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    Exploration of two major boron transport genes BOR1 and NIP5;1 in the genomes of different plants
    (Taylor & Francis Ltd, 2020) Ozyigit, Ibrahim Ilker; Filiz, Ertugrul; Saracoglu, Ibrahim Adnan; Karadeniz, Sedat
    Boron (B) is an essential plant micronutrient but studies regarding its transport are still limited to a few plants. This work identified two major B transport sequences in plants, NIP5;1 boric acid channel protein and BOR1 transporter. 80 BOR1 and 34 NIP5;1 homologs were identified in 18 different plant genomes. BOR1 homologs had a HCO3-transporter domain, 649-737 amino-acid residues with mainly basic nature, putative 8-11 transmembrane domains (TMDs) and 11-13 exons. NIP5;1 homologs had a MIP family domain, 294-311 amino-acid residues with basic nature, 5-6 putative TMDs and 3-5 exons. Tyrosine-based motif, acidic di-leucine motif and lysine residue, reported for polarity, vacuolar sorting and B-dependent degradation, were identified in BOR1 homologs. Two NPA motifs and an ar/R selectivity filter with AIGR residues, reportedly essential in B transport, were also found in NIP5;1 homologs. Two NPA motifs in AtNIP5;1 and OsNIP3;1 homologs were NPS and NPV, whereas in sequences homologous to AtNIP6;1 were NPA/V. Besides, ar/R selectivity filters were identified with A(N/S/T)IGR residues in NIP5;1 and NIP3;1 homologs. The BOR1 and NIP5;1 model structures were mainly conserved. Under different perturbations, Arabidopsis thaliana NIP5;1 and NIP6;1 genes demonstrated similar expression patterns although they act in different tissues, suggesting a common regulatory mechanism, whereas BOR1 showed a different expression pattern. BOR1 was substantially expressed in primary root, radicle and flower; NIP5;1 in primary root and roots, and NIP6;1 in petiole. NIP5;1, 6;1 and BOR1 expression in other plant organs implied their involvement in different pathways in addition to B uptake and its mobilization.
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    Genetic diversity and phylogenetic analysis of Robinia pseudoacacia L. populations using ISSR markers, ITS1 and trnL-F intergenic spacer sequences
    (Czech Academy Agricultural Sciences, 2024) Uras, Mehmet Emin; Filiz, Ertugrul; Sen, Ugur; Ozyigit, Ibrahim Ilker
    Robinia pseudoacacia L. is a deciduous tree planted almost all around the world for a wide variety of uses such as ornamental in urban ecosystems and forest trees in afforestation. This study aims to evaluate the genetic diversity and phylogenetic relations of R. pseudoacacia using some selected populations in Istanbul and Kocaeli cities. For this aim, molecular marker-assisted and DNA sequence-based analyses were performed. According to the results, nine of 15 inter simple sequence repeats (ISSR) primers gave clear and distinguishable bands with a total of 100 loci. The percentage of polymorphic loci (PPL) was calculated as 100% for multi-populations and ranged from 46% to 76% for single populations. Nei's gene diversity value was calculated between 0.165 and 0.251. The lowest and highest PPL were found in populations of Barbaros Boulevard and Dilovasi District, respectively. Population structure analysis showed seven different genetic structures for five populations. Internal transcribed spacer 1 region (ITS1) and trnL-F intergenic spacer region were used to examine the phylogenetic relationships of R. pseudoacacia, and both regions showed a high discriminative power at the family level. Based on the findings, R. pseudoacacia, as a forest tree residing in the urban ecosystem, may face the risk of population decline in the upcoming years due to its moderate/low genetic diversity and susceptibility to environmental pressures.