The way this question is asked, the answer can be sure, why not can it be possible.

But the main question is should you use MiSeq? Why do you want to sequence on MiSeq anyway?

For Plant genome seq, depth would be required and for that you need to have data volume according to the genome size and complexity of your plant.

It could also be dependent on how much efforts and money you want to put in the sequenceing. I can recommend you to consider two points:

1) Read the literature related to your plant which you should be doing in the first place to get the information about the genome size and sequencing tech used by them. How the analysis was done and what were the problems if the authors mention it.

2) Talk to your sequencing facility/company and they can surely help you with finding the best strategy.

Hi @abhijeet, thank you for sharing your opinion.

We are trying to use MiSeq because of the unavailability of other HiSeq platforms.

The plant we would like to sequence is of 340 mb long.

Miseqs are generally not suitable for plant/human WGS (they do not have have the capacity to get enough reads + multiplex to drive the cost down). They're more geared towards targeted amplicon sequencing and bacterial/viral WGS, 16S or anything that's relatively small genome wise and doesn't require ultra deep sequencing.

Illumina has an online tool for you to take a look at, you'll need to start with NextSeq and upwards to get a chance to pool library and get 50x level of coverages.

https://emea.support.illumina.com/downloads/sequencing_coverage_calculator.html

Alternatively, you can consider Nanopore devices and flow cells which is relatively cheap:

https://nanoporetech.com/products/promethion

@kiessling thanks a lot for your kind suggestions. I have understood the limitation.

I would recommend having a look at the Nanopore reads. Reason being, Nanopore can generate long reads (10,000 bp or several Kbs) which can help in De Novo assembly. The quality of reads are a parameter to consider here too, nowadays Nanopore reads with the new Kit 14 and flow cells (>R10.4) can generate >Q20 reads which are pretty decent for De Novo assembly. So you have the potential to generate a lot of reads for cheap that are long and decent quality which can help with De Novo assembly of a genome if you went for that sort of a thing. If you are aligning to a reference, the long reads might not be that helpful but if you want an assembly then that's a nice perk of Nanopore reads. But consider the bioinformatics in advance, this is not necessarily hard or easy depending on many factors (hardware, throughput, choice of software/coding skills). This video might help:

https://www.youtube.com/watch?v=FxFjgCRCxp8