The chromosome-scale genome assembly, annotation and evolution of Rhododendron henanense subsp. lingbaoense.

Rhododendron henanense subsp. lingbaoense (hereafter referred to as R. henanense) is an endemic species naturally distributed in the Henan province, China, with high horticultural, ornamental and medicinal value. Herein, we report a de novo genome assembly for R. henanense using a combination of PacBio long read and Illumina short read sequencing technologies. In total, we assembled 634.07 Mb with a contig N50 of 2.5 Mb, representing ~96.93% of the estimated genome size. By applying Hi-C data, 13 pseudochromosomes of R. henanense genome were assembled, covering ~98.21% of the genome assembly. The genome was composed of ~65.76% repetitive sequences and 31,098 protein-coding genes, 88.77% of which could be functionally annotated. Rhododendron henanense displayed a high level of synteny with other Rhododendron species from the Hymenanthes subgenus. Our data also suggests that R. henanense genes related to stress responses have undergone expansion, which may underly the unique abiotic and biotic stress resistance of the species. This alpine Rhododendron chromosome-scale genome assembly provides fundamental molecular resources for germplasm conservation, breeding efforts, evolutionary studies, and elucidating the unique biological characteristics of R. henanense.

[Determination of 9 isoflavonoids in Puerariae Lobatae Radix with quantitative analysis of multi-components by single marker].

A method for determination of 9 isoflavones in Puerariae Lobatae Radix was established and the accuracy and feasibility of the method were verified. The relative correction factors of eight isoflavonoids,3'-hydroxy puerarin,puerarinapioside,3'-methoxy puerarin,puerarin 6″-O-xyloside,daidzin,genistin,formononetin and daidzein were determined by HPLC method with puerarin as the internal standard. The contents of 9 isoflavonoids in 11 batches of samples were determined by external standard method and QAMS.The accuracy and feasibility of the methods were evaluated by comparison of the quantitative results between external standard method and QAMS. The reproducibility of the relative correction factors was good under different experimental conditions,and there was no significant difference between the external standard method of the 9 compounds and the content of QAMS method. The results showed that using puerarin as an internal standard to simultaneously determine the 8 isoflavonoids mentioned above is accurate and feasible. Thus,it can be used as quality control of Puerariae Lobatae Radix.

The complete chloroplast genome sequence of Gentiana lawrencei var. farreri (Gentianaceae) and comparative analysis with its congeneric species.

BACKGROUND: The chloroplast (cp) genome is useful in plant systematics, genetic diversity analysis, molecular identification and divergence dating. The genus Gentiana contains 362 species, but there are only two valuable complete cp genomes. The purpose of this study is to report the characterization of complete cp genome of G. lawrencei var. farreri, which is endemic to the Qinghai-Tibetan Plateau (QTP). METHODS: Using high throughput sequencing technology, we got the complete nucleotide sequence of the G. lawrencei var. farreri cp genome. The comparison analysis including genome difference and gene divergence was performed with its congeneric species G. straminea. The simple sequence repeats (SSRs) and phylogenetics were studied as well. RESULTS: The cp genome of G. lawrencei var. farreri is a circular molecule of 138,750 bp, containing a pair of 24,653 bp inverted repeats which are separated by small and large single-copy regions of 11,365 and 78,082 bp, respectively. The cp genome contains 130 known genes, including 85 protein coding genes (PCGs), eight ribosomal RNA genes and 37 tRNA genes. Comparative analyses indicated that G. lawrencei var. farreri is 10,241 bp shorter than its congeneric species G. straminea. Four large gaps were detected that are responsible for 85% of the total sequence loss. Further detailed analyses revealed that 10 PCGs were included in the four gaps that encode nine NADH dehydrogenase subunits. The cp gene content, order and orientation are similar to those of its congeneric species, but with some variation among the PCGs. Three genes, ndhB, ndhF and clpP, have high nonsynonymous to synonymous values. There are 34 SSRs in the G. lawrencei var. farreri cp genome, of which 25 are mononucleotide repeats: no dinucleotide repeats were detected. Comparison with the G. straminea cp genome indicated that five SSRs have length polymorphisms and 23 SSRs are species-specific. The phylogenetic analysis of 48 PCGs from 12 Gentianales taxa cp genomes clearly identified three clades, which indicated the potential of cp genomes in phylogenetics. DISCUSSION: The "missing" sequence of G. lawrencei var. farreri mainly consistent of ndh genes which could be dispensable under chilling-stressed conditions in the QTP. The complete cp genome sequence of G. lawrencei var. farreri provides intragenic information that will contribute to genetic and phylogenetic research in the Gentianaceae.

Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.).

Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae]), native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR) markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1-6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assembled genome of jujube. The density of SSRs in jujube was 872.60 loci/Mb, which was much higher than in A. thaliana (221.78 loci/Mb). (A+ T)-rich repeats were dominant in the jujube genome. We then randomly selected 100 SSRs in the jujube genome with long repeats and used them to successfully design 70 primer pairs. After screening using a series of criteria, a set of 20 fluorescently labeled primer pairs was further selected and screened for polymorphisms among three jujube populations. The average number of alleles per locus was 12.8. Among the three populations, mean observed and expected heterozygosities ranged from 0.858 to 0.967 and 0.578 to 0.844, respectively. After testing in three populations, all SSRs loci were in Hardy-Weinberg equilibrium (HWE) in at least one population. Finally, removing high null allele frequency loci and linked loci, a set of 17 unlinked loci was in HWE. These markers will facilitate the study of jujube genetic structure and help elucidate the evolutionary history of this important fruit crop.

[Spatial distributions of OH radicals and O atoms in argon hollow needle-plate discharge in ambient air].

In the present work, the spatial distributions of OH radicals and O atoms were studied in argon hollowneedle-plate discharge in ambient air. A 3 cm long plasma torch was generated in the discharge. The optical emission spectrum from 300 to 800 nm was collected. Besides Ar I lines and N2 second positive band system, OH emission band around 309 nm, O line at 777.4 nm and weaker H line were found in the optical emission spectrum. Because OH radicals and O atoms play an important role in material surface modification, the relative intensities of the OH radicals band (around 309 nm) and O atom line (777.4 nm) were analyzed. The results show that the number of OH radicals decreases rapidly and the number of O atoms follows a rule of increasing firstly and then decreasing from are root to arc tip.

Feasibility of building robust surface electromyography-based hand gesture interfaces.

This study explored the feasibility of building robust surface electromyography (EMG)-based gesture interfaces starting from the definition of input command gestures. As a first step, an offline experimental scheme was carried out for extracting user-independent input command sets with high class separability, reliability and low individual variations from 23 classes of hand gestures. Then three types (same-user, multi-user and cross-user test) of online experiments were conducted to demonstrate the feasibility of building robust surface EMG-based interfaces with the hand gesture sets recommended by the offline experiments. The research results reported in this paper are useful for the development and popularization of surface EMG-based gesture interaction technology.