Abstract
Phylogenomics is the study of evolutionary histories among organismal lineages based on comparative analysis of genome-scale data. Until recent years, the application of phylogenomics in algal research had been limited by data availability. With the increasing affordability of sequencing technologies, algal research, alongside other disciplines of life sciences, is now inundated with large amount of sequencing data, including but not limited to genomes, transcriptomes and epigenomes. In the past 5 years, we have seen a surge of published reports and data of new algal genomes, and this trend is showing no signs of slowing down. These novel genomes provide an exciting analysis platform for understanding algal biology, ecophysiology and diversity, and at a broader scale, eukaryote evolution. Phylogenomic approaches allow for addressing interesting biological questions at scale that was previously unimaginable. This chapter highlights the importance and current trends of phylogenomics in algal research. The limitations and future perspectives of algal phylogenomics are discussed in light of the on-going deluge of sequencing data.
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