Chilo suppressalis


Species: Chilo suppressalis

(striped rice stem borer)

Order: Lepidoptera

Family: Crambidae

Genus: Chilo

C. suppressalis ranges from Australasia and the Pacific Islands through Asia to Europe (where it was probably accidentally introduced). The larvae are a serious pest of rice, more under temperate and sub-tropical than tropical conditions. The larvae feed on the stems causing similar symptoms to other rice stem borers. The larvae tunnel into the stems, through the internodes towards the base of the plant, causing stems to wilt and die, a condition known as 'deadheart'. The stems are easily pulled out. Feeding at the base of the panicles may prevent emergence or result in white unfilled grain of those that have emerged, a symptom called 'whitehead'.

Unlike other Chilo species it is adapted to temperate climates. Host plants include: Rice, sorghum and maize are major hosts, but it is also found on sugarcane, millet, and many wild grasses.

CABI states that this is one of the most important pests of rice in East Asia, India and Indonesia. It is a threat to Africa. In Asia, Scirpophaga incertulas and Chilo suppressalis are responsible for a steady annual damage of 5-10% of the rice crop, with occasional localized outbreaks of up to 60%.

Source: Pacific Pests, Pathogens & Weeds

Sample collection

Syngenta received this strain from Aventis in April 2000.

Next Generation Sequencing

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

234,532,466 reads and 45x coverage.

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

328,141,794 reads and 63x coverage.

iii) PacBio CLR data, of mean read length 11,591, total reads 11,066,056, read length N50 14,892, and total bases 128,275,638,188. DNA was extracted using DNAzol at Rothamsted Research (2250ng gDNA) and BluePippin purified before library preparation.


Non-sexed single-individual used for PacBio CLR (University of Maryland, USA), 10X genomics Illumina, 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 (Redundans). 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 10X library data using freebayes.

RNA-seq data PRJNA89435 (midgut), PRJNA183730 (Parasitization by a braconid wasp, Cotesia chilonis), PRJNA375715 (6th instar larvae and prepupae), PRJNA551080 (adult) assembled with a BUSCO: C:99.5%[S:61.3%,D:38.2%],F:0.1%,M:0.4% 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 and IRAC gene models were found and curated using mapped RNA-seq and a Maker gene annotation.

An endosymbiont Enterobacter species was assembled (4,762,943 bp).

Final Results

A complete annotated 30 chromosome assembly deposited at NCBI under accession PRJEB37827 (incl. raw data).

BUSCO (Insecta odb 10): C:98.2%,F:0.6%,M:1.2%

11,366 gene - BUSCO C:94.7%[S:85.2%,D:9.5%],F:0.8%,M:4.5%

Scaffold No. (incl Mt): 52

N50: 28,297,866

N bases (bp): 56,583

Repeat: 49.49%

Total size (bp) (chr no.): 778,668,679 (30)

Curated: 79x P450, 46x ABC transporter, 26x UGT, and 119/130 IRAC gene models.

One endosymbiont was assembled as an Enterobacter (4,762,943 bp).

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