Recent progress in phylogenomic methods

Phylogenomics is the intersection of the fields of phylogenetics and genomics, aiming to use genome-scale molecular data to resolve the phylogenetic relationships among organisms. In this review, we briefly introduced five methods of data collection in phylogenomics by high-throughput sequencing: targeted amplicon sequencing, transcriptome sequencing, reduced-genome-representation sequencing, target sequence capture, and low coverage whole-genome shotgun sequencing. We summarized and compared the characteristics, applications and costs of each method. In addition, we reviewed the current work flow of data processing of a typical phylogenomic analysis, including five steps: data preprocessing and assembly, orthologous sequences identification, sequence alignment, data quality control and phylogenetic tree reconstruction. We also summarized the key points of each step and introduced software that are used in these steps. Phylogenomics is a promising way to reconstruct the Tree of Life. However, it also faces a series of problems at present. For example, the analysis of genome-scale data will lead to a significant increase in computation time, the impact of systematic error will become more serious when the data size increases and different data sets may yield strongly supported but inconsistent results. In the end of this review, we summarized and discussed the latest studies concerning these issues and made some suggestions to deal with these problems in the future.