Create phylogenetic tree of 144 species

Question

[anasjamshed]

I have 144 plant species and I want to their sequences to build a phylogenetic tree.

How can I get the sequences?

[manaswwm]

I think understanding what you want to base the phylogeny on is probably an even more important question. If you want to align the entire genomes of these 144 species and construct phylogeny then I do not know if that would be feasible at all. Not that I am an expert in phylogeny, but the amount of noise introduced within phylogenetic inferences is directly proportional to the number of species you use in making the tree, and, in my opinion, 144 is a very large number. You would first need to know exactly which regions of the genomes are you claiming to be potentially conserved/similar across all 144 species that you could base your phylogeny on.

[anasjamshed]

I dont want to take complete genome

[manaswwm]

Which is understandable, but what regions do you want to base the phylogeny on? If it is genes, then which genes? Do you have annotations for all 144 species?

[anasjamshed]

I don't have annotation, how can i get these?

[manaswwm]

One place would be Ensembl Plants but I doubt you would find all 144 species there so you will need to search elsewhere too