Genome Survey Sequencing and Genetic Background Characterization of Ilex chinensis Sims (Aquifoliaceae) Based on Next-Generation Sequencing

Abstract

Ilex chinensis Sims. is an evergreen arbor species with high ornamental and medicinal value that is widely distributed in China. However, there is a lack of molecular and genomic data for this plant, which severely restricts the development of its relevant research. To obtain the whole reference genome, we first conducted a genome survey of I. chinensis by next-generation sequencing (NGS) to perform de novo whole-genome sequencing. As a result, our estimates using k-mer and flow cytometric analysis suggested the genome size of I. chinensis to be around 618–655 Mb, with the GC content, heterozygous rate, and repeat sequence rate of 37.52%, 1.1%, and 38%, respectively. A total of 334,649 microsatellite motifs were detected from the I. chinensis genome data, which will provide basic molecular markers for germplasm characterization, genetic diversity, and QTL mapping studies for I. chinensis. In summary, the I. chinensis genome is complex with high heterozygosity and few repeated sequences. Overall, this is the first report on the genome features of I. chinensis, and the information may lay a strong groundwork for future whole-genome sequencing and molecular breeding studies of this species.