Study of tergal glands morphogenesis through an integrative analysis of genomic data

Curs 2013-2014About 50% of living species are holometabolan insects. Therefore, unraveling the ori- gin of insect metamorphosis from the hemimetabolan (gradual metamorphosis) to the holometabolan (sudden metamorphosis at the end of the life cycle) mode is equivalent to explaining how all this biodiversity originated. One of the problems with studying the evolution from hemimetaboly to holometaboly is that most information is available only in holometabolan species. Within the hemimetabolan group, our model, the cock- roach Blattella germanica, is the most studied species. However, given that the study of adult morphogenesis at organismic level is still complex, we focused on the study of the tergal gland (TG) as a minimal model of metamorphosis. The TG is formed in tergites 7 and 8 (T7-8) in the last days of the last nymphal instar (nymph 6). The comparative study of four T7-T8 transcriptomes provided us with crucial keys of TG formation, but also essential information about the mechanisms and circuitry that allows the shift from nymphal to adult morphogenesis.Director/a: Xavier Bellé

Distinct gene expression dynamics in germ line and somatic tissue during ovariole morphogenesis in Drosophila melanogaster

The survival and evolution of a species is a function of the number of offspring it can produce. In insects, the number of eggs that an ovary can produce is a major determinant of reproductive capacity. Insect ovaries are made up of tubular egg-producing subunits called ovarioles, whose number largely determines the number of eggs that can be potentially laid. Ovariole number in Drosophila is directly determined by the number of cellular structures called terminal filaments, which are stacks of cells that assemble in the larval ovary. Elucidating the developmental and regulatory mechanisms of terminal filament formation is thus key to understanding the regulation of insect reproduction through ovariole number regulation. We systematically measured mRNA expression of all cells in the larval ovary at the beginning, middle, and end of terminal filament formation. We also separated somatic and germ line cells during these stages and assessed their tissue-specific gene expression during larval ovary development. We found that the number of differentially expressed somatic genes is highest during the late stages of terminal filament formation and includes many signaling pathways that govern ovary development. We also show that germ line tissue, in contrast, shows greater differential expression during early stages of terminal filament formation, and highly expressed germ line genes at these stages largely control cell division and DNA repair. We provide a tissue-specific and temporal transcriptomic dataset of gene expression in the developing larval ovary as a resource to study insect reproduction

Role-shifting threads: Increasing OpenMP malleability to address load imbalance at MPI and OpenMP

This paper presents the evolution of the free agent threads for OpenMP to the new role-shifting threads model and their integration with the Dynamic Load Balancing (DLB) library. We demonstrate how free agent threads can improve resource utilization in OpenMP applications with load imbalance in their nested parallel regions. We also demonstrate how DLB efficiently manages the malleability exposed by the role-shifting threads to address load imbalance issues. We use three real-world scientific applications, one of them to demonstrate that free agents alone can improve the OpenMP model without external tools, and two other MPI+OpenMP applications, one of them with a coupling case, to illustrate the potential of the free agent threads’ malleability with an external resource manager to increase the efficiency of the system. In addition, we demonstrate that the new implementation is more usable than the former one, letting the runtime system automatically make decisions that were made by the programmer previously. All software is released open-source.This work has received funding from the DEEP Projects, at the European Commission’s FP7, H2020, and EuroHPC Programmes, under Grant Agreements 287530, 610476, 754304, and 955606. The PCI2021-121958 financed by the Spanish State Research Agency - Ministry of Science and Innovation. And it also has the support of the Spanish Ministry of Science and Innovation (Computacion de Altas Prestaciones VIII: PID2019-107255GB).Peer ReviewedPostprint (author's final draft

Cluster of emerging technology: evaluation of a production HPC system based on A64FX

Clusters of emerging technologies are appearing with more and more frequency in HPC. After years of skepticism, data-centers are adopting them as production systems thanks to several geopolitical and technological factors. The most honorable example is the Fugaku supercomputer, powered by the latest Fujitsu A64FX CPU. Which is the behavior of mature HPC codes on such emerging technology clusters? Which performance will obtain scientists when running their HPC applications “as is” on these clusters? This paper presents the evaluation of CTE-Arm, a Fugaku-like system, including both fine-tuned micro-benchmarks and five scientific applications run without prior fine-tuning: Alya, NEMO, Gromacs, OpenIFS, and WRF. Results show that while micro-architectural benchmarks show performance as expected, the performance obtained running HPC applications not tuned for a specific architecture are between 2× and 4× slower compared with a standard Intel-based HPC system. Therefore further effort is needed to improve tools (e.g., compilers) and system software (e.g., MPI libraries) to ease applications deployment and improve their performance.This work is partially supported by the Spanish Government (SEV-2015-0493), by the Spanish Ministry of Science and Technology (TIN2015-65316-P), by the Generalitat de Catalunya (2017-SGR-1414), by the European and Horizon 2020 POP CoE (GA n. 824080).Peer ReviewedPostprint (author's final draft

