Phylogenetic tree analysis for Bali Cattle based on partial sequence 16S rRNA Mitochondrial DNA

Mitochondria DNA (mtDNA) as a source of genetic information based on the maternal genome, can provide important information for phylogenetic analysis and evolutionary biology. The objective of this study was to analyze the phylogenetic tree of Bali cattle with seven gene bank references (Bos indicus, Bos taurus, Bos frontalis, and Bos grunniens) based on partial sequence 16S rRNA mitochondria DNA. The Bayesian phylogenetic tree was constructed using BEAST 2.4. and visualization in Figtree 1.4.4 (tree.bio.ed.ac.uk/software/figtree/). The best model of evolution was carried out using jModelTest 2.1.7. The most optimal was the evolutionary models GTR + I + G with p-inv (I) 0,1990 and gamma shape 0.1960. The main result indicated that the Bali cattle were grouped into Bos javanicus. Phylogenetic analysis also successfully classifying Bos javanicus, Bos indicus, Bos taurus, Bos frontalis and Bos grunniens. These results will complete information about Bali cattle and useful for the preservation and conservation strategies of Indonesian animal genetic resources.

Screening and Evaluation of a Potential Bacteriocin Producing Lactobacillus in Milk and Dairy Products Collected from Puducherry

In an array of identifying safe antimicrobial compounds, bacteriocin producing Lactobacillus strain have been investigated in this study from the daily consuming food resources of humans. Till now, the best studied bacteriocins are nisin A produced by Lactobacillus lactis and pedocin PA-1 synthesized by Pediococcus acidilactici which have been accredited as a preservative in the food industries by the World Health Organization (WHO). For this study, four different milk and dairy products viz., curd, cheese, yoghurt and butter were collected from the local markets of Karaikal region, Puducherry, India and were used for the isolation of Lactobacillus species using MRS agar. Totally, five morphologically distinct strains were collected and were initially named as MPD 1 to MPD 5. During the screening process of bacteriocin production, the strain MPD 5 showed maximum antimicrobial activity against Vibrio cholerae MTCC 3906 with 900AU/ml. This strain was molecular identified as Lactiplantibacillus plantarum MDP 5 based on 16S rRNA partial sequence method. This 16S rRNA partial sequence was submitted to the NCBI nucleotide GenBank and provided with the accession number, MW301154.1. Further, this strain revealed an enhanced production of bacteriocin using the standardized physicochemical factors such as pH 7, 35°C, 2% fructose and 1% peptone. Furthermore, these optimal conditions revealed more than 2-fold increase in the bacteriocin production. All the above information suggesting the possibilities of bacteriocin for the bioindustrial production using the L. plantarum MDP 5 of this study and its future prospects for the investigation of biocidal activities against many highly infectious pathogens of human and veterinary.

Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene

Basith A, Abinawanto, Kusrini E, Yasman. 2021. Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas 22: 4282-4290. Groupers populations in Indonesia, particularly from Madura Island, East Java are indicated to be over-fished, thereby requiring data collection of more accurate genetic resources as an important step for grouper conservation. A total of 14 samples of the Epinepheplus groupers were obtained from the fish landing port on Madura Island. The 617 bp CO1 gene sequence was utilized for genetic diversity analysis and phylogenetic tree reconstruction. Genetic diversity is based on the value of haplotype diversity (Hd) and nucleotide diversity (?). Reconstruction of the phylogenetic tree includes neighbor-joining (NJ) implementing K2P substitution model, while maximum likelihood (ML) is conducted by implementing HKY+G+I substitution model, both of which were evaluated by employing a bootstrap of 1000 replications. Analysis of genetic distance between species indicated that the farthest distance between E. heniochus and E. fasciatus was 0.189, while the closest distance between E. erythrurus and E. ongus was 0.099. Intrapopulation genetic diversity indicated a high value with details of Hd=0.978 and ?=0.12107. Furthermore, NJ and ML phylogenetic tree demonstrated similar topology in the observed Epinephelus spp. obtained from Madura Island grouped into 7 clades, that is Epinephelus coioides, E. bleekeri, E. areolatus, E. erythrurus, E. heniochus, E. fasciatus, and E. ongus.

Studies of some genes of Bacillus subtilis MN99 local strains against plant diseases

The objective of this study was the isolation and characterization of Bacillus subtilis local strains from the soil in Mongolia. These local strains of B. subtilis are showed to have high antagonistic activities against some plant pathogenic fungi and bacteria. Six strains of B. subtilis were isolated and characterized morphologically, physiologically and biochemically according the Bergey’s Manual of Systematic Bacteriology. In order to identify species of the isolated strains, we amplified and sequenced 16S rRNA gene, essential funtinal genes bmyB, spoVG and srfAA, which are related to antagonistic activity of these strains. The sequences were aligned using CLASTALW multiple sequence alignment tool. Phylogenetic tree was drawn according to Maximum likelihood”method and “Tamura-Nei” model using “MEGA-X version 10.2.6 program. Among all isolates of B. subtilis MN99 and 7/24 strains had higher antagonist activity against plant diseases. According to partial sequence of srfAA (620bp) gene of MN99, the local strain belongs to B. subtilis and partial sequence of bmyB (370bp), spoVG (22bp) gene of MN7/24 strain showed that the it belongs to B. atrophaeus species. All local strains of B. subtilis had bacillomycin synthesis gene, and B. subtilis MN99 strain had only surfactine synthesis gene, while did not have spore formation and hemolysis gene SpoVG.

