High throughput technology has prompted the progressive omics studies, including genomics and transcriptomics. We have reviewed the improvement of comparative omic studies, which are attributed to the high throughput measurement of next generation sequencing technology. Comparative genomics have been successfully applied to evolution analysis while comparative transcriptomics are adopted in com...

Comparative transcriptomics can now be conducted on organisms in natural settings, which has greatly enhanced understanding of genome-environment interactions. Here, we demonstrate the utility and potential pitfalls of comparative transcriptomics of wild organisms, with an example from three cyprinid fish species (Teleostei:Cypriniformes). We present extensively filtered and annotated transcrip...

INTRODUCTION: Transcriptomics and metabolomics are high-throughput technologies that are critical to contemporary biomedical sciences, measuring gene expression levels and metabolite concentrations, respectively. Effective methods of integrating metabolomics and transcriptomics data are highly desired. Gene and metabolic pathways represent accumulated expert knowledge in particular domains. LAS...

The evolution of new organs is difficult to study because most vertebrate organs evolved only once, more than 500 million years ago. An ideal model for understanding complex organ evolution is the placenta, a structure that is present in live bearing reptiles and mammals (amniotes), which has evolved independently more than 115 times. Using transcriptomics, we characterized the uterine gene exp...

Hydra continuously differentiates a sophisticated nervous system made of mechanosensory cells (nematocytes) and sensory-motor and ganglionic neurons from interstitial stem cells. However, this dynamic adult neurogenesis is dispensable for morphogenesis. Indeed animals depleted of their interstitial stem cells and interstitial progenitors lose their active behaviours but maintain their developme...

Evolution refers to the historic ‘‘unfolding’’ of organismal life on Earth, which already intrigued Greek philosophers. It cannot be studied directly—just as the plot of a theatre play cannot be inferred from watching the last second. Instead; we study the fossil record; also, synthetic biology has increasing power to mimic key steps in evolution. The comparative approach, however, remains most...

We have collected several valuable lessons that will help improve transcriptomics experimentation. These lessons relate to experiment design, execution, and analysis. The cautions, but also the pointers, may help biologists avoid common pitfalls in transcriptomics experimentation and achieve better results with their transcriptome studies.