Whole-genome sequencing and analysis of Apocynum cannabinum

Abstract

Backgroud Apocynum cannabinum is an important plant resource from the Apocynaceae family. However, the lack of complete genome information has severely impeded research progress of molecular biology research in this plant. Whole-genome sequencing can provide an in-depth understanding of species growth, development, and evolutionary origin, and is the most effective method for scientifically exploring the ecological and economic value of a plant. Methods and results In this study, we employed Illumina HiSeq, single-molecule real-time sequencing, 10X genomics linked reads, and chromatin interaction (Hi-C), a new assembly technique, to successfully assemble the whole draft genome for A.cannabinum (260 Mb). The super-scaffold N50 genome size from the Hi-C assisted assembly was 21.16 Mb and was anchored to 11 chromosome, resulting in a high-quality reference genome at the chromosome level (2n = 2x = 22). We further annotated, analyzed, and predicted 22,793 protein-coding genes, of which the functions of 95.6% were already annotated, 92.3% contained conserved protein domains, and 78.7% were aligned to known metabolic pathways. Colclushions This high-quality A.cannabinum genome can be used to analyze growth and development and evaluate gene evolution at the genome level, as well as assist in the comparative genomics and genetic modification of other important medicinal plants in Apocynaceae. Comparative analysis of the gene families showed that A. cannabinum speciated around 35.8 (27.0–46.9) million years ago.