New Citrus Genome Sequence Resources

The International Citrus Genome Consortium (ICGC) released 2 annotated genome assemblies in January 2011, one a Sanger based sequence of a haploid derived from Clementine mandarin to serve as the citrus reference genome, and the other a 454 technology-based sequence of a diploid sweet orange, Ridge Pineapple. Since then, additional work has been carried out by ICGC collaborators to integrate the haploid genome sequence with a high density genetic linkage map populated with sequence derived markers. This has enabled the assembly of the genome into 9 pseudomolecules, representing the basic citrus chromosome number. Efforts to improve the more fragmented sweet orange genome assembly are proceeding, as well. SNPs have been mined from BAC end sequences of Ridge Pineapple, and 1536 were selected for a GoldenGate Custom Panel to be used for genotyping a family of hybrids between sweet orange and Poncirus trifoliata, leading to subsequent integration of the sweet orange genome sequence with physical and genetic linkage maps. Currently there are several models proposed that describe the possible phylogenic origins of sweet orange and Clementine mandarin, which address the complex introgressions of pummelo and mandarin germplasm. Several additional citrus genomes have been or will be sequenced, including Ponkan mandarin, Willowleaf mandarin (believed to be one parent of Clementine mandarin), and a typical pummelo accession. Together, assignment of haplotypes throughout the genomes made possible by these additional sequence resources should lead to a robust and consistent model to explain the phylogeny of sweet orange, the most commercially significant citrus fruit.