Identification of RNA Editing Sites in Chloroplast Transcripts of Phalaenopsis aphrodite and Comparative Analysis with Those of Other Seed Plants

Abstract Background The Stephania tetrandra S. Moore (S. tetrandra) is a medicinal plant belonging to the family Menispermaceae that has high medicinal value and is well worth doing further exploration. The wild resources of S. tetrandra were widely distributed in tropical and subtropical regions of China, generating potential genetic diversity and unique population structures. The geographical origin of S. tetrandra is an important factor influencing its quality and price in the market. In addition, the species relationship within Stephania genus still remains uncertain due to high morphological similarity and low support values of molecular analysis approach. The complete chloroplast (cp) genome data has become a promising strategy to determine geographical origin and understand species evolution for closely related plant species. Herein, we sequenced the complete cp genome of S. tetrandra from Zhejiang Province and conducted a comparative analysis within Stephania plants to reveal the structural variations, informative markers and phylogenetic relationship of Stephania species. Results The cp genome of S. tetrandra voucher ZJ was 157,725 bp, consisting of a large single copy region (89,468 bp), a small single copy region (19,685 bp) and a pair of inverted repeat regions (24,286 bp each). A total of 134 genes were identified in the cp genome of S. tetrandra, including 87 protein-coding genes, 8 rRNA genes, 37 tRNA genes and 2 pseudogene copies (ycf1 and rps19). The gene order and GC content were highly consistent in the Stephania species according to the comparative analysis results, with the highest RSCU value in arginine (1.79) and lowest RSCU value in serine of S. tetrandra, respectively. A total of 90 SSRs have been identified in the cp genome of S. tetrandra, where repeats that consisting of A or T bases were much higher than that of G or C bases. In addition, 92 potential RNA editing sites were identified in 25 protein-coding genes, with the most predicted RNA editing sites in ndhB gene. The variations on length and expansion extent to the junction of ycf1 gene were observed between S. tetrandra vouchers from different regions, indicating potential markers for further geographical origin discrimination. Moreover, the values of transition to transversion ratio (Ts/Tv) in the Stephania species were significantly higher than 1 using Pericampylus glaucus as reference. Comparative analysis of the Stephania cp genomes revealed 5 highly variable regions, including 3 intergenic regions (trnH-psbA, trnD-trnY, trnP) and two protein coding genes (rps16 and ndhA). The identified mutational hotspots of Stephania plants exhibited multiple SNP sites and Gaps, as well as different Ka/Ks ratio values. In addition, five pairs of specific primers targeting the divergence regions were accordingly designed, which could be utilized as potential molecular markers for species identification, population genetic and phylogenetic analysis in Stephania species. Phylogenetic tree analysis based on the conserved chloroplast protein coding genes indicated a sister relationship between S. tetrandra and the monophyletic group of S. japonica and S. kwangsiensis with high support values, suggesting a close genetic relationship within Stephania plants. However, two S. tetrandra vouches from different regions failed to cluster into one clade, confirming the occurrences of genetic diversities and requiring further investigation for geographical tracing strategy. Conclusions Overall, we provided comprehensive and detailed information on the complete chloroplast genome and identified nucleotide diversity hotspots of Stephania species. The obtained genetic resource of S. tetrandra from Zhejiang Province would facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of Stephania plants.

Download Full-text

Criminal and Administrative Measures to Protect Forests from Illegal Logging in Ukraine

Всероссийский криминологический журнал ◽

10.17150/2500-4255.2021.15(5).605-612 ◽

2021 ◽

Vol 15 (5) ◽

pp. 605-612

Author(s):

Aleksandr Khan ◽

Stanislav Pevko ◽

Elena Yushkevich

Keyword(s):

Comparative Analysis ◽

Public Relations ◽

Criminal Liability ◽

Criminal Code ◽

Seed Plants ◽

Forest Plantations ◽

Illegal Logging ◽

Natural Origin ◽

Considerable Damage

The conducted research showed a lack of coordination between different norms of Ukrainian criminal and administrative laws that define the offences in the sphere of illegal logging, and determine the type and degree of liability for committing them. This lack of coordination is manifested, specifically, in the competition of certain norms, their ineffectiveness, and the absence of liability for certain publicly dangerous actions connected with illegal logging and damaging trees. The authors carried out a comparative analysis of criminal administrative offences in this sphere and formulated recommendation on improving criminal and administrative legislations that protect public relations in the sphere of protecting forests in Ukraine. They suggest the following: 1) amending Art. 65 of the Code of Ukraine on Administrative Offences by establishing liability for selling illegally logged timber or shrubs; 2) amending Art. 246 of the Criminal Code of Ukraine and Art. 65 the Code of Ukraine on Administrative Offences by introducing administrative liability for buying illegally logged timber or shrubs, as well as criminal liability for buying illegally logged timber or shrubs if it inflicted considerable damage; 3) amending Art. 246 of the Criminal Code of Ukraine by introducing criminal liability for destroying or damaging forest plantations, seedlings, young plants in tree nurseries and plantations, as well as young trees of natural origin and self-seed plants in the areas designated for reforestation if that inflicted considerable damage on protected public relations. The presented suggestions on improving current criminal and administrative legislations of Ukraine are aimed at improving the effectiveness of counteracting illegal logging in the country.

Download Full-text

The ADAR Family in Amphioxus: RNA Editing and Conserved Orthologous Site Predictions

Genes ◽

10.3390/genes11121440 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1440

Author(s):

Michał Zawisza-Álvarez ◽

Claudia Pérez-Calles ◽

Giacomo Gattoni ◽

Jordi Garcia-Fernàndez ◽

Èlia Benito-Gutiérrez ◽

...

Keyword(s):

Gene Expression ◽

Nervous System ◽

Comparative Analysis ◽

Gene Family ◽

Rna Editing ◽

Regulation Of Gene Expression ◽

The Other ◽

Phylogenetic Position ◽

Evolutionary Perspective ◽

Regulatory Complexity

RNA editing is a relatively unexplored process in which transcribed RNA is modified at specific nucleotides before translation, adding another level of regulation of gene expression. Cephalopods use it extensively to increase the regulatory complexity of their nervous systems, and mammals use it too, but less prominently. Nevertheless, little is known about the specifics of RNA editing in most of the other clades and the relevance of RNA editing from an evolutionary perspective remains unknown. Here we analyze a key element of the editing machinery, the ADAR (adenosine deaminase acting on RNA) gene family, in an animal with a key phylogenetic position at the root of chordates: the cephalochordate amphioxus. We show, that as in cephalopods, ADAR genes in amphioxus are predominantly expressed in the nervous system; we identify a number of RNA editing events in amphioxus; and we provide a newly developed method to identify RNA editing events in highly polymorphic genomes using orthology as a guide. Overall, our work lays the foundations for future comparative analysis of RNA-editing events across the metazoan tree.

Download Full-text