Abstract
Background Among beetles, the rice weevil Sitophilus oryzae is one of the most important pests causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions.
Results We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 Kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino-acids required for insect development and cuticle biosynthesis.
Conclusions In addition to being an agricultural pest and a valuable endosymbiotic system, S. oryzae can be a remarkable model for studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
NP: nicolas.parisot{at}insa-lyon.fr
CV-C: carlos.vargas{at}uv.es
CG: goubert.clement{at}gmail.com
PB-P: patrice.baa-puyoulet{at}inrae.fr
SB: severine.balmand{at}inrae.fr
LB: beranger.louis.bio{at}gmail.com
CB: blancbillard.caroline{at}gmail.com
AB: aymeric.bonnamour{at}gmail.com
MB: matthieu.boulesteix{at}univ-lyon1.fr
NB: nelly.burlet{at}univ-lyon1.fr
FC: federica.calevro{at}insa-lyon.fr
PC: patrick.callaerts{at}kuleuven.be
TC: theo.chancy{at}hotmail.fr
HC: hubert.charles{at}insa-lyon.fr
SC: stefano.colella{at}inrae.fr
ASB: andredsb.2b{at}gmail.com
ED: elisa.dell-aglio{at}insa-lyon.fr
ADG: digenova{at}gmail.com
GF: gerard.febvay{at}inrae.fr
TG: toni.gabaldon{at}bsc.es
MGF: mari.ferrarini{at}gmail.com
AG: alegerber{at}lncc.br
BG: benjamin.gillet{at}ens-lyon.fr
RH: robert.hubley{at}isbscience.org
SH: sandrine.hughes{at}ens-lyon.fr
EJ-J: emmanuelle.joly{at}inrae.fr
JM: justin.maire{at}unimelb.edu.au
MM-H: marina.marcet{at}bsc.es
FM: masson.ff{at}gmail.com
CM: camille.meslin{at}inrae.fr
NM: nicolas.montagne{at}sorbonne-universite.fr
AM: andres.moya{at}uv.es
ATRV: atrv{at}lncc.br
GR: gautier.richard{at}inrae.fr
JR: jeb.rosen{at}isbscience.org
M-FS: Marie-France.Sagot{at}inria.fr
AFAS: arian.smit{at}isbscience.org
JMS: jessica.storer{at}isbscience.org
CV-M: carole.monegat{at}insa-lyon.fr
AVa: agnes.vallier{at}inrae.fr
AVi: avignero{at}uni-mainz.de
AZ-R: anna.zaidman{at}insa-lyon.fr
WZ: wzamoum{at}gmail.com
CV: cristina.vieira{at}univ-lyon1.fr
RR: rita.rebollo{at}inrae.fr
AL: amparo.latorre{at}uv.es
AH: abdelaziz.heddi{at}insa-lyon.fr
- Abbreviations
- AMPs
- AntiMicrobial Peptides
- CPs
- cuticle proteins
- HGT
- horizontal gene transfer
- IMP
- Inosine MonoPhosphate
- K2P
- Kimura 2 Parameters
- LINE
- long INterspersed Element
- LTR
- Long Terminal Repeat
- MAMPs
- Microbial Associated Molecular Patterns
- MITEs
- miniature inverted repeat elements
- ORs
- odorant receptors
- PRR
- Pattern Recognition Receptors
- PLE
- penelope-like
- RC
- rolling circle
- SINE
- Short INterspersed Element
- TIR
- terminal inverted repeat
- TSS
- transcription start sites
- TEs
- transposable elements
- TTSS
- Type Three Secretion Systems
- UTR
- untranslated regions
- UMP
- Uridine MonoPhosphate