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Τύπος: Άρθρο σε επιστημονικό περιοδικό
Τίτλος: De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly.
Συγγραφέας: [EN] Bayega, Anthony
[EN] Djambazian, Haig
[EL] Τσουμάνη, Κωνσταντίνα[EN] Tsoumani, Konstantina
[EL] Γρηγορίου, Μαρία-Ελένη[EN] Gregoriou, Maria-Eleni
[EL] Σαγρή, Ευθυμία[EN] Sagri, Efthimia
[EL] Δροσοπούλου, Ελένη[EN] Drosopoulou, Elena
[EL] Μαυραγάνη-Τσιπίδου, Πηνελόπη[EN] Mavragani-Tsipidou, Penelope
[EN] Giorda, Kristina
[EL] Τσιάμης, Γεώργιος[EN] Tsiamis, George
[EL] Μπούρτζης, Κώστας[EN] Bourtzis, Kostas
[EL] Οικονομόπουλος, Σπυρίδων[EN] Oikonomopoulos, Spyros
[EN] Dewar, Ken
[EN] Church, Deanna
[EL] Παπανικολάου, Αλέξης[EN] Papanicolaou, Alexie
[EL] Ματθιόπουλος, Κώστας[EN] Mathiopoulos, Kostas
[EL] Ραγκούσης, Γιάννης[EN] Ragoussis, Jiannis
Ημερομηνία: 30-Μαρ-2020
Περίληψη: Background The olive fruit fly, Bactrocera oleae, is the most important pest in the olive fruit agribusiness industry. This is because female flies lay their eggs in the unripe fruits and upon hatching the larvae feed on the fruits thus destroying them. The lack of a high-quality genome and other genomic and transcriptomic data has hindered progress in understanding the fly’s biology and proposing alternative control methods to pesticide use. Results Genomic DNA was sequenced from male and female Demokritos strain flies, maintained in the laboratory for over 45 years. We used short-, mate-pair-, and long-read sequencing technologies to generate a combined male-female genome assembly (GenBank accession GCA_001188975.2). Genomic DNA sequencing from male insects using 10x Genomics linked-reads technology followed by mate-pair and long-read scaffolding and gap-closing generated a highly contiguous 489 Mb genome with a scaffold N50 of 4.69 Mb and L50 of 30 scaffolds (GenBank accession GCA_001188975.4). RNA-seq data generated from 12 tissues and/or developmental stages allowed for genome annotation. Short reads from both males and females and the chromosome quotient method enabled identification of Y-chromosome scaffolds which were extensively validated by PCR. Conclusions The high-quality genome generated represents a critical tool in olive fruit fly research. We provide an extensive RNA-seq data set, and genome annotation, critical towards gaining an insight into the biology of the olive fruit fly. In addition, elucidation of Y-chromosome sequences will advance our understanding of the Y-chromosome’s organization, function and evolution and is poised to provide avenues for sterile insect technique approaches.
Γλώσσα: Αγγλικά
Σελίδες: 21
DOI: 10.1186/s12864-020-6672-3
ISSN: 1471-2164
Θεματική κατηγορία: [EL] Άλλες Επιστήμες Μηχανικού και Τεχνολογίες[EN] Other Engineering and Technologies
[EL] Γεωπονική Βιοτεχνολογία[EN] Agricultural Biotechnology
Λέξεις-κλειδιά: Olive fruit fly genomeBactrocera oleaeLinked readsLong readsY chromosome assemblyInsect developmental genes
Κάτοχος πνευματικών δικαιωμάτων: © The Author(s). 2020
Όροι και προϋποθέσεις δικαιωμάτων: Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
Διατίθεται ανοιχτά στην τοποθεσία: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6672-3
Ηλεκτρονική διεύθυνση του τεκμηρίου στον εκδότη: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6672-3
Ηλεκτρονική διεύθυνση περιοδικού: https://bmcgenomics.biomedcentral.com/
Τίτλος πηγής δημοσίευσης: BMC Genomics
Τόμος: 21
Σελίδες τεκμηρίου (στην πηγή): Article no 259
Σημειώσεις: The genome and transcriptome sequencing were supported by a Stavros Niarchos Fulbright Greek Diaspora Scholarship, Genome Canada Genomics Technology Platform grant, the Canada Foundation for Innovation (CFI) and the CFI Leaders Opportunity Fund (32557), Compute Canada Resource Allocation Project (WST-164-AB) and Genome Innovation Node (244819) to JR. AB is a Queen Elizabeth II PhD scholarship recipient. Part of the sequencing cost of this research was also supported by the “ARISTEIA” (MIS524938) Action of the “Operational programme Education and Lifelong Learning”, co-funded by the European Social Fund (ESF) and Hellenic National Resources. Further support was provided by the two postgraduate programs of the Department of Biochemistry and Biotechnology of the University of Thessaly (“Biotechnology – Quality Assessment in Nutrition and the Environment” and “Applications of Molecular Biology -Genetics –Diagnostic Biomarkers”). KTT was funded through a postdoctoral studies scholarship from the Hellenic State Scholarship Foundation (IKY); this research is co-financed by Greece and the European Union (European Social Fund-ESF) through the Operational Programme «Human Resources Development, Education and Lifelong Learning» in the context of the project “Reinforcement of Postdoctoral Researchers” (MIS-5001552), implemented by the State Scholarships Foundation (IKΥ). The NIH Intramural Research Program, National Library of Medicine funded the NCBI Gnomon annotation and the USDA-National Agricultural Library (NAL) provided support for the WebApollo curation website
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