Genetic Diversity and Phylogenetic Analyses of Laurus nobilis L. (Lauraceae) Populations Revealed Chloroplast (cpDNA) trnL Intron and trnL-F Region

Canbolat

Moral

et al. 2021

Nova Biotechnol. Chim.

Self Cite

In this study, sequences analysis of some Citrus species distributed in Turkey's Aegean region was based on the cpDNA psbA-trnH region. The sequences for psbA-trnH regions of the outgroups were retrieved from NCBI GenBank. Genomic DNA was isolated from healthy and green leaves. Total genomic DNA was extracted using GeneMark DNA isolation Plant Kit. The psbA-trnH region was amplified using primers psbA and trnH. DNA sequences were edited using the Sequencher 5.4.6. Sequencing data were analyzed using MEGA 6.0 software. Maximum likelihood (ML) tree was created to determine the relationships between Citrus taxa. cpDNA psbA-trnH sequences ranged between 426 and 470 nucleotides. Maximum likelihood phylogenetic tree is composed of two clades. The divergence values differed between 0.000 and 0.012. According to the results of the study, the separation of Citrus species in phylogenetic tree obtained with psbA-trnH sequence data was realized. However, it has been found that cpDNA psbA-trnH sequence populations of species belong together. In addition, the phylogenetic relationship between the sequence data of some species belonging to the Rutaceae family taken from NCBI and Citrus species was revealed.

Section: Resultsmentioning

confidence: 99%

Sequences analysis of chloroplast psbA-trnH region in Citrus L. (Rutaceae) species from the Aegean region of Turkey

Canbolat

Moral

et al. 2021

Nova Biotechnol. Chim.

Self Cite

“…However, compared to nuclear molecular markers used in phylogenetic study, the chloroplast genome based molecular markers are ideal system phylogeny studies as chloroplastis small genome with very low rate of nucleotide substitutions (Wei et al, 2005). Hence, chloroplast DNA (cpDNA) sequencing technology has been widely used to investigate phylogenetic relationships between various plant groups as it is an important research object in the field of molecular evolution, phylogeny, and molecular markers (Daniell et al, 2016;Sevindik and Okan, 2020). Particularly the non-coding regions of chloroplast DNA sequences such as cemA-petA, clpP-psbB, ndhF-rpl32, petA-psbJ, psbA-trnK, trnL-ccsA, rpl32-trnL, trnE-trnT, trnK-rps16, trnP-psaJ, trnT-trnL molecular markers are used in resolution of phylogenetic relationships of closely related species as it contained parsimony-informative (Liu et al, 2005).…”

Section: Open Accessmentioning

confidence: 99%

“…The last two decades, the plant molecular systematics has been rapidly advancing by analyzing the sequences and using that sequences in discovery of new phylogenetic analyzes methods (Sevindik and Okan, 2020). This advancement in sequence analysis methods is proving very useful in plant systematics studies and phylogenetic analyzes when there are insufficient morphological traits/ parameters in terms of phylogenetic knowledge (İnal et al, 2017).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Phylogenetic Analysis of Strawberry, Fragaria x ananassa (Rosaceae: Fragaria) using Cytochrome C Heme Attachment Protein (ccsA) Gene

Jadhao

Dey

2021

Research Biotica

Phylogenetic relationships and genetic diversity were inferred using nucleotide sequences of chloroplast ccsAgene (cytochrome c heme attachment protein, for c-type cytochrome synthesis) of strawberry, F. x ananassa and other Fragaria species. Genomic DNA was isolated from fresh and green leaves of strawberry cultivar 'Chandler' seedlings. The ccsA gene sequence was amplified and isolated by using gene specific primers designed from consensus sequences of Fragaria species. After sequencing, the isolated ccsA gene sequence was corrected using BioEdit programs. Then ccsA nucleotide sequence isolated from cultivated strawberry (F. x ananassa) cultivar 'Chandler' was deposited in GeneBank at NCBI with accession number MK872805.1. Based on the BLASTn hit results, two separate datasets were prepared, one for Fragaria genus and other for Rosaceae family species to study the diversity analyses. MEGA 7.0 program was then used for phylogenetic analyzes and the detection of evolutionary genetic divergence between the species. For Fragaria genus which also included cultivated strawberry (F. x ananassa) ccsA gene sequence, the mean nucleotide composition was estimated as 29.3% A, 37.8% T, 15.5% C and 17.4% G. The lowest divergence distance i.e., 0.00 was estimated for Fragaris species, while the highest distance 1.00 was observed only for Fragaria nipponica (KY769125.1). Overall, the molecular phylogenetic analysis revealed that no genetic variation was observed in Fragaria species that was due to the highly conserved chloroplast nucleotide sequences of ccsA gene during evolution. However, the ccsA nucleotide sequences can be useful to study intra genus evolutionary relationship between Rosaceae family members.

“…There have been similar studies in the past with sequences and populations of important plant species, trnL-F such as; Turkish Olea europaea subsp. europaea (Kaya et al, 2018), Turkish rice (Oryza sativa) (Filiz et al, 2018), Turkish cotton (Gossypium hirsutum L.) (Hocaoglu-Ozyigit et al, 2020), Turkish apple (Malus L.) genotypes , Laurus nobilis populations from Turkey (Sevindik and Okan, 2019), Turkish some Centaurea L. (Kalmer and Tekpınar, 2017), Turkish Urtica ssp. (Kolören and Eker, 2018), Fritillaria were collected from different regions of Turkey (Türktaş et al, 2012).…”

Section: Cpdna Trnl-f Sequences Analysismentioning

confidence: 99%

Molecular Genetic Diversity of Prunus armeniaca L. (Rosaceae) Genotypes by RAPD, ISSR-PCR, and Chloroplast DNA (cpDNA) trnL-F Sequences

Murathan

International Journal of Fruit Science

2020

Self Cite

In this study, phylogenetic analysis of some Turkish Prunus armeniaca L. genotypes was conducted based on RAPD-PCR, ISSR-PCR, and chloroplast DNA (trnL-F) sequence analyses. Prunus armeniaca genotypes were obtained from Malatya province, and brought to the laboratory for genomic DNA isolation. Eleven RAPD and fifteen ISSR primers were used to determine molecular characterization of Prunus armeniaca genotypes. For the amplification of the trnL-F region, trne and trnf primers were used in Polymerase Chain Reaction (PCR). A total of 46 and 95 bands were obtained with RAPD and ISSR analysis, respectively. The trnL-F sequences varied from 398 to 403 nucleotides. Average nucleotide composition of trnL-F sequences was 31.0% T, 14.4% C, 37.4% A and 17.2% G. The genetic distance between the five apricot genotypes is 0.00. A maximum likelihood tree was generated to determine genetic relationships among Prunus armeniaca genotypes. Analysis of Prunus armeniaca genotypes based on RAPD, ISSR, and trnL-F sequences revealed that the rate of polymorphism obtained using RAPD and ISSR were higher than those obtained through the trnL-F sequences.