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I'am trying to create a phylogeny tree from some plants, as the post's title says, to help me conclude which of those plants are closer genetically with another one plant.

So let's say that this is the plant list:

Nicotiana tabacum , Zea mays, Oryza sativa, Solanum lycopersicum, Solanum tuberosum, Erythranthe guttata, Hordeum vulgare, Vitis vinifera, Prunus persica, Glycine max, Populus trichocarpa, Medicago truncatula, Phaseolus vulgaris, Morus notabilis, Citrus clementina, Setaria italica, Theobroma cacao, Acacia mangium, Cicer arietinum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Panax ginseng

and i want to see which of those species is closer with Sorghum bicolor.

Is there any easy way to conclude something like that or it needs to get results out of bioinformatics using a specific gene , align it , and then see the tree ?

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  • $\begingroup$ If you want to compare the relationship, you need to use a gene which is present in all plants you list here and then do a comparision. This will allow you to build such a tree. $\endgroup$ – Chris Jun 2 '14 at 14:05
  • $\begingroup$ Ok. i have took one gene and translated into protein for all these plants. Aligned them and now which algorithm should i use to produce the phylogeny tree ? $\endgroup$ – F.N Jun 2 '14 at 16:15
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    $\begingroup$ Single gene trees are unreliable. You should concatenate and align at least 50 genes, e.g. ribosomal proteins, and then build a tree with e.g. RAxML and PhyloBayes. Be sure to pick an out group wisely too.. $\endgroup$ – 5heikki Jun 2 '14 at 20:05
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In general for plants, before you start trying to make your own phylogeny, you should try to find an existing phylogeny. Phylogenetics is complex, and a lot of people have already done the hard work. You can start by looking at the Angiosperm Phylogeny to figure out which species are most closely related. To make use of the tree you will usually have to look up each species to figure out what order or family it is in.

Angiosperm Phylogeny 3 model species tree

In this particular case, Sorghum bicolor is a grass, so of course it's going to be closed to Zea, Oryza, Setaria and Brachypodium (all grasses) than any of the others. You can see where it places relative to the other grasses by looking at a grass-specific phylogeny. Because all three are model species, their phylogenetic placement relative to one another is well established. A simple Google image search for [grass model species phylogeny] gives you your answer (from the Setaria genome paper):

enter image description here

This shows you that Sorghum is closest to Zea out of the species you listed.

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