scholarly journals De novo genome assembly of the olive fruit fly (Bactrocera oleae) developed through a combination of linked-reads and long-read technologies

2018 ◽  
Author(s):  
Haig Djambazian ◽  
Anthony Bayega ◽  
Konstantina T. Tsoumani ◽  
Efthimia Sagri ◽  
Maria-Eleni Gregoriou ◽  
...  
Keyword(s):  
Y Chromosome ◽  
De Novo ◽  
Fruit Fly ◽  
Bactrocera Oleae ◽  
Olive Fruit Fly ◽  
Olive Fruit ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

AbstractLong-read sequencing has greatly contributed to the generation of high quality assemblies, albeit at a high cost. It is also not always clear how to combine sequencing platforms. We sequenced the genome of the olive fruit fly (Bactrocera oleae), the most important pest in the olive fruits agribusiness industry, using Illumina short-reads, mate-pairs, 10x Genomics linked-reads, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT). The 10x linked-reads assembly gave the most contiguous assembly with an N50 of 2.16 Mb. Scaffolding the linked-reads assembly using long-reads from ONT gave a more contiguous assembly with scaffold N50 of 4.59 Mb. We also present the most extensive transcriptome datasets of the olive fly derived from different tissues and stages of development. Finally, we used the Chromosome Quotient method to identify Y-chromosome scaffolds and show that the long-reads based assembly generates very highly contiguous Y-chromosome assembly.JR is a member of the MinION Access Program (MAP) and has received free-of-charge flow cells and sequencing kits from Oxford Nanopore Technologies for other projects. JR has had no other financial support from ONT.AB has received re-imbursement for travel costs associated with attending Nanopore Community meeting 2018, a meeting organized my Oxford Nanopore Technologies.

scholarly journals 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

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Anthony Bayega ◽  
Haig Djambazian ◽  
Konstantina T. Tsoumani ◽  
Maria-Eleni Gregoriou ◽  
Efthimia Sagri ◽  
...  
Keyword(s):  
Y Chromosome ◽  
De Novo Assembly ◽  
De Novo ◽  
Fruit Fly ◽  
Bactrocera Oleae ◽  
Olive Fruit Fly ◽  
Olive Fruit ◽  
Long Read

scholarly journals De novo clustering of long-read transcriptome data using a greedy, quality-value based algorithm

2018 ◽  
Author(s):  
Kristoffer Sahlin ◽  
Paul Medvedev
Keyword(s):  
Clustering Algorithm ◽  
De Novo ◽  
Substantial Improvement ◽  
Error Rates ◽  
Reconstruction Algorithms ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Long Read ◽  
Transcript Reconstruction ◽  
Oxford Nanopore Technologies

AbstractLong-read sequencing of transcripts with PacBio Iso-Seq and Oxford Nanopore Technologies has proven to be central to the study of complex isoform landscapes in many organisms. However, current de novo transcript reconstruction algorithms from long-read data are limited, leaving the potential of these technologies unfulfilled. A common bottleneck is the dearth of scalable and accurate algorithms for clustering long reads according to their gene family of origin. To address this challenge, we develop isONclust, a clustering algorithm that is greedy (in order to scale) and makes use of quality values (in order to handle variable error rates). We test isONclust on three simulated and five biological datasets, across a breadth of organisms, technologies, and read depths. Our results demonstrate that isONclust is a substantial improvement over previous approaches, both in terms of overall accuracy and/or scalability to large datasets. Our tool is available at https://github.com/ksahlin/isONclust.

scholarly journals De-novo Assembly of Limnospira fusiformis Using Ultra-Long Reads

2021 ◽  
Vol 12 ◽  
Author(s):  
McKenna Hicks ◽  
Thuy-Khanh Tran-Dao ◽  
Logan Mulroney ◽  
David L. Bernick
Keyword(s):  
Phylogenetic Analysis ◽  
Type Strain ◽  
Reference Genome ◽  
De Novo ◽  
Illumina Miseq ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies ◽  
Rdna Analysis

The Limnospira genus is a recently established clade that is economically important due to its worldwide use in biotechnology and agriculture. This genus includes organisms that were reclassified from Arthrospira, which are commercially marketed as “Spirulina.” Limnospira are photoautotrophic organisms that are widely used for research in nutrition, medicine, bioremediation, and biomanufacturing. Despite its widespread use, there is no closed genome for the Limnospira genus, and no reference genome for the type strain, Limnospira fusiformis. In this work, the L. fusiformis genome was sequenced using Oxford Nanopore Technologies MinION and assembled using only ultra-long reads (>35 kb). This assembly was polished with Illumina MiSeq reads sourced from an axenic L. fusiformis culture; axenicity was verified via microscopy and rDNA analysis. Ultra-long read sequencing resulted in a 6.42 Mb closed genome assembled as a single contig with no plasmid. Phylogenetic analysis placed L. fusiformis in the Limnospira clade; some Arthrospira were also placed in this clade, suggesting a misclassification of these strains. This work provides a fully closed and accurate reference genome for the economically important type strain, L. fusiformis. We also present a rapid axenicity method to isolate L. fusiformis. These contributions enable future biotechnological development of L. fusiformis by way of genetic engineering.

scholarly journals Transcriptome landscape of the developing olive fruit fly embryo delineated by Oxford Nanopore long-read RNA-Seq

