Citrus genomes: past, present and future

Over the past decade, genome sequencing and assembly approaches have been greatly improved, resulting in the assembly of many genomes for citrus, including wild, domesticated, and citrus-related genomes. Improvements in technologies have led to assembled genomes with higher completeness, contiguity, quality, and accuracy that have greatly facilitated annotation and analysis. This review summarizes the evolution of the sequencing, assembly, and annotation technologies leading to citrus genomes over the past 11 years, a comprehensive evaluation of their quality, contiguity, and completeness, and the major findings and applications. Of the 50 genomes now available, 35 have been assembled to chromosome level and 15 to draft level, and 14 were haplotype-resolved assemblies. To date there have been four pangenome-wide studies for citrus. The very recent genomes assembled with long-read sequencing have achieved >99% and >98% assembly and annotation completeness (BUSCO), respectively. However, some early genomes are not of the same high quality as more recently sequenced genomes and would benefit from re-sequencing. A more comprehensive pangenome based upon a larger set of species and genotypes assembled at the haplotype level would allow genomics to deliver the maximum benefits for citrus improvement and research.