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https://hdl.handle.net/123456789/630| Τύπος: | Αναρτημένη ανακοίνωση (poster) |
| Τίτλος: | Development of a bioinformatic approach to discern between high-throughput genetic data of metazoan and prokaryotic origin for complex holobionts |
| Συγγραφέας: | [EL] Νταϊλιάνης, Αθανάσιος[EN] Dailianis, Thanos [EL] Μανουσάκη, Τερέζα[EN] Manousaki, Tereza [EN] Koutsouveli, Vasiliki [EN] Lagnel, Jacques [EN] Kollias, Spyridon [EL] Τσιγκενόπουλος, Κωνσταντίνος[EN] Tsigenopoulos, Constantinos [EL] Αρβανιτίδης, Χρήστος[EN] Arvanitidis, Christos [EL] Μαγουλάς, Αντώνιος[EN] Magoulas, Antonios [EL] Ντούνας, Κωνσταντίνος[EN] Dounas, Costas |
| Ημερομηνία: | 2019 |
| Περίληψη: | Sponges are organisms with simple body plan, without true tissue differentiation. Moreover, they are notorious for hosting rich, regulated symbiotic bacterial communities, thus creating the sponge holobiont. These traits, combined with the expansive and diverse nature of the poriferan phylum and the fact that only two sponge species have been sequenced, imposes challenges to genomic approaches. For example, although transcriptome assembly facilitated through NGS can provide sound answers to ecological questions, a de novo assembly approach is required for non-model organisms, due to absence of a reference genome. This becomes more challenging in sponges as it is often difficult to discriminate between signals of metazoan and prokaryotic origin, thus introducing biases to interpretation. T o overcome this impediment, we developed and present a novel bioinformatics pipeline that efficiently separates between bacterial expressed genes from those of eukaryotic origin, overcoming this challenge. This method was used towards the transcriptome acquisition for the common Mediterranean bath sponge Spongia officinalis. The pipeline involves standard read pre-processing steps and incorporates extra analyses to identify and filter prokaryotic reads out of the analysis. Following multiple quality control filters, the surviving reads were scanned for non-sponge sequences. First, the reads were mapped against the bacterial sequences available in the NCBI RefSeq database with the tool ribopicker. The unmapped reads were consequently used for the transcriptome reconstruction. The resulting draft transcriptome assembly was annotated with standard pipelines and the annotation was used to notify further on the presence of prokaryote data. As a final filtering step, the top blast hits of each contig were scanned and the taxon identity of the corresponding organisms were retrieved. Contigs with top hits taxon identities that matched bacterial sequences were eliminated to end up with a high-quality, prokaryote-free assembly. The proposed pipeline can be followed to overcome the technical RNASeq problems characteristic for symbiont-rich metazoan organisms with low or non-existent tissue differentiation, such as sponges and cnidarians. At the same time, however, it can be valuable towards the development of targeted experimental approaches that specifically examine the symbiotic communities of these organisms. This is highly important, since as is often the case, several important functions and properties of these complex holobionts cannot be confidently attributed to the host metazoan or the symbiont community. |
| Γλώσσα: | Αγγλικά |
| Τόπος δημοσίευσης: | Patras, Greece |
| Σελίδες: | 1 |
| Θεματική κατηγορία: | [EL] Θαλάσσια βιολογία και Βιολογία γλυκών υδάτων[EN] Marine and Freshwater Biology |
| Λέξεις-κλειδιά: | Porifera; marine invertebrate; prokaryotic symbionts; RNAseq; heat stress; bioinformatics |
| Κάτοχος πνευματικών δικαιωμάτων: | © by the author(s) |
| Όνομα εκδήλωσης: | 8th Conference of the Hellenic Society of Mikrobiokosmos |
| Τοποθεσία εκδήλωσης: | University of Patras, Greece |
| Ημ/νία έναρξης εκδήλωσης: | 18/04/2019 |
| Ημ/νία λήξης εκδήλωσης: | 20/04/2019 |
| Σημειώσεις: | This research was implemented through an IKY scholarship funded by the action
"Reinforcemen of Postdoctoral Researchers" of the operational programme "Human
Resources Development, Education and Life Lifelong Learning" with priority axes 6, 8, 9 and
was co-financed by the European Social Fund (ESF) and the Hellenic Republic. Conference site: http://mikrobiokosmos8.org/ |
| Εμφανίζεται στις συλλογές: | Μεταδιδακτορικοί ερευνητές |
Αρχεία σε αυτό το τεκμήριο:
| Αρχείο | Περιγραφή | Σελίδες | Μέγεθος | Μορφότυπος | Έκδοση | Άδεια | |
|---|---|---|---|---|---|---|---|
| Dailianis 2019 MBK8.pdf | Περίληψη σε πρακτικά συνεδρίου και αναρτημένη ανακοίνωση | 1 σελίδα σελίδες | 4.96 MB | Adobe PDF | Άλλη |  | Δείτε/ανοίξτε |