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Bactrocera oleae
Summary
| Type |
organism
|
|---|---|
| Genus |
Bactrocera
|
| Species |
oleae
|
| Common Name |
Olive fruit fly
|
| Description | |
| Publication |
Bayega A, Djambazian H, Tsoumani KT, Gregoriou ME, Sagri E, Drosopoulou E, Mavragani-Tsipidou P, Giorda K, Tsiamis G, Bourtzis K, Oikonomopoulos S, Dewar K, Church DM, Papanicolaou A, Mathiopoulos KD, Ragoussis J. 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 Mar 30; 21(1):259.
|
| Organism Image |
|
| Image Credit |
Courtesy of Nikos Papadopoulos, University of Thessaly
|
Assembly Stats
| Contig N50 |
187.7 kb
|
|---|---|
| GC Content |
34.5%
|
| Scaffold N50 |
4.6 Mb
|
Other Information
| Community Contact |
Haig Djambazian, McGill University
|
|---|---|
| Links |
Analyses
| Name | Program |
|---|---|
| JAMg Official Gene Set v1 | JAMg (Just Annotate My genome) |
| Bactrocera oleae genome assembly gapfilled_joined_lt9474.gt500.covgt10 | ray |
| NCBI Bactrocera oleae Annotation Release 100 | NCBI Eukaryotic Genome Annotation Pipeline |
| Functional annotation of NCBI Bactrocera oleae Annotation Release 100 | AgBase functional annotation pipeline |
| Functional annotation of NCBI Bactrocera oleae Annotation Release 101 | AgBase functional annotation pipeline |
| NCBI Bactrocera oleae Annotation Release 101 | NCBI Eukaryotic Genome Annotation Pipeline |
| Bactrocera oleae genome assembly MU_Boleae_v2 (GCF_001188975.3) | 10x Genomics Supernova v. 1.2; Sspace standard v. 3.0; Pbjelly v. 15.8.24; NPSCARF v. 1.7-05b |
| Bactrocera oleae annotations JAMg OGSv1.1 | JAMg (Just Annotate My genome), 2015-03-01; Liftoff, 1.6.3 |
1. Description
The olive fruit fly, Bactrocera oleae (Rossi), is the primary pest of olives. Olive fly’s larvae are monophagous, feeding exclusively on olive sap. Under favorable weather conditions, the flies have three to five generations per year, reaching extremely high population densities. The species expansion range closely follows that of the olive tree. It includes the entire Mediterranean basin, South and Central Africa, Canary Islands, the Near and Middle East, California and Central America. There have also been reports of Bactrocera species collected from wild olive trees in China, suggesting the presence of the olive fly in Asia, thus leaving Australia and South America as the only olive producing areas that are still olive fly free. Despite its importance, complete absence of classical genetic tools has hampered the study of the insect, compared to other species of the Tephritid family. The analysis of the fly’s genome and transcriptome can now give new insights into complex biological processes of the insect.
2. Project description:
We have sequenced the olive fruit fly (Bactrocera oleae) with Illumina short reads, Illumina mate pairs, PacBio long reads and have also performed a de novo transcriptome assembly with Illumina RNA sequencing.
The total genome size we have obtained is 512,888,968 bp in 77,416 sequences. By combining all the technologies starting with the initial short read assembly and using Illumina mate pairs we were able to increase the GN50 from 9,039 bp in 9,547 sequences to 113,040 bp in 608 sequences. This scaffolded assembly was then upgraded to a GN50 of 205,997 bp in 373 sequences using a PacBio continuous long reads and submitted to NCBI as GenBank: LGAM00000000.1
Finally we have used reassembled transcripts to further increase the size of the scaffolded assembly to a GN50 of 250,814 bp in 324 sequences.
The work represents a collaboration between Greek and Canadian Teams lead by Drs Kostas Mathiopoulos and Jiannis Ragoussis respectively. The University of Thessaly team in Greece consists of Kostas Mathiopoulos, Konstantina Tsoumani, Maria-Eleni Gregoriou, Efthimia Sagri. The BSRC Fleming team in Athens, Greece includes Martin Reczko and Jiannis Ragoussis (Affiliated Member). The McGill University and Genome Quebec Innovation Centre team in Montreal includes Jiannis Ragoussis, Haig Djambazian, Ken Dewar, and Louis Letourneau. The work is supported by the Action “ARISTEIA” of the “Operational program “Education and Life Long Learning”, co-funded by the European Social Fund and Greek National Resources”; and Genome Canada.
Genome update. Previously, the i5k Workspace@NAL hosted Bactrocera oleae genome assembly gapfilled_joined_lt9474.gt500.covgt10), NCBI Bactrocera oleae Annotation Release 100, JAMg Official Gene Set v1 and Functional annotation of NCBI Bactrocera oleae Annotation Release 100. The assembly and annotations have updated to the most recent assembly, Bactrocera oleae genome assembly MU_Boleae_v2 (GCF_001188975.3), Bactrocera oleae annotations JAMg OGSv1.1, NCBI Bactrocera oleae Annotation Release 101, and Functional annotation of NCBI Bactrocera oleae Annotation Release 101.