A draft genome for Spatholobus suberectus

Abstract

Spatholobus suberectus Dunn (S. suberectus), which belongs to the Leguminosae, is an important medicinal plant in China. Owing to its long growth cycle and increased use in human medicine, wild resources of S. suberectus have decreased rapidly and may be on the verge of extinction. De novo assembly of the whole S. suberectus genome provides us a critical potential resource towards biosynthesis of the main bioactive components and seed development regulation mechanism of this plant. Utilizing several sequencing technologies such as Illumina HiSeq X Ten, single-molecule real-time sequencing, 10x Genomics, as well as new assembly techniques such as FALCON and chromatin interaction mapping (Hi-C), we assembled a chromosome-scale genome about 798 Mb in size. In total, 748 Mb (93.73%) of the contig sequences were anchored onto nine chromosomes with the longest scaffold being 103.57 Mb. Further annotation analyses predicted 31,634 protein-coding genes, of which 93.9% have been functionally annotated. All data generated in this study is available in public databases.

Fig. 1

Morphological character of S. suberectus. (a) A picture of S. suberectus plant. (b) The vine stem of S. suberectus is called “chicken blood vines”. (c) The pod of S. suberectus has only one seed.

Fig. 2

Estimation of S. suberectus genome size by K-mer analysis.

Fig. 3

Diagrammatic sketch of the annotation pipeline.

Fig. 4

Circos Plot Showing the Genomic Features of S. suberectus. Concentric circles, from outermost to innermost, show (a) gene density (blue), (b) tandem repeats density (green), (c) transposon element density (purple), (d) LTR-Copia density (yellow), (e) LTR-Gypsy density (red) and intra-genome collinear blocks connected by curved lines. All distributions are drawn in a window size of 300 kb, chromosomes_ scale = 5,000,000 bp.