. Both schistosomes have a complete set of minor spliceosomal snRNAs. Several ncRNAs that are expected to exist in the <it>S. mansoni </it>genome were not found, among them the telomerase RNA, vault RNAs, and Y RNAs.</p> <p>Conclusion</p> <p>The ncRNA sequences and structures presented here represent the most complete dataset of ncRNA from any lophotrochozoan reported so far. This data set provides an important reference for further analysis of the genomes of schistosomes and indeed eukaryotic genomes at large.</p

Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean

Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to&nbsp;serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency

Introducing evolutionary biologists to the analysis of big data: guidelines to organize extended bioinformatics training courses

Research in evolutionary biology has been progressively influenced by big data such as massive genome and transcriptome sequencing data, scalar measurements of several phenotypes on tens to thousands of individuals, as well as from collecting worldwide environmental data at an increasingly detailed scale. The handling and analysis of such data require computational skills that usually exceed the abilities of most traditionally trained evolutionary biologists. Here we discuss the advantages, challenges and considerations for organizing and running bioinformatics training courses of 2–3 weeks in length to introduce evolutionary biologists to the computational analysis of big data. Extended courses have the advantage of offering trainees the opportunity to learn a more comprehensive set of complementary topics and skills and allowing for more time to practice newly acquired competences. Many organizational aspects are common to any course, as the need to define precise learning objectives and the selection of appropriate and highly motivated instructors and trainees, among others. However, other features assume particular importance in extended bioinformatics training courses. To successfully implement a learning-by-doing philosophy, sufficient and enthusiastic teaching assistants (TAs) are necessary to offer prompt help to trainees. Further, a good balance between theoretical background and practice time needs to be provided and assured that the schedule includes enough flexibility for extra review sessions or further discussions if desired. A final project enables trainees to apply their newly learned skills to real data or case studies of their interest. To promote a friendly atmosphere throughout the course and to build a close-knit community after the course, allow time for some scientific discussions and social activities. In addition, to not exhaust trainees and TAs, some leisure time needs to be organized. Finally, all organization should be done while keeping the budget within fair limits. In order to create a sustainable course that constantly improves and adapts to the trainees’ needs, gathering short- and long-term feedback after the end of the course is important. Based on our experience we have collected a set of recommendations to effectively organize and run extended bioinformatics training courses for evolutionary biologists, which we here want to share with the community. They offer a complementary way for the practical teaching of modern evolutionary biology and reaching out to the biological community.Peer reviewe

Canagliflozin and renal outcomes in type 2 diabetes and nephropathy

BACKGROUND Type 2 diabetes mellitus is the leading cause of kidney failure worldwide, but few effective long-term treatments are available. In cardiovascular trials of inhibitors of sodium–glucose cotransporter 2 (SGLT2), exploratory results have suggested that such drugs may improve renal outcomes in patients with type 2 diabetes. METHODS In this double-blind, randomized trial, we assigned patients with type 2 diabetes and albuminuric chronic kidney disease to receive canagliflozin, an oral SGLT2 inhibitor, at a dose of 100 mg daily or placebo. All the patients had an estimated glomerular filtration rate (GFR) of 30 to &lt;90 ml per minute per 1.73 m2 of body-surface area and albuminuria (ratio of albumin [mg] to creatinine [g], &gt;300 to 5000) and were treated with renin–angiotensin system blockade. The primary outcome was a composite of end-stage kidney disease (dialysis, transplantation, or a sustained estimated GFR of &lt;15 ml per minute per 1.73 m2), a doubling of the serum creatinine level, or death from renal or cardiovascular causes. Prespecified secondary outcomes were tested hierarchically. RESULTS The trial was stopped early after a planned interim analysis on the recommendation of the data and safety monitoring committee. At that time, 4401 patients had undergone randomization, with a median follow-up of 2.62 years. The relative risk of the primary outcome was 30% lower in the canagliflozin group than in the placebo group, with event rates of 43.2 and 61.2 per 1000 patient-years, respectively (hazard ratio, 0.70; 95% confidence interval [CI], 0.59 to 0.82; P=0.00001). The relative risk of the renal-specific composite of end-stage kidney disease, a doubling of the creatinine level, or death from renal causes was lower by 34% (hazard ratio, 0.66; 95% CI, 0.53 to 0.81; P&lt;0.001), and the relative risk of end-stage kidney disease was lower by 32% (hazard ratio, 0.68; 95% CI, 0.54 to 0.86; P=0.002). The canagliflozin group also had a lower risk of cardiovascular death, myocardial infarction, or stroke (hazard ratio, 0.80; 95% CI, 0.67 to 0.95; P=0.01) and hospitalization for heart failure (hazard ratio, 0.61; 95% CI, 0.47 to 0.80; P&lt;0.001). There were no significant differences in rates of amputation or fracture. CONCLUSIONS In patients with type 2 diabetes and kidney disease, the risk of kidney failure and cardiovascular events was lower in the canagliflozin group than in the placebo group at a median follow-up of 2.62 years

