Jiabin Deng

Genome-Wide Identification and Analyses of Calmodulins and Calmodulin-like Proteins in Lotus japonicas

L. japonicus, a model plant of legumes plants, is widely used in symbiotic nitrogen fixation. A large number of studies on it have been published based on the genetic, biochemical, structural studies. These results are secondhand reports that CaM is a key regulator during Rhizobial infection. In plants, there are multiple CaM genes encoding several CaM isoforms with only minor amino acid differences. Moreover, the regulation mechanism of this family of proteins during rhizobia infection is still unclear. In the current study, a family of genes encoding CaMs and CMLs that possess only the Ca2+-binding EF-hand motifs were analyzed. Using ML and BI tree based on amino acid sequence similarity, seven loci defined as CaMs and 19 CMLs, with at least 23% identity to CaM, were identified. The phylogenetics, gene structures, EF hand motif organization, and expression characteristics were evaluated. Seven CaM genes, encoding only 4 isoforms, were found in L. japonicus. According to qRT-PCR, four LjCaM isoforms are involved in different rhizobia infection stages. LjCaM1 might be involved in the early rhizobia infection epidermal cells stage. Furthermore, additional structural differences and expression behaviors indicated that LjCMLs may have different potential functions from LjCaMs.

Phylogenetic relationships among Elymus and related diploid genera (Triticeae: Poaceae) based on nuclear rDNA ITS sequences

Abstract To investigate the phylogenetic relationships among Elymus and related diploid genera, the genome donor of Elymus, and the evolutionary history of polyploid Elymus species, nuclear ribosomal internal transcribed spacer (ITS) sequences were analyzed for 10 Elymus species, together with 17 diploid taxa from 5 monogenomic genera. The phylogenetic analyses (Neighbor-Joining) supported two major clades (St and H). Sequence diversity and genealogical analysis suggested that (1) Elymus species were unambiguously closely related to Pseudoroegeria; (2) Pse. stipifolia might be serve as the St genome donor of polyploid Elymus species; (3) the Y genome might be originated from ancestral lineage of Pseudoroegneria (St); (4) the ITS sequences of Elymus were evolutionarily distinct and may clarify parental lineages and phylogenetic relationships in Elymus.

Ecotypic adaptations in Bermuda grass (Cynodon dactylon) for altitudinal stress tolerance

Abstract Three ecotypes [foot hill (700 m), mid hill (1571 m) and top hill (2804 m)] of a Bermuda grass Cynodon dactylon (L.) Pers. from Pir Chinasi Hill in Western Himalaya were evaluated for their degree of tolerance to altitudinal stress. Differential response of all ecotypes in terms of adequate structural modifications to different elevation levels was an evident to confirm the hypothesis that plants inhabiting different altitudes show variation in structure (internal modifications) and strategic (response) due to heterogeneity in environmental gradients. Soil at top hill site was more acidic and displayed significant increase in ionic content and total nitrogen. High elevation had severe impact on morphoanatomical and physiological attributes. A significant decline in shoot fresh weight and total leaf area was observed in top hill ecotype. With exception of Ca2+ and carotenoid, other ionic and chlorophyll content were significantly declined at high elevations. Anatomical alterations such as, increased leaf thickness, intensive sclerification around the vascular bundle and pith area, reduced metaxylem vessel area, high number of silica bodies, high pubescence (increased microhair and trichome density) were some of the promising anatomical adaptations in top hill ecotype which played an important role in high degree of tolerance of this grass to cope with altitudinal stresses. Increased leaf thickness might be a response to lower temperature that protects mesophyll cells and high density of trichomes may be involved in blocking transpiration water and internal heat. The pattern of constant variation suggests that differential response of these ecotypes is highly related to air temperature, pattern of rainfall, availability of nutrients.

Ethnopharmacological studies of indigenous plants in Kel village, Neelum Valley, Azad Kashmir, Pakistan

