Nilaparvata lugens


Species: Nilaparvata lugens - brown planthopper

Order: Hemiptera

Suborder: Auchenorrhyncha

Family: Delphacidae

Genus: Nilaparvata

N. lugens is probably the most serious insect pest of rice in Asia. Its feeding causes plants to wilt and causes a symptom called hopperburn. It also transmits grassy stunt and ragged stunt virus diseases. N. lugens was a minor rice pest until the mid-1960s in much of tropical Asia. However, it assumed the status of the most destructive pest in the 1970s.

N. lugens damages plants by sucking sap from the mesophyll and blocking the xylem and phloem by laying egg masses in the midribs of the leaf sheath and leaf blade. Affected plants become chlorotic. Older leaves turn progressively yellow from the tip to the midpoint of the leaf, then gradually dry up and die. This feeding damage is commonly referred to as hopperburn. Hopperburn begins in patches but can spread rapidly as the planthoppers move from dying plants to adjacent plants. Excreted honeydew on infested plants may also become a medium for sooty mould fungus.

In addition to direct feeding damage, N. lugens is also the vector of rice grassy stunt tenuivirus and rice ragged stunt oryzavirus.


Sample collection

An insecticide susceptible strain which has become wingless during long-term culture. The strain has been maintained at Rothamsted since 2012, when it was supplied by Bayer.

Next Generation Sequencing

i) Illumina Hi-C sequencing 150 bp paired end data:

824,808,638 reads and 132x coverage.

ii) PacBio CLR data, of mean read length 9,519, total reads 26,277,464, read length N50 13,526, and total bases 250,138,790,988. DNA was extracted using 6 individuals using the MagAttract kit at Rothamsted Research (2000ng gDNA).

iii) Illumina 10X sequencing 150 bp paired end data:

417,294,921 reads and 134x coverage.

iv) Nanopore sequencing of 2 flow cells, totalling 7,235,072 reads, 24,277,531,149 bp and 26x coverage.


Multi-individual used for PacBio CLR (University of Georgia, USA) and multi-individual for Hi-C Illumina sequencing (Arima Genomics USA). Falcon was used to assemble the PacBio CLR, with Juicer then 3d-dna using Hi-C data for chromosome level assembly. Haplotigs were removed (purge_haplotigs). Manual curation was done to bring the genome together and check for miss-assemblies. Unmapped reads were mapped back to the original assembly to check for missing sequence and incorporated into the final assembly. Error correction was done with Illumina Hi-C data using freebayes.

Public RNA-seq data was assembled into a transcriptome (BUSCO: C:97.6%[S:59.8%,D:37.8%],F:1.5%,M:0.9%) and used in the Maker2 annotation pipeline with trained Augustus and Genemark gene predictors. PASA was used to update the gene models to add UTR, correct existing models and add isoforms. Non-coding RNA was annotated using infernal v1.1.4.

A Pfam genomic track was created by converting to six reading frames and utilizing hmmer to identify loci of interest i.e. P450 pfam domains on the genome. Using this information, loci of interest including UDP, P450, ABC were curated.

Endosymbiont Arsenophonus (2,858,500 bp) was assembled and submitted.

Final Results

A complete annotated 15 chromosome assembly deposited at NCBI under accession PRJEB47894 (incl. raw data).

BUSCO (Insecta odb10): C:93.9%,F:2.9%,M:3.2%

16,672 gene models - BUSCO C:90.6%[S:79.8%,D:10.8%],F:3.4%,M:6.0%

Scaffold No. (incl Mt): 31

N50: 100,452,519

N bases (bp): 3,359,422

Repeat: 47.9%

Total size (bp) (chr no.) 931,071,774 (15)

Curated: 56x P450, 54x ABC transporter, 19x UGT, and 0/130 IRAC gene models.

One Endosymbiont Arsenophonus was assembled (2,858,500 bp).


Assembly did not assemble well (in terms of large contigs) for this species even though nanopore data was good and PacBio CLR data was good. Similar problem with grasshopper reported elsewhere. Might be something to do with the species heterozygosity. Would be good try trio binning on this species and reuse the Hi-C that is now available.

Other files

These are files that were not submitted to NCBI but might be useful.

Genomic PFAM annotation track

Non-coding RNA annotation track

Repeat annotation track

Repeat library