How to perform RT-qPCR accurately in plant species? A case study on flower colour gene expression in an azalea (Rhododendron simsii hybrids) mapping population

AbstractSacred lotus (Nelumbo nucifera, or lotus) is one of the most widely grown aquatic plant species with important uses, such as in water gardening and in vegetable and herbal medicine. A public genomic database of lotus would facilitate studies of lotus and other aquatic plant species. Here, we constructed an integrative database: the Nelumbo Genome Database (NGD, http://nelumbo.biocloud.net). This database is a collection of the most updated lotus genome assembly and contains information on both gene expression in different tissues and coexpression networks. In the NGD, we also integrated genetic variants and key traits from our 62 newly sequenced lotus cultivars and 26 previously reported cultivars, which are valuable for lotus germplasm studies. As applications including BLAST, BLAT, Primer, Annotation Search, Variant and Trait Search are deployed, users can perform sequence analyses and gene searches via the NGD. Overall, the valuable genomic resources provided in the NGD will facilitate future studies on population genetics and molecular breeding of lotus.

Download Full-text

Can we save critically endangered relict endemic plant species? A case study of Primula boveana Decne ex Duby in Egypt

Journal for Nature Conservation ◽

10.1016/j.jnc.2021.126005 ◽

2021 ◽

Vol 61 ◽

pp. 126005

Author(s):

Karim Omar ◽

Ibrahim Elgamal

Keyword(s):

Plant Species ◽

Critically Endangered ◽

Endemic Plant ◽

Endemic Plant Species

Download Full-text

A TRIPARTITE CLUSTERING ANALYSIS ON MICRORNA, GENE AND DISEASE MODEL

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720012400070 ◽

2012 ◽

Vol 10 (01) ◽

pp. 1240007 ◽

Cited By ~ 2

Author(s):

CHENGCHENG SHEN ◽

YING LIU

Keyword(s):

Gene Expression ◽

Clustering Algorithm ◽

Target Genes ◽

Regulation Of Gene Expression ◽

Disease Model ◽

Relational Information ◽

Microrna Gene ◽

Research Findings ◽

Family Based

Alteration of gene expression in response to regulatory molecules or mutations could lead to different diseases. MicroRNAs (miRNAs) have been discovered to be involved in regulation of gene expression and a wide variety of diseases. In a tripartite biological network of human miRNAs, their predicted target genes and the diseases caused by altered expressions of these genes, valuable knowledge about the pathogenicity of miRNAs, involved genes and related disease classes can be revealed by co-clustering miRNAs, target genes and diseases simultaneously. Tripartite co-clustering can lead to more informative results than traditional co-clustering with only two kinds of members and pass the hidden relational information along the relation chain by considering multi-type members. Here we report a spectral co-clustering algorithm for k-partite graph to find clusters with heterogeneous members. We use the method to explore the potential relationships among miRNAs, genes and diseases. The clusters obtained from the algorithm have significantly higher density than randomly selected clusters, which means members in the same cluster are more likely to have common connections. Results also show that miRNAs in the same family based on the hairpin sequences tend to belong to the same cluster. We also validate the clustering results by checking the correlation of enriched gene functions and disease classes in the same cluster. Finally, widely studied miR-17-92 and its paralogs are analyzed as a case study to reveal that genes and diseases co-clustered with the miRNAs are in accordance with current research findings.

Download Full-text

Altitudinally coordinated pattern of plant community structure in the Shivapuri National Park, Nepal

Banko Janakari ◽

10.3126/banko.v18i1.2161 ◽

1970 ◽

Vol 18 (1) ◽

pp. 11-17 ◽

Cited By ~ 1

Author(s):

Shalik Ram Sigdel

Keyword(s):

Community Structure ◽

Species Diversity ◽

Plant Species ◽

Plant Community ◽

National Park ◽

Climatic Factors ◽

Flower Colour ◽

Basal Area ◽

Plant Community Structure ◽

Closed Canopy

Study on plant community structure was undertaken in different altitudinal ranges of Shivapuri National Park. The general objective of this study is to analyse different plant community structure in Shivapuri National Park with regards to altitudinal variation. The forest was divided into three distinct altitudinal ranges on the basis of dominancy. In each altitudinal range standard quadrats method was applied for vegetation analysis. The highest number of species was found in site II. All the ecological parameters of the plant species were higher in site II except Basal Area of tree that was highest in site III. The pattern of distribution of plant species was not uniform according to altitude. At higher elevation, the forest was mature with almost closed canopy and trees were large; so the tree density was low. Species richness was highest in site II. Species diversity among tree and shrub species was higher in site I. But for herb species diversity was higher in site II for both seasons. Such type of variations may be due to nature of soil i.e. acidity, nutrient availability and other micro-climatic factors. The most noteworthy thing was that variation in flower colour of Rhododendron arboreum i.e. deep scarlet at low altitude, but it gradually changed into pinkish white as altitude increased. Key words: Altitude, Density, Plant community, Species diversity doi: 10.3126/banko.v18i1.2161 Banko Janakari, Vol. 18, No. 1, 11-17

Download Full-text

Ethnomedicinal Knowledge of Kisan Community - A Case Study

Himalayan Journal of Science and Technology ◽

10.3126/hijost.v4i0.33861 ◽

2020 ◽

pp. 16-23

Author(s):

Manisha KC ◽

Nanda Bahadur Singh

Keyword(s):

Indigenous Knowledge ◽

Plant Species ◽

Common Cold ◽

Animal Species ◽

Traditional Practices ◽

Medicinal Purpose ◽

Group Discussions ◽

Key Informants ◽

Ethnomedicinal Knowledge

In the context of depleting indigenous knowledge and their values in the Kisan Community, they seem unaware of their culturally rich traditional practices of using animals and plants for medicinal purpose. It has been essential to document those knowledge of practices for future references. The paper tried to explore and document those knowledge and practices by the Kisan community of Mechinagar 9 and 11 of Jhapa, Nepal. For this purpose, the data were collected through interviews with key informants including conjurer (Dhami/Jhakri), elders of the society and also focal group discussions with the local people. Analysis of the data has shown that 29 animal species belonging to 24 families are used to treat 29 ailments and 57 plant species belonging to 37 families are used for treating 39 different ailments. The commonly treated ailments were common cold, cuts, wounds, diarrhoea, dysentery, etc.

Download Full-text