Hi Sachin:

For phylogenetic analysis in insects  you can combine data: total evidence (combined molecular and morphological data), combined molecular data, morphological data, mitochondrial DNA and nuclear DNA. All datasets can be subjected to maximum-parsimony (MP), parsimony bootstrap (BS) and partitioned Bayesian likelihood analyses. Genes selected for sequencing are widely used across phylogenetic studies of insects and selected to allow comparison between species.  For partitioned Bayesian likelihood analyses you can amplify and sequence several molecular partitions or gene regions: the mtDNA genes COI, leucine tRNA and COII and the autosomal genes Wingless (Wg), Elongation factor 1-alpha (Ef1a), Tektin, Ribosomal Protein L5 (RpL5) and the sex-linked gene,Triose phosphate isomerase (Tpi). You can use published primers for specific groups of insects or specific orders to analize your samples.

Regards,

Luis Miguel

I agree with Luis Miguel. Good information.

Thanks for useful information

Both COI (mitochondreal) and ITS2 (ribosomal DNA), which are used with plant feeding mites.