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이성일,Kabwe Nkongolo,박두리,최익영,최아영,김남수 한국유전학회 2019 Genes & Genomics Vol.41 No.3
Objective Betulaceae is a relatively small birch family that comprises about 160 deciduous trees and shrubs. Chloroplast (cp) genome sequencing of Alnus rubra and Betula cordifolia was carried out to elucidate their molecular features and phylogenetic relationship among species in Betulaceae family. Methods Chloroplast genome sequencing was carried out using next generation sequencing method. Molecular and genomic features of the two cp genomes were characterized with other cp genomes in Betulaceae. Also, molecular phylogenetic analysis was performed using the whole cp genome sequences. Results The average cp genome length was 160,136 bp among the Betulaceae species. Base compositions of the cp genomes were skewed toward a high AT ratio, with an average of 63.4%. We identified 117 different genes 83 with protein coding, 4 with ribosomal RNA, and 30 with tRNA. Eighteen genes contained introns which were conserved among the cp genomes of all Betulaceae. We mined 82 SSRs from the cp genomes of A. rubra, A. cordifolia, and A. nana. The SSRs were variable in motif repeat numbers and presence/absence among the cp genomes. Conclusion Chloroplast genome-wide sequence comparison from 11 Betulaceae species and one cp genome of evergreen oak revealed that the patterns of sequence variations were congruent with two subfamily classification Betuloideae (Alnus and Betula) and Corylaceae (Corylus, Ostrya, and Carpinus). Subsequent phylogenetic analysis also supports the subclassifications of these species.
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Neha Samir Roy,이성일,Kabwe Nkongolo,김남수 한국유전학회 2018 Genes & Genomics Vol.40 No.5
The Betulaceae family comprises two subfamilies, Betuloideae and Corylaceae. The subfamily Betuloideae contains two genera, Alnus Mill. and Betula L. Twenty putative long terminal repeat (LTR) retrotransposons were mined from 171 scaffolds containing 5,208,995 bp of dwarf birch (Betula nana) genome sequences. Five retrotransposons were finally selected after filtering the retrotransposon canonical features and nucleotide similarities between left and right LTR sequences. Of the five retroelements, three elements were found to be Ty1/Copia retrotransposons; identity of the other two elements could not be ascertained due to sequence undetermined ‘N’ bases in the sequence database. Inter-retrotranposon amplified polymorphism (IRAP) analysis, based on the LTR sequences of the mined LTR-retrotransposons, produced 179 discernible IRAP bands among the Alnus and Betula genera. Sequence analysis revealed no size homoplasy among the homologous IRAP bands. Phylogenetic and principle coordinate analysis, based on the band sharing among the taxa, showed the species in two different genera were clearly separated. The subgenera in each genus of Alnus and Betula were also distinguishable from the IRAP profiles. In the genus Betula, the species in subgenus Betula showed mixed clustering between species. This is incongruent with the phylogeographical distribution of the species.
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Gabriel Theriault,Paul Michael,Kabwe Nkongolo 한국유전학회 2016 Genes & Genomics Vol.38 No.4
Recent studies have found that many transporters, metabolic products and chelators play a role in heavy metal (HM) resistance in model plants. Knowledge of mechanisms involved in resistance to HM in higher plant species is limited. In the present study, the expression of four novel genes (AT2G16800, GR, ZAT11, and IREG1) in white birch (Betula papyrifera) growing in soil contaminated with different levels of nickel were investigated. B. papyrifera seedlings were treated with different doses of nickel including 5.56, 1600, and 4800 mg/kg in growth chamber screening trials. The expression of targeted genes in nickel resistant and susceptible genotypes was measured using RT-qPCR. Field trials were also conducted to assess the regulation of these genes in B. papyrifera growing in metal-contaminated and uncontaminated sites. The transcription factor ZAT11 was the only gene affected (downregulation) by nickel at the low dose of 5.56 mg/kg. The expression of all the four genes was affected by the high dose of 1600 mg/kg resulting in the downregulation of AT2G16800, GR, and ZAT11 and the upregulation of IREG1. ZAT11 and IREG1 were differentially expressed in resistant genotypes. No differences in gene expression were found when samples from metalcontaminated and reference field sites were compared, but the expression of AT2G16800 and IREG1 was higher in roots compared to leaves. The findings of this study suggest that the bioavailable amounts of nickel that is usually found in highly metal-contaminated soils in mining regions cannot trigger a measurable genetic response in plants.
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DNA methylation and histone modifications induced by abiotic stressors in plants
Czajka Karolina,Mehes-Smith Melanie,Nkongolo Kabwe 한국유전학회 2022 Genes & Genomics Vol.44 No.3
Background: A review of research shows that methylation in plants is more complex and sophisticated than in microorganisms and animals. Overall, studies on the effects of abiotic stress on epigenetic modifications in plants are still scarce and limited to few species. Epigenetic regulation of plant responses to environmental stresses has not been elucidated. This study summarizes key effects of abiotic stressors on DNA methylation and histone modifications in plants. Discussion: Plant DNA methylation and histone modifications in responses to abiotic stressors varied and depended on the type and level of stress, plant tissues, age, and species. A critical analysis of the literature available revealed that 44% of the epigenetic modifications induced by abiotic stressors in plants involved DNA hypomethylation, 40% DNA hypermethylation, and 16% histone modification. The epigenetic changes in plants might be underestimated since most authors used methods such as methylation-sensitive amplification polymorphism (MSAP), High performance liquid chromatography (HPLC), and immunolabeling that are less sensitive compared to bisulfite sequencing and single-base resolution methylome analyses. More over, mechanisms underlying epigenetic changes in plants have not yet been determined since most reports showed only the level or/and distribution of DNA methylation and histone modifications. Conclusions: Various epigenetic mechanisms are involved in response to abiotic stressors, and several of them are still unknown. Integrated analysis of the changes in the genome by omic approaches should help to identify novel components underlying mechanisms involved in DNA methylation and histone modifications associated with plant response to environmental stressors.
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