The development of SSR markers based on RNA-sequencing and its validation between and within Carex L. species.

BACKGROUND: Carex L. is one of the largest genera in the Cyperaceae family and an important vascular plant in the ecosystem. However, the genetic background of Carex is complex and the classification is not clear. In order to investigate the gene function annotation of Carex, RNA-sequencing analysis was performed. Simple sequence repeats (SSRs) were generated based on the Illumina data and then were utilized to investigate the genetic characteristics of the 79 Carex germplasms. RESULTS: In this study, 36,403 unigenes with a total length of 41,724,615 bp were obtained and annotated based on GO, KOG, KEGG, NR databases. The results provide a theoretical basis for gene function exploration. Out of 8776 SSRs, 96 pairs of primers were randomly selected. One hundred eighty polymorphic bands were amplified with a polymorphism rate of 100% based on 42 pairs of primers with higher polymorphism levels. The average band number was 4.3 per primer, the average distance value was 0.548, and the polymorphic information content was ranged from 0.133 to 0.494. The number of observed alleles (Na), effective alleles (Ne), Nei's (1973) gene diversity (H), and the Shannon information index (I) were 2.000, 1.376, 0.243, and 0.391, respectively. NJ clustering divided into three groups and the accessions from New Zealand showed a similar genetic attribute and clustered into one group. UPGMA and PCoA analysis also revealed the same result. The analysis of molecular variance (AMOVA) revealed a superior genetic diversity within accessions than between accessions based on geographic origin cluster and NJ cluster. What's more, the fingerprints of 79 Carex species are established in this study. Different combinations of primer pairs can be used to identify multiple Carex at one time, which overcomes the difficulties of traditional identification methods. CONCLUSIONS: The transcriptomic analysis shed new light on the function categories from the annotated genes and will facilitate future gene functional studies. The genetic characteristics analysis indicated that gene flow was extensive among 79 Carex species. These markers can be used to investigate the evolutionary history of Carex and related species, as well as to serve as a guide in future breeding projects.

Hedysarumqilianshanense sp. nov. (Fabaceae, Hedysareae), a new species from the Qilianshan Mountains in Gansu, China.

Hedysarumqilianshanensesp. nov. (Fabaceae, Hedysareae) is described and illustrated from the Qilianshan Mountains in Gansu, China. This new species is similar to H.przewalskii, but can be distinguished by its corolla being light purple to purple, standard 15-19 mm long, wings 14-16 mm long, keels 16-19 mm long, and the ovary and legume being glabrous. The new species can be easily distinguished from H.neglectum Ledeb. by its bract being shorter than the pedicel, and the ovary and legume being glabrous. Phylogenetic tree based on the nuclear ITS and ETS sequences shows that H.qilianshanense is sister to H.przewalskii, while the tree based on the plastid psbA-trnH, trnC-petN, trnL-F, trnS-G and petN-psbM sequences shows H.qilianshanense as sister to a clade consisting of H.hedysaroides, H.inundatum, H.americanum and H.neglectum. The new species is a diploid with the chromosome number 2n = 14. Based on morphological, phylogenetic and karyotypic evidence, the new species may originate from an ancient homoploid hybrid speciation event.

Developmental Programmed Cell Death Involved in Ontogenesis of Dictamnus dasycarpus Capitate Glandular Hairs.

Plant glandular trichomes have received much attention due to their commercial and biological value. Recent studies have focused on the development of various glands in plants, suggesting that programmed cell death (PCD) may play an important role during the development of plant secretory structures. However, the development processes and cytological characteristics in different types of plant secretory structures differed significantly. This study aims to provide new data on the developmental PCD of the capitate glandular hairs in Dictamnus dasycarpus. Light, scanning, immunofluorescence labeling, and transmission electron microscopy were used to determine the different developmental processes of the capitate glandular hairs from a cytological perspective. Morphologically, the capitate glandular hair originates from one initial epidermal cell and differentiates into a multicellular trichome characterized by two basal cells, two lines of stalk cells, and a multicellular head. It is also histochemically detected by essential oils. TUNEL-positive reactions identified nuclei with diffused fluorescence or an irregular figure by DAPI, and Evans blue staining showed that the head and stalk cells lost their viability. Ultrastructural evidence revealed the developmental process by two possible modes of PCD. Non-autolytic PCD was characterized by buckling cell walls and degenerated nuclei, mitochondria, plastids, multivesicular body (MVB), and end-expanded endoplasmic reticulum in the condensed cytoplasm, which were mainly observed in the head cells. The MVB was detected in the degraded vacuole, a degraded nucleus with condensed chromatin and diffused membrane, and eventual loss of the vacuole membrane integrity exhibited typical evidence of vacuole-mediated autolytic PCD in the stalk cells. Furthermore, protoplasm degeneration coupled with dark oil droplets and numerous micro-dark osmiophilic substances was observed during late stages. The secretion mode of essential oils is also described in this paper.

