Genome Survey Sequencing of Nomocharis forrestii, Assembly of Its Complete Chloroplast Genome and Analysis of Simple Sequence Repeat (SSR) Markers

Abstract

Background: Nomocharis is a genus that is closely related to Lilium in the Liliaceae family. It’s useful to study the influence of the uplift of the Qinghai-Tibet Plateau on plants and their biological diversity. Nomocharis is a genus of such plants, and research on this genus will be especially informative, considering the genetic diversity of flowers. However, the genetic information of Nomocharis has not been fully elucidated. Results: To obtain a complete Nomocharis reference genome, the paper first performed a general survey. Next-generation sequencing (NGS) was utilized to perform de novo sequencing of the entire Nomocharis forrestii genome. In this study, the sequencing process yielded approximately 137.4 Gb of high-quality data, the total sequencing depth was approximately 63X, and the Q30 ratio was 91.95%; the estimated genome size was approximately 2.17 Gb; the repetitive sequence content was approximately 84.7%, the heterozygosity rate was 3.99%, and the estimated GC content of the genome was 43%. Furthermore, an annotated circular chloroplast gene map was generated, and a preliminary evolutionary analysis was performed. In addition, a total of 78,045 high-quality SSR markers were developed. Conclusion: Nomocharis forrestii has a 2.17 Gb heterozygous genome, its SSR markers are predominantly dinucleotides, and its chloroplast genome shows that Nomocharis forrestii and Lilium bakerianum have the highest homology followed by Lilium distichum. To the best of our knowledge, this report describes the first de novo whole-genome sequencing and assembly process to be performed for Nomocharis. The results of this study may provide new resources for the future genetic analysis and molecular breeding of Nomocharis.