I have some experience in Human, SARS-CoV-2, Dengue and whole Genome Sequencing, and bacterial metagenomics. Now I want to do some work on plant genomics. Can anyone share some knowledge regarding plant genomics? How I will start? From where can get the reference genome? Is BaseSpace is enough to assemble the sequence?
The main differences are:
1. plants have cell wall, so DNA-extraction protocol is different. CTAB-method is the best of the best according to our experience.
2. The plant genomes are usually very big. So the combination of long-read methods (PacBIO, Nanopore) with the short-read methods (Illumina) is often necessary.
Thanks to all. Do you have the practical experience to work with this?@
Shahina Akter. I am not sure I understood exactly what you are looking for, since you mentioned that you have experience/ exposure in genomics. The basics are the same across all living things. Perhaps processing materials for nucleic acids (as Lidia Samarina has alluded to), and post-processing handling might have variations here and there - depending on the nature of the tissues or organic matter in question.
For reference genomes (completed or incomplete or dedicated specific genomic features), there are many plant genomic meta-databases like phytozome, and dedicated, plant species-specific databases all over the place. Remember, not all species are fully sequenced or have well-curated seq datasets; so you'll need to piggyback on the sequences of their close relative and 'assume' some synteny through comparative genomic inferences.
There are many proprietary and publicly available software to do assembly. Once you set your goal, you will be spoiled for choice.
Thank you very much@Henry Awika. Surely I will follow your instructions. I hope you will help me if I fall in any difficulty in future. Could you please share your email, so that I can contact you if I fall in any trouble?
Shahina, you can send me a message to my inbox here and I will respond to you with my email.
These review papers will answer your questions. Must read
Article A guide to sequence your favorite plant genomes
https://academic.oup.com/gigascience/article/8/3/giy163/5281243
https://www.frontiersin.org/articles/10.3389/fpls.2018.01660/full
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