The 0.2 scale bar at the bottom makes the distances seem huge.  Did you translated the mRNA open reading frames to protein?  Is the tree based on the protein alignment, or RNA?  What program did you use for the multiple sequence alignment?

thanks Brian, no i did not translate the sequences. the tree is based on RNA (cDNA). I used MEGA 6 software.

Did the multiple sequence alignment look good? 

since the sequences are of variable length, some very short and others very long, even though alignment was pretty good.

Actually i want to know if someone has done it or some other related study in some other plant or there is any paper which is directly related to it.

if there are recognised groups of zinc fingers like MYBs in arabidopsis, so that i could use those sequences as check or template sequences to see if my genes conform with that grouping.

hope you understood me.

thanks again for your kind reply.

MEGA has many methods of phylogenetic reconstruction included in the package.  Some of those methods such as neighbor-joining will not do well if the sequences do not all have at least several hundred bases of overlap.  Usually there is no error message if the data is not appropriate, it just produces a tree even if the tree is essentially meaningless.  I suspect you will get far better results if you translate each zinc finger protein cDNA sequence into its zing finger protein and then use the protein sequence to categorize which group it belongs to.  It may only be reasonable to attempt phylogenetic reconstruction within each group and not between all groups.

Zinc fiinger domains are fairly small and most likely did not all share a common ancestor but instead were derived by convergent evolution.

http://www.rcsb.org/pdb/101/motm.do?momID=87