Characterization of Firmiana danxiaensis plastomes and comparative analysis of Firmiana: insight into its phylogeny and evolution

BACKGROUND

Firmiana danxiaensis is a critically endangered and ecologically important tree currently only found in four locations in Danxia or Karst habitats in northern Guangdong Province, China. The specialized habitat preference makes it an ideal model species for study of adaptive evolution. Meanwhile, the phylogenetic relationships of F. danxiaensis in four locations under two landforms are unclear. Therefore, we sequenced its complete chloroplast (cp.) genomes and conducted comprehensive interspecific and intrageneric plastome studies.

RESULTS

The F. danxiaensis plastomes in four locations showed a typical quadripartite and circular structure that ranged from 160,832 to 161,206 bp in size, with 112 unique genes encoded. Comparative genomics showed that the plastomes of F. danxiaensis were relatively conserved with high similarity of genome organization, gene number, GC content and SSRs. While the genomes revealed higher biased codon preferences in Karst habitat than those in Danxia habitats. Eighteen and 11 divergent hotpots were identified at interspecific and intrageneric levels for species identification and further phylogenetic studies. Seven genes (clpP, accD, ccsA, ndhH, rpl20, rpoC2, and rps4) were under positive selection and may be related to adaptation. Phylogenetic analysis revealed that F. danxiaensis is sister to F. major and F. simplex. However, the interspecific relationships are not consistent with the habitat types.

CONCLUSIONS

The characteristics and interspecific relationship of F. danxiaensis plastomes provide new insights into further integration of geographical factors, environmental factors, and genetic variations on the genomic study of F. danxiaensis. Together, our study will contribute to the study of species identification, population genetics, and conservation biology of F. danxiaensis.

Proposal to recognise the tribes Adinobotryeae and Glycyrrhizeae (Leguminosae subfamily Papilionoideae) based on chloroplast phylogenomic evidence

Within the legume family, the taxonomic status of subtribe Glycyrrhizinae of tribe Galegeae and of the genus Adinobotrys has been re-assessed. Based on genome skimming data, we conducted phylogenomic analyses of the inverted repeat-lacking clade within subfamily Papilionoideae. The results support the sister relationship between Glycyrrhizeae and Adinobotrys. Glycyrrhizeae is resurrected based on Glycyrrhiza and Glycyrrhizopsis, and a new tribe, Adinobotryeae, is proposed to accommodate Adinobotrys.

The complete chloroplast genome of desert spiny semi-shrub Alhagi sparsifolia (Fabaceae) from Central Asia

Alhagi sparsifolia is a sand-resistant subshrub and food resource for camels in the desert and semi-desert areas of Central Asia. In China, this is the olny Alhagi species and it is restricted in the Northwestern region. Its complete chloroplast genome was sequenced using the Illumina Hiseq X-Ten platform. The genome lacks an inverted repeat (IR) region, containing 74 protein-coding genes, 30 tRNAs genes, and four rRNAs. The overall GC content is 43.6%. Based on the chloroplast genome sequence, a maximum-likelihood (ML) tree was constructed along with its 15 taxa, indicating that A. sparsifolia belong to the tribe Hedysareae, which nested in IRLC group of the subfamily Papilionoideae (Fabaceae).

[Epidemiological study of bone and joint injury based on urban medical insurance database]

OBJECTIVE

To estimate the prevalence rate of bone and joint injury in China and to describe the three-dimension distribution of the disease (area, time and people).

METHODS

Based on a cross-sectional design, a retrospective study was conducted by using Chinese basic medical insurance database from January 1, 2013 to December 31, 2017 to analyze the epidemiological characteristics of bone and joint injury. The prevalence rate of bone and joint injury in each city was calculated, and then using meta-analyses to estimate the pooled prevalence of each area and the whole country. The pooled prevalence rates were compared among the different groups of populations, in terms of geographical area, time and population characteristics (age and gender).

RESULTS

A total of 28 419 264 subjects were included in this study, including 705 793 patients with bone and joint injury. From 2013 to 2017, in Chinese basic medical insurance database, the overall prevalence rate of bone and joint injury was 141.5(95%CI: 90.4－203.7) per 10 000 population, and the prevalence rates of non-specific or polyarticular disease, knee disease, and shoulder disease were 101.6 (95%CI: 63.5－148.4)per 10 000 population, 22.5(95%CI:15.1－31.4)per 10 000 population and 10.9 (95%CI: 6.4－16.4)per 10 000 population. The prevalence rates varied across the areas, the highest rate was observed in North China, with the prevalence of 310.6 (95%CI: 12.6－989.7) per 10 000 population, and the lowest rate was observed in Southwest China, with the prevalence of 59.0 (95%CI: 37.5－85.2) per 10 000 population. The prevalence rate of bone and joint injury increased over the study period, from 111.1 (95%CI: 56.0－182.5)per 10 000 population in 2013 to 175.5 (95%CI: 116.8－245.5)per 10 000 population in 2017. The prevalence of bone and joint injury in the female population was 149.1 (95%CI: 94.2－215.9) per 10 000 population, which was higher than that of men [133.6(95%CI: 86.2－190.9) per 10 000 population]. The higher prevalence of knee disease, unspecified or polyarticular disease, and bone and joint injury were observed in people aged 60 years and older, while the prevalence of shoulder disease peaked in 40－59 years old people [20.6 (95%CI: 12.5－30.5) per 10 000 population].

