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Surbhi Grewal

Surbhi Grewal

Jan 23
16 tweets

As a wet lab biologist who is now doing more #Bioinformatics projects than lab work, I just want to share my journey of how I got here. And thank some of the many people that helped along the way. It all started with my first @PAG / PAG ASIA in 2014…

It was all about the @wheatgenome sequencing project and I was amazed by how it had all come together. All I was interested in though was how to track wild relative introgressions in wheat using the array we developed with @University of Bristol Biological Sciences…Simples. Umm not so much..
It took a year and another @PAG / PAG ASIA before I learnt how to use the softwares, command line and configured the process to suit our unique germplasm. Lots of emails that started with…you probably don’t know me but I saw your talk and was wondering if you can help me out.
Our first paper in 2016 on tracking Am. muticum introgressions in wheat was a step change. We published similar studies with other wild species then hit another roadblock. The array couldn’t tell if segments were now homozygous in selfed lines.
We needed a new genotyping method and with BLAST as my only bioinformatics skill I felt a bit helpless & out of my depth. With support from many of my peers @homonecloco @Laura-Jayne Gardiner I spent the next 2 years developing chromosome specific KASP that tracked our introgressions.
My skills were so limited that everything was a long winded process. SNP discovery was cumbersome - happening through sequence alignment of PCR products! The whole lab stepped in to do the PCRs while I analysed the sequencing data. Took ages and a baby to publish the results!
@Anthony Hall Lab 🌾 stepped in with whole genome sequencing of the wild species under @Designing Future Wheat programme & provided us with invaluable SNPs for KASP development… thanks @Ryan Joynson @Benedict Coombes
But as things went on I wanted to be able to do what everyone else was doing. Basic genomics and maybe if I was crazy enough de novo genome assembly of our wild species. Turns out I was crazy enough.
I needed bioinformatics skills & so at the height of the first lockdown I took basic online courses and then started a part time apprenticeship MRes Bioinformatics Scientist. Thanks @Adam Blanchard @Michael Wilson @Dr Sarah Storr @Angus Davidson 🇿🇦 for your support over the last 2.5 yrs
It gave me the confidence to explore established & new pipelines, google the right questions (& errors!), implement solutions from forums, understand and customise code. I have a long way to go but couldn’t have done it without this course. Also, I passed with minor corrections!
It gave me the basic skills to take on some advanced courses by @Physalia-courses@ONLINE on genome assembly and comparative genomics. Thanks to instructors @Marcela Uliano-Silva @Fritz Sedlazeck @Vertebrate Genomes Project (VGP) who showed us how to do it step by step.
It has been a steep (vertical almost) learning curve but I’m happy to report that over the last 6 months I’ve produced a chromosome-scale genome assembly of a wheat relative using @PacBio HiFi and @Arima Genomics HiC & with support on curation by @Wellcome Sanger Tree of Life Programme …watch this space 😉
Massive effort and not possible without everyone @Wheat_ResearchCentre I’m especially grateful for the support of my mentors Ian @Ian King and Julie King and @Stella Edwards over all these years and many of my colleagues @UoNBiosciences @Plant Science Nottingham @UoNFutureFood
As I prepare for my maternity leave next week I just want to say to all our junior lab members @Nikki Walter @Jack Walker @Jake Hill @veronicaguwela @Manel Othmeni thanks for your support too and remember the learning never stops! So never give up…keep the flame going!
Surbhi Grewal

Surbhi Grewal

Assistant Professor at BBSRC Nottingham Wheat Research Centre @Notts_WRC Special interest in wild relatives (of wheat), indian street food and cricket
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