Genome Annotation, In silico Tools and Databases with Special Reference to Moso Bamboo

The first complete plant genome sequence, Arabidopsis thaliana, was reported and published in 2000, marking the beginning of the plant genome era. Over the past 20 years, draft or reference genomes of approximately 800 plant species have been sequenced and the number continues to grow exponentially. The release of these plant genomes has dramatically advanced studies in various disciplines of plant biology. With tremendous advances in sequencing technology and the initiation of many genome sequencing and updating projects, improving the accuracy of the genome annotation stage remains challenging. This is because only a few genomes are available as annotation standards achieved through enormous investments in human curation efforts. Therefore, high-quality genome annotation, as one way of summarizing the existing knowledge of the genomic characteristics of an organism, will be one of the principal research focuses for the plant genome. In addition, genome annotation will play an essential role in some challenging fields in the future, i.e., dissecting information from plant pan-genomes. Here, we summarize the progress of plant genome annotation and the challenges of annotating more complex plant genomes and present state-of-the-art tools and databases for this process.