CONCLUSION

This study reported a relative low prevalence of bone and joint injury in China from 2013 to 2017. The prevalence increased over the study period, and the highest prevalence rate was observed in North China. The prevalence rate showed differences among different groups of populations, and higher rates were observed in females and people aged 60 years and older.

The complete chloroplast genomes of rare medical herb Glycyrrhiza inflata and its relative G. aspera (Fabaceae)

Glycyrrhiza inflata is a threatened perennial herb with medicinal value, which restricts in NW China and Mongolia. Its ally species, G. aspera, is widely distributed from northern China to Turkey. The complete chloroplast genomes were sequenced using the Illumina Hiseq X-Ten platform. Each of the genomes lacks an inverted repeat (IR) region, containing 76 protein-coding genes, 30 tRNAs genes, and 4 rRNAs. The overall GC contents are both 34.3%. A phylogenetic tree based on the whole chloroplast genomes of 15 species indicated that G. aspera and G. inflata belonged to a monophyletic Glycyrrhiza, which was nested in IRLC group of the subfamily Papilionoideae (Leguminosae).

Ethnobotanical survey of herbal tea plants from the traditional markets in Chaoshan, China

ETHNOPHARMACOLOGICAL RELEVANCE

Herbal tea, which refers to "cooling tea", "cool beverage", or "liáng chá" in China, includes a range of drinks with heat-clearing and detoxification qualities. Herbal tea plants are great contributive to the health and prosperity of Chaoshan people. The aim of the study was to document herbal tea plant species used and commercialized as "liáng chá" in Chaoshan area, to facilitate the use and development of herbal tea enterprises, and to promote the further development of national herbal tea.

MATERIALS AND METHODS

Information and data were obtained from all 83 stall holders in 12 traditional markets, semi-structured informant interviews were carried out individually with the stall holders, 10 questions were asked.

RESULTS

In this study, 186 species of herbal tea plants belonging to 65 families and 156 genera were indicated by 83 stall holders, with Asteraceae being the most prevalent family with 22 species. Herbs are main sources of herbal tea plants in Chaoshan area, with whole plants (97 species) being the most used parts. Herbal drinks are mostly consumed for heat-clearing and detoxification, and a large number of plant species were reported to treat coughs, colds, dysentery, dampness and sore throats. The most cited species were Hedyotis corymbosa (L.) Lam. (47 times mentioned), Hedyotis diffusa Willd. (46), Plantago asiatica L. (43), Houttuynia cordata Thunb (42), Centella asiatica (L.) Urban (36), Desmodium styracifolium (Osbeck) Merr. (35) and Morus alba L. (31), and 5 protected species were recorded in the list of the nationally protected species of China: Dendrobium officinale Kimura et Migo, Dendrobium nobile Lindl., Anoectochilus formosanus Hayata, Bulbophyllum odoratissimum (J. E. Smith) Lindl. and Pholidota chinensis Lindl. The selling price of most fresh herbal tea plants in the market varied from￥10-16/kg, with the profit margin of sales ranging from 12.5% to 20%. The consumption of herbal tea for one family costs about ￥3-5/day.

CONCLUSION

Chaoshan herbal teas, prepared by diverse plant species, are regarded as a long tradition inseparable part in daily life of local people. Although they can effectively prevent and treat different kinds of diseases, they are not suitable for everyone (e.g. the elderly, children, and pregnant or breastfeeding women), even in healthy people, improper use of herbal tea can lead to physical discomfort. Furthermore, in order to appropriately understand the function, efficacy, and safety of herbal tea plants, additional research of traditional practices and phytochemistry, nutrient, physiological and toxicity properties should be analyzed.

Parallel, self-organizing, hierarchical neural networks with continuous inputs and outputs

Parallel, self-organizing, hierarchical neural networks (PSHNN's) are multistage networks in which stages operate in parallel rather than in series during testing. Each stage can be any particular type of network. Previous PSHNN's assume quantized, say, binary outputs. A new type of PSHNN is discussed such that the outputs are allowed to be continuous-valued. The performance of the resulting networks is tested in the problem of predicting speech signal samples from past samples. Three types of networks in which the stages are learned by the delta rule, sequential least-squares, and the backpropagation (BP) algorithm, respectively, are described. In all cases studied, the new networks achieve better performance than linear prediction. A revised BP algorithm is discussed for learning input nonlinearities. When the BP algorithm is to be used, better performance is achieved when a single BP network is replaced by a PSHNN of equal complexity in which each stage is a BP network of smaller complexity than the single BP network.