Genome sequencing for biodiversity, from one genome study to the phylogenomic study

Genomic researches on non-human model organisms have been tremendously developed during these ten years after finishing human genome project. The recent emergency of sequencing technologies have greatly reduced the sequencing cost, thus promoted the larger scale of genomic researches, e.g. from individual genome to population genomics, from single species to the whole phylogenomic sequencing. Within these two years, we at BGI have finished over 150 animal genomes, covering various taxonomies from the basal Nematode and Platyhelminthes to primates, and have revealed their unique genome features which consistent with their molecular adaptations.

For example, the naked mole rat is one of the animals with various extremely special traits. They are strictly subterranean, extraordinarily long-lived eusocial mammal, living in full darkness, at low oxygen and high carbon dioxide concentrations, and are unable to sustain thermogenesis nor feel certain types of pain.  With the available of the naked mole rat genome and the transcriptome information, we have uncovered many distinct gene evolutionary events and gene regulation patterns in this animal. For instant, a large number of genes have loss or pseudogenized leading to the poor visual function of naked mole rats and their dark adaptation.

Since the genomic tools have become routine, genomics has penetrated all areas of the life science. Group of species genome sequencing and digital decoding the tree of life are not longer the mirage. Several large scope international consortiums, in which BGI plays as a key role, like the Vertebrate Genome 10K Project, 1K Insect Transcriptome Evolution Project, and Insect 5K Project have been initiated and will soon provide new insights for our understanding of biodiversity. For example, the systematic relationships within the class Aves have been heavily debated for centuries. We have initiated the phylogenomic analysis of complete genome sequences of 50 carefully chosen key bird taxa, to resolve the systematics of the class Aves once and for all. This trial would provide a demo case for building the real digital tree of life. Overall, we are just entering a new era of the phylogenomic study, a filed that will provide us a comprehensive view of the biodiversity.