Hemimetabolous genomes reveal molecular basis of termite eusociality

Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity

Comparative transcriptomics of hemimetabolan and holometabolan metamorphosis

The evolutionary success of insects was particularly shaped by the innovation of the metamorphosis, especially by the transition from hemimetaboly to holometaboly. The mechanisms underlying this evolutionary transition represent an unsolved question, although different approaches have been used to study them. In the present thesis we followed a transcriptomic approach, comparing data on mRNA and miRNA expression in key developmental moments, comprising embryonic and postembryonic stages, in species representing the hemimetabolan and holometabolan modes. Most of the work has been carried out in the hemimetabolan species Blattella germanica, but we have used also other reference species for comparison, especially the holometabolan Drosophila melanogaster and Tribolium castaneum. The results show that there are not qualitative gene differences between holometabolan and hemimetabolan species, but differences in patterns of expression and potential networking of orthologous genes. Transcription factors, epigenetic modifiers, and miRNAs appear as important players in both developmental modes.L'èxit evolutiu dels insectes ha estat mercat per la innovació de la metamorfosi i, en especial, per la transició de la metamorfosi hemimetàbola a holometàbola. Els mecanismes subjacents en aquesta transició evolutiva representen una qüestió no resolta. Per tal d'estudiar aquesta transició, en aquesta tesi hem utilitzat un enfocament transcriptomic comparant dades de mRNA i miRNA en estadis clau del desenvolupament, incloent-hi estadis embrionaris i post embrionaris en espècies representatives de metamorfosis hemimetàbola i holometàbola. La major part dels anàlisis s'han centrat en l'hemimetàbola Blattella germanica, tot i que s'han utilitzat dades d'altres espècies com a contrast, especialment dels holometàbols Drosophila melanogaster i Tribolium castaneum. Els resultats mostren que no hi ha diferències qualitatives en relació a gens dels hemimetàbols i holometàbols, en canvi les principals diferències consisteixen en els diferents perfils d'expressió de gens comuns i la seva xarxa de d'interacció. Els factors de transcripció, els modificadors epigenètics i els miRNAs emergeixen com a principals protagonistes dels mecanismes reguladors en ambdós models de desenvolupament

Towards understanding the molecular basis of cockroach tergal gland morphogenesis. A transcriptomic approach

The tergal gland is a structure exclusive of adult male cockroaches that produces substances attractive to the female and facilitates mating. It is formed de novo in tergites 7 and 8 during the transition from the last nymphal instar to the adult. Thus, the tergal gland can afford a suitable case study to investigate the molecular basis of a morphogenetic process occurring during metamorphosis. Using Blattella germanica as model, we constructed transcriptomes from male tergites 7–8 in non-metamorphosing specimens, and from the same tergites in metamorphosing specimens. We performed a de novo assembly all available transcriptomes to construct a reference transcriptome and we identified transcripts by homology. Finally we mapped all reads into the reference transcriptome in order to perform analysis of differentially expressed genes and a GO-enrichment test. A total of 5622 contigs appeared to be overrepresented in the transcriptome of metamorphosing specimens with respect to those specimens that did not metamorphose. Among these genes, there were six GO-terms with a p-value lower than 0.05 and among them GO: 0003676 (“nucleic acid binding”) was especially interesting since it included transcription factors (TFs). Examination of TF-Pfam-motifs revealed that the transcriptome of metamorphosing specimens contains the highest diversity of these motifs, with 29 different types (seven of them exclusively expressed in this stage) compared with that of non-metamorphosing specimens, which contained 24 motif types. Transcriptome comparisons suggest that TFs are important drivers of the process of tergal gland formation during metamorphosis.Support for this research was provided by the Spanish MICINN (grant CGL2008-03517/BOS to XB) and MINECO (grant CGL2012-36251 to XB) and by the Catalan Government (2014 SGR 619 to XB). The research has also benefited from FEDER funds.Peer reviewe

Development of cockroach tergal glands as a minimal model of insect metamorphosis

Trabajo presentado en la 4th Meeting of the Spanish Society of the Evolutionary Biology (SESBE 2013) celebrada en Barcelona del 27 al 29 de noviembre de 2013.N

The tergal glands of male cockroaches as a minimal model of insect metamorphosis

Trabajo presentado en el Seventh International Symposium on Molecular Insect Science, celebrado en Amsterdam del 13 al 16 de julio de 2014.N

Comparative Transcriptomics in Two Extreme Neopterans Reveals General Trends in the Evolution of Modern Insects

The success of neopteran insects, with 1 million species described, is associated with developmental innovations such as holometaboly and the evolution from short to long germband embryogenesis. To unveil the mechanisms underlining these innovations, we compared gene expression during the ontogeny of two extreme neopterans, the cockroach Blattella germanica (polyneopteran, hemimetabolan, and short germband species) and the fly Drosophila melanogaster (endopterygote, holometabolan, and long germband species). Results revealed that genes associated with metamorphosis are predominantly expressed in late nymphal stages in B. germanica and in the early-mid embryo in D. melanogaster. In B. germanica the maternal to zygotic transition (MZT) concentrates early in embryogenesis, when juvenile hormone factors are significantly expressed. In D. melanogaster, the MZT extends throughout embryogenesis, during which time juvenile hormone factors appear to be unimportant. These differences possibly reflect broad trends in the evolution of development within neopterans, related to the germband type and the metamorphosis mode.This work was supported by the Spanish Ministry of Economy and Competitiveness (grants CGL2012-36251 and CGL2015-64727-P to X.B., including FEDER funds), Spanish Ministry of Science and Innovation (grants BFU2011–22404 and CGL2016–76011-R to M.-D.P., including FEDER funds), and Catalan Government (grants 2014 SGR 619 and 2017 SGR 1030).Peer reviewe