Intergeneric Hybridization between Phalaenopsis 2166 and Vanda ‘saint valentine’: Characterization of Parents Using ndhE cpDNA Partial Sequence

An intergeneric cross between Phalaenopsis 2166 and Vanda ‘saint valentine’ has successfully produced protocorms that will be grown further to form seedlings. The present study aims to genetically characterize both parents by using ndhE partial gene as its sequence is shown polymorphic among five orchid genera of the subtribe Oncidiinae. The results reveal that the ndhE partial sequences of Phalaenopsis 2166 and Vanda ‘saint valentine’ are considerably homologous with those of Oncidium. However, alignment of ndhE partial sequences between both parents shows only 58% similarity, leading to the conclusion that a relatively high genetic difference between them may occur.

Epidemiology and molecular characterization of re-emerged virulent strains of Peste des Petits Ruminants virus among sheep in Kassala State, Eastern Sudan

Background Peste des Petits Ruminants (PPR) is a severe contagious viral disease, which mainly affects small ruminants. PPR is caused by a Morbillivirus that belongs to the family Paramyxoviridae. In this study 12 suspected PPR outbreaks among sheep and goats were investigated in four localities in Kassala State, Eastern Sudan, during 2015—2017. The causative agent was confirmed by a Sandwich Enzyme-Linked Immunosorbent Assay (sELISA), and a Reverse Transcription Polymerase Chain Reaction (RT-PCR) targeting a partial sequence of nucleocapsid protein gene (N- gene) and a partial sequence of fusion protein gene (F- gene). Sequencing and phylogenetic analysis were carried out on six N- gene based RT-PCR products selected from two outbreaks occurred on border and inner localities of Kassala State to determine the circulating lineages of PPRV strains. Identity percentages were determined between isolates in this study and previous Sudanese, and other (African and Asian) isolates which clustered along with them. Results Out of 30 samples, 22 (73.3%) were positive using sandwich ELISA. From 22 s ELISA positive samples, 17 (77.3%) were positive by Ngene based RT-PCR and only 7(43.8%) out of 16 positive samples by N gene based RT-PCR were positive using Fgene based RT-PCR. The sequencing and phylogenetic analysis confirmed involvement of the lineage IV of PPRV in outbreaks among small ruminants in Kassala State and high identity percentage between our isolates and previous Sudanese and other (African and Asian) isolates. Conclusions The present study demonstrates that genetic relationship between PPRV strains circulating in sheep in Kassala State, Eastern Sudan, and PPRV strains characterized as lineage IV in neighboring African countries such as Eretria,Ethiopia, Egypt, and other Asian countries

Elatostema qinzhouense (Urticaceae), a new species from limestone karst in Guangxi, China

Elatostema qinzhouense L.F. Fu, A.K. Monro & Y.G. Wei, a new species from Guangxi, China is described and illustrated. Morphologically, E. qinzhouense is most similar to E. hezhouense from which it differs by having smaller size of leaf laminae, fewer and smaller staminate peduncle bracts, longer pistillate peduncle bracts and a larger achene. This result is supported by the molecular evidence. The phylogenetic position of the new species within Elatostema is evaluated using three DNA regions, ITS, trnH-psbA and psbM-trnD, for 107 taxa of Elatostema s.l. (including E. qinzhouense). Bayesian inference (BI) and maximum likelihood (ML) analyses each recovered the same strongly supported tree topologies, indicating that E. qinzhouense is a member of the core Elatostema clade and sister to E. hezhouense. Along with the phylogenetic studies, plastid genome and ribosomal DNA (rDNA) sequences of the new species are assembled and annotated. The plastid genome is 150,398 bp in length and comprises two inverted repeats (IRs) of 24,688 bp separated by a large single-copy of 83,919 bp and a small single-copy of 17,103 bp. A total of 113 functional genes are recovered, comprising 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The rDNA is 5,804 bp in length and comprised the 18S ribosomal RNA partial sequence (1,809 bp), internal transcribed spacer 1 (213 bp), 5.8S ribosomal RNA (164 bp), internal transcribed spacer 2 (248 bp) and 26S ribosomal RNA partial sequence (3,370 bp). In addition, the chromosome number of E. qinzhouense is observed to be 2n = 26, suggesting that the species is diploid. Given a consistent relationship between ploidy level and reproductive system in Elatostema, the new species is also considered to be sexually reproducing. Our assessment of the extinction threat for E. qinzhouense is that it is Endangered (EN) according to the criteria of the International Union for Conservation of Nature.

A new species of Oneilliella from India with description of the female of Trachynotothrips brevispinis Masumoto & Okajima (Thysanoptera: Thripidae)

Oneilliella shivii sp.n. (Panchaetothripinae) is described from India as the second species in this genus. Trachynotothrips brevispinis and T. striatus (Thripinae) are newly recorded from India, and the first description provided of the female of T. brevispinis. Partial sequence data of mitochondrial cytochrome c oxidase (mtCOI) of these species were generated.