tRNomics: Genomic Organization and Processing Patterns of tRNAs

Surprisingly little is known about the organization and distribution of tRNAs and tRNA-related sequences on a genome-wide scale. While tRNA complements are usually reported in passing as part of genome annotation efforts, and peculiar features such as the tandem arrangements of tRNAs in Entamoeba histolytica have been described in some detail, comparative studies are rare. We therefore set out to systematically survey the genomic arrangement of tRNAs in a wide range of eukaryotes to identify common patterns and taxon-specific peculiarities. We found that tRNA complements evolve rapidly and that tRNA locations are subject to rapid turnover. At the phylum level, distributions of tRNA numbers are very broad, with standard deviations on the order of the mean. Even within fairly closely related species, we observe dramatic changes in local organization. Consistent with this variability, syntenic conservation of tRNAs is also poor in general, with turn-over rates comparable to those of unconstrained sequence elements. We conclude that the genomic organization of tRNAs shows complex, lineage-specific patterns characterized by extensive variability, and that this variability is in striking contrast to the extreme levels of sequence-conservation of the tRNA genes themselves. Our comprehensive analysis of eukaroyotic tRNA distributions provides a basis for further studies into the interplay between tRNA gene arrangements and genome organization in general. Secondly, we focused on the investigation of small non-coding RNAs (ncRNAs) from whole transcriptome data. Since ncRNAs constitute a significant part of the transcriptome, we explore this data to detect and classify patterns derived from transcriptome-associated loci. We selected three distinct ncRNA classes: microRNAs, snoRNAs and tRNAs, all of which undergo maturation processes that lead to the production of shorter RNAs. After mapping the sequences to the reference genome, specific patterns of short reads were observed. These read patterns appeared to reflect RNA processing and, if so, should specify the RNA transcripts from which they are derived. In order to investigate whether the short read patterns carry information on the particular ncRNA class from which they orginate, we performed a random forest classification on the three distinct ncRNA classes listed above. Then, after exploring the potential classification of general groups of ncRNAs, we focused on the identification of small RNA fragments derived from tRNAs. After mapping transcriptome sequence data to reference genomes, we searched for specific short read patterns reflecting tRNA processing. In this context, we devised a common tRNA coordinate system based on conservation and secondary structure information that allows vector representation of processing products and thus comparison of different tRNAs by anticodon and amino acid. We report patterns of tRNA processing that seem to be conserved across species. Though the mechanisms and functional implications underlying these patterns remain to be clarified, our analysis suggests that each type of tRNA exhibits a specific pattern and thus appears to undergo a characteristic maturation process

BUSCANDO AGUJAS EN UN PAJAR: VIAJES DE RNAS PEQUEÑOS IN SILICO E IN VITRO.

Los esfuerzos para estudiar el transcriptoma, implican el análisis cuantitativo y cualitativo del conjunto de moléculas funcionales de RNAs producto de la transcripción genómica. Los estudios dirigidos sobre la fracción asociada a los RNAs que finalmente son traducidos en proteínas, han sido ampliamente reportados en la literatura. Sin embargo, el análisis de la fracción de RNAs que no codifican para proteínas, sino que cumplen otras funciones celulares, representan para la genética, uno de los campos en continua transformación tecnológica, experimental y computacional. De este grupo, los estudios de RNAs pequeños que hacen parte de los caminos de regulación de la expresión génica, conforman un ejemplo que impacta nuestra comprensión sobre la regulación de la expresión de genes en un sentido, y representan un ejemplo del trabajo interdisciplinario entre experimentalistas y teóricos. En esta revisión, se presenta un ejemplo sobre el desarrollo de métodos de secuenciamiento de última generación, ligado al desarrollo de nuevas herramientas computacionales para el estudio de RNAs pequeños. Palabras clave: transcriptoma, RNA pequeños, secuenciamiento de última generación. ABSTRACT Efforts to study the transcriptome have led quantitative and qualitative analyses of all the functional RNA molecules products of transcription. Most of the studies have been focused on the fraction of coding RNAs and have been broadly published. However, the comprehension of the fraction associated to non-coding RNAs , that are not translated into proteins, but instead, shows a critical role for RNAs in cellular function, it is nowadays one field of Genetics, that has in turn led to the transformation of technologies in both both experimental and computational research. The characterization of small RNAs associated to the RNA interference pathway (whereby RNA can regulate gene expression) corresponds to one example in which frontiers of knowledge have been expanded not only to increase our comprehension of expression regulation, but also to allow interdisciplinary work among experimentalists and theoreticians. As follow it is presented an example based on small RNA biology to link next generation sequencing technologies and computational research. Key Words: transcriptome, small RNAs, next-generation sequencing technology

