⭐️ It is with immense pleasure that we share with you the published #Sitophilus oryzae #genome paper in @BMCBiology doi.org/10.1186/s12915… 1/n
S. oryzae is a #coleopteran capable of destroying entire cereal crops posing a significant threat to the food security of many developing countries. The female #weevil lays ~300 eggs during its lifetime. They develop within the cereal grain until a ~3 day old adult emerges 2/n Image
Cereal grains are nutritionally poor, and S. oryzae partnered with a gram- bacterium that complements its diet. The bacteria are present within specialized insect cells, called #bacteriocytes. Check here for our latest research on this #symbiosis doi.org/10.1073/pnas.2…. 3/n
“Parenthèse” for a pretty #bacteriocyte figure that I am way too proud of (red: tubulin, green: syto9). Thanks @Severin04682184 for taking it properly! I am definitely not a 🔬 person! 4/n Image
Ok, back to our #genome: more than 6 years ago, A. Heddi, A. Moya & A. Latorre were having dinner in Valencia, @ restaurant in Plaza de San Nicolás, where they decided it was time to sequence S. oryzae’s genome so they could get deep into the #insect-#bacteria partnership. 5/n
This project took a loooong time, it is therefore with immense gratitude ♥️ that we recognize the tenacity and effort of two of the first co-authors @VargasChavezC & @clementgoubert who despite lab, country & project changes, remained on board. Bravo les gars! 6/n
A special acknowledgement also goes to @niparisot, first-author, who took over the project just after his recruitment @INRAE_UMR_BF2I as an assistant professor @insadelyon and managed such an incredible international consortium. 7/n
I only arrived in this project a couple of years ago, just after my recruitment as a @INRAE_DPT_SPE researcher @INRAE_UMR_BF2I so I am really grateful for all the effort that was done before & after the TEs and I (with @clementgoubert) made a putch !
So what did we find? And how crazy did we become in the process ? 9/n
Bear in mind this started 6 years ago which is very different then starting a genome assembly from scratch nowadays. We had @PacBio and @illumina reads but man oh man, we were never satisfied with the assembly 10/n.
We joined forces with @IGFLyon, got some @nanopore reads, and ended up with 142X cov! With the help of @ErableInria @digenoma doi.org/10.1038/s41587… we finally assembled our genome (2000 scaffolds - still room for improvement). It took us 4 years & 3 different assemblies. 11/n
In the last two years, we annotated (3 times!) the genome and discovered that a little over 70% of it is composed of repetitive sequences! That explains why this was soooo hard to assemble ! Below a comparison with other insects 12/n Image
So @clementgoubert and I, with @TreepVieira & DFAM, were able to detect and annotate the repetitive seq., which correspond mainly to DNA transposons. The genome is so dense that when @clementgoubert and I looked at IGV we thought we were looking at a human or mouse genome ! 13/n Image
A special shout out for @MGFerrarini ♥️ who did the analysis for Fig. 5 showing that TE families are expressed & tissue specific. Compared to other insects, S. oryzae has a higher TE-content in its RNAseq reads. Not only is this weevil full of TEs but many are transcribed! 14/n Image
One of our most promising discoveries is that TE content is variable in the Sitophilus taxon going from ~80% for S. oryzae, to ~54% for Sitophilus linearis (done with dnaPipeTE from @clementgoubert). 15/n Image
We are currently digging on these genomes to try to understand why they have such different TE content (and because at the end we are masochists who love to assemble TE-rich genomes) 16/n
But what about the intracellular bacteria in all this? Well, we did find ~50 TE families differentially expressed between symbiotic and aposymbiotic ovaries. But is this biologically relevant? It remains to be seen, and this is one of our questions right now. 17/n Image
Curiously, S. linearis, the weevil harboring the less TE content, is also the only weevil we have in the lab without any bacteria. Coincidence? Hope the future can tell us! tenor.com/bhTmp.gif 18/n
Our work did not revolve only around TEs. Our MASSIVE sup material has chapters describing many different analyses we have done. And for this, I’ll let you follow @niparisot for a twitorial on everything else we found! See you at his twitter feed! 19/n.
This was definitely those roller coaster projects, for a long time period, involving many people, & many labs. We did become a little crazy but I’m happy with everything I learned. Thank you all involved in this! See you soon for more on the bacteria-TE-insect projects! 19/19.

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