Characterization of the complete chloroplast genome of Gypsophila huashanensis Y. W. Tsui & D. Q. Lu, an endemic herb species in China.

Gypsophila huashanensis Y. W. Tsui & D. Q. Lu (Caryophyllaceae) is an endemic herb species to the Qinling Mountains in China. In this study, we characterized its whole plastid genome using the Illumina sequencing platform. The complete plastid genome of G. huashanensis is 152,457 bp in length, including a large single-copy DNA region of 83,476 bp, a small single-copy DNA region of 17,345 bp, and a pair of inverted repeat DNA sequences of 25,818 bp. The genome contains 130 genes comprising 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Evolutionary analysis showed that the non-coding regions of Caryophyllaceae exhibit a higher level of divergence than the exon regions. Gene site selection analysis suggested that 11 coding protein genes (accD, atpF, ndhA, ndhB, petB, petD, rpoCl, rpoC2, rps16, ycfl, and ycf2) have some sites under protein sequence evolution. Phylogenetic analysis showed that G. huashanensis is most closely related to the congeneric species G. oldhamiana. These results are very useful for studying phylogenetic evolution and species divergence in the family Caryophyllaceae.

The complete chloroplast genome of Carex agglomerata C. B. Clarke (Cyperaceae), an endemic species from China.

Carex agglomerata C. B. Clarke is a sedge with excellent ornamental characters, it is an important ecosystem stabilizer. Here we report the complete chloroplast genome of C. agglomerata to provide a foundation for further phylogenetic studies on the Cyperaceae. The chloroplast (cp) genome is 184,157 bp in size and consists of a large single-copy (LSC) region 106,654 bp in length, a small single-copy (SSC) region of 36,099 bp, two inverted repeats (IR) regions each 20,702 bp. The total GC content of the cp genome is 33.9% with the LSC, SSC, and IR regions 32, 32.5, and 42.9%, respectively. The cp genome contains 128 genes, including 80 protein-coding, 40 tRNA, and eight rRNA genes. The phylogenetic analysis showed C. agglomerata is in a clade with Carex neurocarpa Maxim and Carex siderosticta Hance. This study provides a basis for further phylogenetic studies of Carex.

Impact of continuous Panax notoginseng plantation on soil microbial and biochemical properties.

Panax notoginseng is a highly regarded medicinal plant that has been cultivated for more than 400 years in Southwest China. The obstacles associated with the continuous cropping of P. notoginseng are the greatest issues for the development this plant. In the present study, the micro-ecologies of soils differing in the duration of P. notoginseng planting were compared, the results of which could provide important information to aid in solving the problems associated with the continuous cropping of P. notoginseng. Soils in which P. notoginseng had grown for 1, 3 or 5 years, as well as unplanted or fallow soil, which had a P. notoginseng planting interval of 1, 3, 6 or 9 years, were collected in Yunnan Province, China. The numbers and physiological groups of microorganisms, soil enzyme activities and nutrients present in the soil were analyzed to identify the effects of continuous cropping and determine the influence of crop rotation on the soil. After P. notoginseng was planted, the ecological structure of the soil and the balance of soil nutrients changed. These changes in the soil ecosystem prevented the soil from adapting to the continuous cropping of P. notoginseng, which eventually limited the growth of P. notoginseng and increased the incidence of diseases. After rotation of P. notoginseng, some soil indicators were restored, and some indicators with irregular changes may have been caused by crop rotation and field fertilization management practices. Thus, the selection of suitable crop rotations will facilitate the use of continuous cropping for P. notoginseng.