High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant.

Background: Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation remain unknown. Hence, a high-quality reference genome will be very valuable for marker-assisted breeding, genome editing, and molecular genetics. Findings: We generated 66 Gb and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using Pacific Biosciences (PacBio) single-molecule real-time and Illumina HiSeq sequencing platforms. The PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 Mb and a total length of 808 Mb. The repetitive sequences identified accounted for 57.52% of the genome sequence, and 54,008 protein-coding genes were predicted collectively with ab initio and homology-based gene prediction from the masked genome. The divergence time between S. splendens and Salvia miltiorrhiza was estimated at 28.21 million years ago (Mya). Moreover, 3,797 species-specific genes and 1,187 expanded gene families were identified for the scarlet sage genome. Conclusions: We provide the first genome sequence and gene annotation for the scarlet sage. The availability of these resources will be of great importance for further breeding strategies, genome editing, and comparative genomics among related species.

[Effects of root-excision on trunk hydraulic traits and growth status of Ginkgo biloba].

The roots of 8-year-old Ginkgo biloba saplings were partially excised to three degrees to study the effects of root-excision on the trunk hydraulic traits and growth status of the saplings. The three degrees were severe, medium, and light (8:1, 10:1, and 12:1 of excised root diameter to base diameter of tree trunk, respectively). Physiological parameters including trunk ultrasound acoustic emission (UAE) signal, branch percentage loss of hydraulic conductance (PLC), sap flow flux, and leaf stomatal conductance, transpiration rate and water potential were measured periodically after root-excision. In all treatments, a great number of trunk UAE signal produced after a short time of root-excision, peaked at 6 h, and decreased gradually then. The intensity of the UAE signals increased with increasing root-excision degree. After root-excision, the branch PLC increased rapidly in the first 12 h but slowly after 24 h. The sap flow flux, leaf stomatal conductance, transpiration rate and water potential after root-excision decreased obviously, with significant differences among the three treatments. The cumulative number of UAE signals (cUAE) was significantly and positively correlated with branch embolism degree, while negatively correlated with sap flow flux and leaf water potential. The leaf area and new branch length of G. biloba in the next year after root-excision decreased significantly, and the decrement was increased with root-excision degree. Root-excision not only made the degrees of conduits cavitation and branch embolism increased, but also affected water transportation and leaf transpiration rate within a short period of time, which would in turn give an impact on G. biloba plant growth.