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Data released on April 20, 2015

Gene-set of brown planthopper genome

Wang, Z; Yu, L; Zhang, C; Zhou, X (2015): Gene-set of brown planthopper genome GigaScience Database. http://dx.doi.org/10.5524/100139 RIS BibTeX Text

The brown planthopper, Nilaparvata lugens, the most destructive pest of rice, is a typical monophagous herbivore that feeds exclusively on rice sap, which migrates over long distances. Outbreaks of it have re-occurred approximately every three years in Asia. It has also been used as a model system for ecological studies and for developing effective pest management.
The N. lugens population sequenced in the present study was originally collected in Hangzhou, China, in 2008 and had been reared on rice seedlings (strain: TN1). One male and one female were isolated and mated to produce F1 progeny. A single pair was then selected for sibling inbreeding for 13 generations. Genomic DNA was extracted from adult females of the F13 generation. We constructed a series of DNA libraries with varying insert sizes (180 bp, 200 bp, 500 bp, 2 kb, 5 kb, 10 kb, 20 kb, and 40 kb) to perform WGS sequencing. All of the above libraries were sequenced on Illumina HiSeq 2000 or GA-II sequencers. After performing filtering steps to remove adapter-contaminated reads, low-quality reads, and duplicate reads, a total of 158.01 Gbp of clean WGS data (131.67X of the genome) with 131.7-fold of genome coverage depth and were combined with 507.94 Gbp of clean fosmid sequence data was obtained. This was assembled using SOAPdenovo and Rabbit, producing a final draft assembly of 1.141Gbp with a scaffold N50 of 356,597 bp. The Nilaparvata lugens genome should highlight potential directions for effective pest control of the planthopper.

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Related manuscripts:

doi:10.1186/s13059-014-0521-0

Accessions (data included in GigaDB):

BioProject: PRJNA177647

Genomic

http://gigadb.org/images/data/cropped/100139.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN03077662108931 brown planthopperNilaparvata lugens Sex:female
Geographic location (country and/or sea,region):Hangzhou China
Isolate:NLH13
Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
Coding sequenceFASTA31.7 MB2015-04-20
AnnotationGFF1.77 MB2015-04-20
Protein sequenceFASTA6.17 MB2015-04-20
Displaying 1-3 of 3 File(s).

History:

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