ABSTRACT
High throughput sequencing technology is also called Next Generation Sequencing (NGS), which can sequence hundreds and thousands sequences in different samples at the same time. In the present study, the culture-independent high throughput sequencing technology was applied to sequence the fungi metagenomic DNA of the fungal internal transcribed spacer 1(ITS 1) in the root of Sinopodophyllum hexandrum. Sequencing data suggested that after the quality control, 22 565 reads were remained. Cluster similarity analysis was done based on 97% sequence similarity, which obtained 517 OTUs for the three samples (LD1, LD2 and LD3). All the fungi which identified from all the reads of OTUs based on 0.8 classification thresholds using the software of RDP classifier were classified as 13 classes, 35 orders, 44 family, 55 genera. Among these genera, the genus of Tetracladium was the dominant genera in all samples(35.49%, 68.55% and 12.96%).The Shannon's diversity indices and the Simpson indices of the endophytic fungi in the samples ranged from 1.75-2.92, 0.11-0.32, respectively.This is the first time for applying high through put sequencing technol-ogyto analyze the community composition and diversity of endophytic fungi in the medicinal plant, and the results showed that there were hyper diver sity and high community composition complexity of endophytic fungi in the root of S. hexandrum. It is also proved that the high through put sequencing technology has great advantage for analyzing ecommunity composition and diversity of endophtye in the plant.
ABSTRACT
Objective: To analyze the genetic diversity and genetic structure of 245 plant samples in Notopterygium incisum from different regions. Methods: Genetic diversity and genetic structure of 245 samples of N. incisum were studied using chloroplast cpDNA trnT-trnL direct sequencing method and Neighbor-joining (NJ) method. Results: Haplotype diversity (Hd) and nucleotide diversity (Pi) at the species level were 0.873 and 0.00407, respectively. At the population level, Hd ranged with 0.000-0.900, and Pi ranged with 0.000-0.0544. It indicated that N. incisum had a moderate level of genetic diversity than N. franchetii plants of the genus Notopterygium Boiss. Molecular variance analysis (AMOVA) indicated that high genetic differentiation (77.55%) existed among populations, and gene flow was low (Nm=0.145) among populations. Based on the NJ tree, the 31 wild populations tested were clustered into two groups. Conclusion: N. incisum has the midium cpDNA diversity and higher population genetic differentiation.
ABSTRACT
In this study, 31 Notopterygium incisum populations were analyzed using ITS sequences to investigate the genetic structure. The results showed that: the ITS region ranged in size from 634 to 635 bp and base composition was with high G + C content of 57.8%. Thirty-one polymorphic sites were detected from 402 sequences of 31 populations of N. incisum, and the proportion of polymorphic sites was 4.88%, in which parsimony informative sites were up to 12. And 31 haplotypes were identified based on these polymorphic sites. Molecular variance analysis (AMOVA) indicated that high genetic differentiation (57%) existed among population, and gene flow was low (N(m) = 0.38) among populations. Phylogenetic relationships of 31 haplotypes were analyzed using NJ method with N. forbesiias an out-group. Phylogenetic analysis showed that 31 haplotypes from different populations mixed together and did not form distinct geographically separated clades.