APLICACIONES DE LA BIOINFORMÁTICA EN LA MEDICINA: EL GENOMA HUMANO. ¿CÓMO PODEMOS VER TANTO DETALLE?

<p lang="es-ES" align="JUSTIFY">La bioinformática es un campo novedoso que soporta parte de la investigación biológica dirigida a la identificación de variantes génicas que pueden ser descubiertas desde los estudios de genomas completos. Basados en esta motivación se presenta el panorama general de los aportes principales de la bioinformática en el desarrollo del secuenciamiento del primer genoma humano. Adicionalmente se resumen los principales avances en cómputo desarrollados para responder a las demandas requeridas por los métodos de secuenciamiento de última generación para lograr re-secuenciar un genoma humano. Finalmente se introducen algunos de los nuevos retos que deben asumirse para aplicar la genómica personalizada en el desarrollo de la medicina. </p><p lang="es-ES" align="JUSTIFY"> </p><p lang="es-ES" align="JUSTIFY">Abstract</p><p lang="es-ES" align="JUSTIFY">Bioinformatics is a new field that supports part of the biological research aimed at identifying gene variants that can be discovered from studies of whole genomes. Based on this motivation the overview of the main contributions of bioinformatics in the development of sequencing the first human genome is presented. Additionally it is summarized the main advances in computing developed to meet the demands to re-sequence a human genome by using the next generation sequencing technologies. Finally some new challenges that must be faced to apply the personalized genomics into the medicine development are introduced.</p

tRNomics: Genomic Organization and Processing Patterns of tRNAs

Surprisingly little is known about the organization and distribution of tRNAs and tRNA-related sequences on a genome-wide scale. While tRNA complements are usually reported in passing as part of genome annotation efforts, and peculiar features such as the tandem arrangements of tRNAs in Entamoeba histolytica have been described in some detail, comparative studies are rare. We therefore set out to systematically survey the genomic arrangement of tRNAs in a wide range of eukaryotes to identify common patterns and taxon-specific peculiarities. We found that tRNA complements evolve rapidly and that tRNA locations are subject to rapid turnover. At the phylum level, distributions of tRNA numbers are very broad, with standard deviations on the order of the mean. Even within fairly closely related species, we observe dramatic changes in local organization. Consistent with this variability, syntenic conservation of tRNAs is also poor in general, with turn-over rates comparable to those of unconstrained sequence elements. We conclude that the genomic organization of tRNAs shows complex, lineage-specific patterns characterized by extensive variability, and that this variability is in striking contrast to the extreme levels of sequence-conservation of the tRNA genes themselves. Our comprehensive analysis of eukaroyotic tRNA distributions provides a basis for further studies into the interplay between tRNA gene arrangements and genome organization in general. Secondly, we focused on the investigation of small non-coding RNAs (ncRNAs) from whole transcriptome data. Since ncRNAs constitute a significant part of the transcriptome, we explore this data to detect and classify patterns derived from transcriptome-associated loci. We selected three distinct ncRNA classes: microRNAs, snoRNAs and tRNAs, all of which undergo maturation processes that lead to the production of shorter RNAs. After mapping the sequences to the reference genome, specific patterns of short reads were observed. These read patterns appeared to reflect RNA processing and, if so, should specify the RNA transcripts from which they are derived. In order to investigate whether the short read patterns carry information on the particular ncRNA class from which they orginate, we performed a random forest classification on the three distinct ncRNA classes listed above. Then, after exploring the potential classification of general groups of ncRNAs, we focused on the identification of small RNA fragments derived from tRNAs. After mapping transcriptome sequence data to reference genomes, we searched for specific short read patterns reflecting tRNA processing. In this context, we devised a common tRNA coordinate system based on conservation and secondary structure information that allows vector representation of processing products and thus comparison of different tRNAs by anticodon and amino acid. We report patterns of tRNA processing that seem to be conserved across species. Though the mechanisms and functional implications underlying these patterns remain to be clarified, our analysis suggests that each type of tRNA exhibits a specific pattern and thus appears to undergo a characteristic maturation process