I would start first with a structural annotation of your genome and then run a blast of your proteome using strict e-value and coverage. You will get an overview about the most closed organisms. Next step is selecting around 100 proteins from your blast (high identity and coverage) of your organism and at least 12 organisms listed frequently from the blast, make an alignment and phylogenetic tree. This is in my opinion the most reliable way to select closely related organisms.

 Right! But to my knowledge, for structural annotations we need completely annotated genome of reference genome. Can you please comment on how to get it? Thank you!

In case of unknown sequenced genome, the only way to annotate it is to use a well annotated genome (having already some hint there are some how related). Nowadays it s quite complicated not to find it. You have for any specie, a bench of well annotated genomes. In worse cases you uptake the model organism as reference. Later making a blast, you may see more identity to other organisms and I would reuse them again for the structural annotation rather to go for a functional annotation.

Thank you for your explanation! Would you please comment on how can I get annotated genome of closer relative specifically!? 

I have another idea, your organism 's taxonomy is:

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Juncaceae; Juncus

I would go step by step back from genus to family to order, look for the genome sequenced and well annotated and use it as reference to annotate your organism structurally. If this step is precisely elaborated, you have then annotated your organism against the closely relative genome sequenced nowadays.

Later, blast your proteins against whole plant database and select your best hits (using script). Look at these proteins and try to find whether they belong to a sequenced genome or not. I guess not (supposing your search for the genome reference was well done). The blast will only provide information on more closely related organism if many proteins were investigated. Depending on the number you may generate a phylogenetic tree.

I found this hint:

https://books.google.de/books?id=U0D6CAAAQBAJ&pg=PA17&lpg=PA17&dq=genome+of+any+specie+Juncaceae&source=bl&ots=1CIXS3g3aV&sig=jx-WuMqOoTpHIZDbYZ7mnGfA6Vw&hl=de&sa=X&ved=0ahUKEwiipPLWlanUAhUCchQKHbqCAfgQ6AEIXDAG#v=onepage&q=genome%20of%20any%20specie%20Juncaceae&f=false

Poales is the order of oryzae sativa, in worse cases you may use it as reference.

Let me know if my idea was clear.

Best

Loubna

Finding a closest relative is one thing. If you want to use it as a reference for your own annotations, you should also take into account the quality of the annotations.

Many less-well studied organisms only have indirect annotations based on model species. If those are your closest relatives, you could as well go back to a slightly more distantly related species with more trustworthy annotations.