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The total number of species in the world has been estimated to over 874 million.To explore the phylogenetic and evolutionary relationship between species with better resolution,we aimed to explore several useful molecular markers like microsatellite DNA,mitochondrial DNA,chloroplast DNA as well as nuclear DNA from animals and plants in a systematic and cost-effective manner.By using deep sequencing technology with HiSeq/MiSeq platform and de novo assembly,we have successfully fimished the draft genome sequencing for more than 50 different animal and plant species in Taiwan.A simple computational pipeline has been established to deduce the complete mitogenome,plastid genome and rDNA locus from whole genomic reads without pre-isolating the organelles by ultracentrifugation.Furthermore,we also developed a cost-effective skimmed NGS technology to deduce the complete mitogenome and plastid genome from a pooled genomic library.By using species-specific COXI sequence as a bait,we performed gene mapping and de novo assembly to extend the length of mitogenome contigs.Finally,we were able to deduce the species-specific mitogenome from a pooled genomic library containing mixed genomic DNA isolated from multiple species.Due to the success development of skimmed genome decoding technologies,more than 30 scientific papers have been published by our collaborators in the past one years.We would like to take this chance to share the know-how and key steps on performing skimmed NGS technology with the research community.