2018 ◽  
Author(s):  
Anthony Bayega ◽  
Spyros Oikonomopoulos ◽  
Eleftherios Zorbas ◽  
Yu Chang Wang ◽  
Maria-Eleni Gregoriou ◽  
...  
Keyword(s):  
Embryo Development ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Fruit Fly ◽  
Full Length ◽  
Olive Fruit Fly ◽  
Rna Seq ◽  
Olive Fruit ◽  
Olive Fly ◽  
Oxford Nanopore

AbstractThe olive fruit fly or olive fly (Bactrocera oleae) is the most important pest of cultivated olive trees. Like all insects the olive fly undergoes complete metamorphosis. However, the transcription dynamics that occur during early embryonic development have not been explored, while detailed transcriptomic analysis in the absence of a fully annotated genome is challenging. We collected olive fly embryos at hourly intervals for the first 6 hours of development and performed full-length cDNA-Seq using a purpose designed SMARTer cDNA synthesis protocol followed by sequencing on the MinION (Oxford Nanopore Technologies). We generated 31 million total reads across the timepoints (median yield 4.2 million per timepoint). The reads showed 98 % alignment rate to the olive fly genome and 91 % alignment rate to the NBCI predicted B. oleae gene models. Over 50 % of the expressed genes had at least one read covering its entire length validating our full-length RNA-Seq procedure. Expression of 68 % of the predicted B. oleae genes was detected in the first six hours of development. We generated a de novo transcriptome assembly of the olive fly and identified 3553 novel genes and a total of 79,810 transcripts; a fourfold increase in transcriptome diversity compared to the NCBI predicted transcriptome. On a global scale, the first six hours of embryo development were characterized by dramatic transcriptome changes with the total number of transcripts per embryo dropping to half from the first hour to the second hour of embryo development. Clustering of genes based on temporal co-expression followed by gene-set enrichment analysiss of genes expressed in the first six hours of embryo development showed that genes involved in transcription and translation, macro-molecule biosynthesis, and neurodevelopment were highly enriched. These data provide the first insight into the transcriptome landscape of the developing olive fly embryo. The data also reveal transcript signatures of sex development. Overall, full-length sequencing of the cDNA molecules permitted a detailed characterization of the isoform complexity and the transcriptional dynamics of the first embryonic stages of the B. oleae.

Choice response of the olive fruit fly, Bactrocera oleae, to various bait/insecticide combinations: hydrolyzed proteins or ammonium salts?

2021 ◽  
pp. 1-12
Author(s):  
Kiki Varikou ◽  
Antonis Nikolakakis ◽  
Dimitris Bitsakis ◽  
Zacharias Skarakis ◽  
Nikos Garantonakis ◽  
...  
Keyword(s):  
Fruit Fly ◽  
Ammonium Salts ◽  
Bactrocera Oleae ◽  
Choice Response ◽  
Olive Fruit Fly ◽  
Olive Fruit

scholarly journals Population dynamics of pre-imaginal stages of olive fruit fly Bactrocera oleae Gmel. (Diptera, Tephritidae) in the region of Bar (Montenegro)

2013 ◽  
Vol 28 (1) ◽  
pp. 23-29 ◽  
Author(s):  
Tatjana Perovic ◽  
Snjezana Hrncic
Keyword(s):  
Population Dynamics ◽  
Developmental Stages ◽  
Fruit Fly ◽  
Bactrocera Oleae ◽  
Yield Reduction ◽  
Olive Fruit Fly ◽  
Application Timing ◽  
Olive Fruit ◽  
Fruit Drop

Olive fruit fly is the most harmful pest of olive fruits and important for oil production. Damage involves yield reduction as a consequence of premature fruit drop, but also a reduced quality of olive oil and olive products. There is little available data regarding the biology of Bactrocera oleae in Montenegro. Knowledge of the pest life cycle and development would improve optimization of insecticide application timing and protection of fruits, and reduce adverse effects on the environment. Investigation was conducted on the Zutica variety in an olive grove located in Bar during a three-year period. Population dynamics of the pre-imaginal stages and level of fruit infestation were monitored from mid-July until the end of October. The results of this three-year investigation showed that the beginning of infestation was always at the end of July. It was also found that, depending on environmental conditions, the level of infestation was low until the end of August. In September and October it multiplied, and reached maximum by the end of October. Regarding infestation structure, eggs and first instar larvae were the dominant developmental stages of the pest until the middle of September. From mid-September until mid-October all developmental stages (eggs, larvae, pupae) were equally present in infested fruits. Pupae, cocoons and abandoned galleries prevailed until the harvest.

scholarly journals Olive Fruit Fly, Bactrocera oleae (Gmelin) (Insecta: Diptera: Tephritidae)

EDIS ◽  
1969 ◽  
Vol 2002 (8) ◽  
Author(s):  
Howard V. Weems ◽  
James L. Nation
Keyword(s):  
Cooperative Extension ◽  
Fruit Fly ◽  
Cooperative Extension Service ◽  
Bactrocera Oleae ◽  
Extension Service ◽  
Olive Fruit Fly ◽  
University Of Florida ◽  
Olive Fruit ◽  
Agricultural Sciences

This document is EENY-113 (originally published as DPI Entomology Circular No. 44), one of a series of Featured Creatures from the Entomology and Nematology Department, Florida Cooperative Extension Service, Institute of Food and Agricultural Sciences, University of Florida. Published: September 1999. Revised: June 2003.

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