Sequence analysis of Erianthus arundinaceus chromosome 1 isolated by flow sorting after genomic in situ hybridization in suspension

Erianthus arundinaceus is a wild relative of sugarcane (Saccharum officinarum L.) with many desirable agronomic traits for sugarcane genetic improvement. However, limited knowledge of the complex genome of hexaploid E. arundinaceus has impeded the development of required molecular tools. Dissecting complex genomes into single chromosomes can simplify analyses. The flow-cytometric sorting of a single chromosome of E. arundinaceus in a Saccharum–Erianthus introgression line is reported. A novel approach called genomic in situ hybridization in suspension was used to discriminate the alien chromosome from sugarcane chromosomes at the same size. A total of 218,000 E. arundinaceus chromosome 1 (EaC1) were sorted to >97% purity and amplified DNA was sequenced using Illumina and PacBio technologies. The resulting assembly had a 70.93 Mb contig sequence with an N50 of 19.62 kb. A total of 56.69 Mb repeat sequences were predicted, accounting for 79.1% of the chromosome and 2646 genes having a total length of 1.84 Mb that represented 2.59% of the chromosome. Of these genes, 1877 (70.9%) genes were functionally annotated. The phylogenetic relationship of E. arundinaceus with other species using the chromosome 1 sequence revealed that E. arundinaceus was distantly related to Oryza sativa and Zea mays, followed by Sorghum bicolor, and was closely related to S. spontaneum and Saccharum spp. hybrids. This study provides the first insights into the characteristics of EaC1, and the results will provide tools to support molecular improvement and alien introgression breeding of sugarcane.