BackgroundThis explorative study was undertaken for the first time in Kel village located in the Upper Neelum Valley, Azad Kashmir, Pakistan. The purpose was to document the indigenous knowledge of the native people used in the preparation of herbal medicines.MethodsTo get the data on traditional uses of medicinal plants, 20 informants were interviewed. Quantitative ethnobotanical indices, i.e., use value (UV), relative frequencies of citation (RFC), informant consensus factor (Fic), fidelity level (FL), data matrix ranking (DMR), preference ranking (PR), and jaccard index (JI), were calculated for the recorded medicinal plants.ResultsA total of 50 medicinal plants belonging to 33 families used in 13 disease categories were documented. Leaves were the frequently used plant parts, and decoction was the commonly used method for herbal medicine. Plants with high use value were Berberis lycium (2.05), Impatiens glandulifera (1.95), Artemisia scoparia (1.75), Ageratum conozoides (1.75), and Achillea millefolium (1.7). The highest RFC value was calculated for Berberis lycium (0.75), Cynoglossum lanceolatum (0.65), and Impatiens glandulifera and Achillea millefolium (0.60 each). The maximum informant consensus factor was for urinary system, cardiac diseases, baldness, and abortion and miscarriage (1.00). Berberis lyceum (95%) used in jaundice, hepatitis, typhoid, fever, and tuberculosis disorders. Plants with maximum fidelity level (FL) were Berberis lycium (95%) followed by Dioscorea bulbifera, Impatiens glandulifera, and Artemisia vulgaris (90%). Olea ferruginea was the most multipurpose plant and exports (21.2%) was the leading threat in the area. The pearson correlation coefficient (0.500) showed a positive correlation between the use value and relative frequency of citation.ConclusionThe present study provides useful information about traditional uses of medicinal plants used by local communities in different ailments. The plants with the highest use values could be employed in pharmacological research and biotechnological approaches in order to achieve adequate revenue. Some of the plants in the study area are facing high threats of becoming rare, and conservation initiatives are needed to conserve them for sustainable management in the region.

Phylogeny and maternal donor of Elymus (Triticeae: Poaceae) in China based on chloroplast matK sequences

Abstract Hybridization and polyploidization can be major mechanisms for plant evolution and speciation. Thus, the process of polyploidization and evolutionary history of polyploids is of widespread interest. The chloroplast DNA regionsmatK was used to analyze to phylogenetic relationships and maternal donor of Elymus species and their closely related species. The Neighbor-Joining phylogenetic reconstructions partitioned the species into one monophyletic groups. All the Elymus species were related to species of Pseudoroegneria. These results indicated that Pseudoroegneria (St genome) was the maternal donor of the polyploidy Elymus. In addition, the St genome of Elymus had several origins and diverse species of Pseudoroegneria might have taken part in the formation of polyploid species of Elymus.

The complete chloroplast genome sequence of Curcuma flaviflora (Curcuma).

Abstract The complete chloroplast (cp) genome of Curcuma flaviflora, a medicinal plant in Southeast Asia, was sequenced. The genome size was 160 478 bp in length, with 36.3% GC content. A pair of inverted repeats (IRs) of 26 946 bp were separated by a large single copy (LSC) of 88 008 bp and a small single copy (SSC) of 18 578 bp, respectively. The cp genome contained 132 annotated genes, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. And 19 of these genes were duplicated in inverted repeat regions.

Phylogenetic relationships and Y genome origin in Kengyilia (Triticeae: Poaceae) based on single copy gene DMC1

Abstract To investigate the phylogenetic relationships among Kengyilia and related diploid genera, the genome donor of Kengyilia, and the evolutionary history of polyploid Kengyilia species, disrupted meiotic cDNA1 (DMC1) sequences were analyzed for 11 Kengyilia species, together with 34 diploid taxa from 12 monogenomic genera. Sequence diversity and genealogical analysis suggested that (1) the St and P genomes were donated by Pseudoroegneria and Agropyron, respectively; (2) phylogenetic analyses separated the Y sequences from the St sequences, it confirmed that St and Y genome in Kengyilia species have originated from different donors; (3) the St genome of Kengyilia had several origins and diverse species of Pseudoroegneria might have taken part in the formation of polyploid species of Kengyilia.

Phylogenetic analysis of Leymus (Poaceae: Triticeae) based on random amplified polymorphic DNA

Abstract To investigate the Ns genome donor of Leymus and to elucidate the origin of Xm genome of Leymus, Random Amplified Polymorphic DNA (RAPD) markers were used to analyze 13 Leymus accessions, together with 14 taxa from related Triticeae genera. A total of 156 clear and reproducible DNA fragments were amplified by 24 RAPD primers, among which 154 fragments (98.72%) were found to be polymorphic. The main results showed as following: (1) the Leymus species were clustered together first, and there is the closest phylogenetic relationship between L. akmolinensis and L. angustus; (2) Leymus species have Ns genome, which come from Psathyrostachys, and different Psathyrostachys species could serve as the donor for different Leymus species; (3) The partial Leymus species had a close phylogenetic relationship with Hordeum chilense, Australopyrum retrofractum, Lophyrum elongatum.