TY  - JOUR
AU  - Ahmadi-Teshniz, Fereshteh
AU  - Shiran, Behrouz
AU  - Mousavi-Fard, Sadegh
AU  - Fallahi, Hossein
AU  - Banović Đeri, Bojana
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1549
AB  - Background Novel strategies for improvement of ornamental plants and their properties relay on miRNA control of differential plant gene expression modulation. Still, in response to the same abiotic stresses, some conserved miRNA families show different expression patterns in different plant species. In parallel, the use of deep sequencing technologies reveals new levels of complexity of regulatory networks in plants through identification of new miRNAs. Methods and results Fritillaria imperialis plants were collected from their natural habitats in Koohrang, Chaharmahal va Bakhtiari, Iran. Several tissues including stamen, pistil, petal, sepal, leaf, stem, bulb and fruit were collected during three developmental stages (stem elongation, flower development and seed head stages). Using RNAseq and qRT-PCR approach, this research revealed 21 conserved miRNAs, matching 15 miRNA families, in Fritilaria imperialis. Conclusions The expression of seven conserved miRNAs (Fim-miR156b, Fim-miR159, Fim-miR166a-5p, Fim-miR169d-5p, Fim-miR171c, Fim-miR393 and Fim-miR396e-3p) was further investigated in different tissues and three developmental stages, suggesting different roles for these miRNAs during growth and development of crown imperial. Gained knowledge from this research can open the door to find efficient ways to secure crown imperial survival, preservation and utilization and if proven useful may be applied in other plant species as well.
PB  - Springer, Dordrecht
T2  - Molecular Biology Reports
T1  - Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing
EP  - 1132
IS  - 2
SP  - 1121
VL  - 49
DO  - 10.1007/s11033-021-06938-1
ER  - 

@article{
author = "Ahmadi-Teshniz, Fereshteh and Shiran, Behrouz and Mousavi-Fard, Sadegh and Fallahi, Hossein and Banović Đeri, Bojana",
year = "2022",
abstract = "Background Novel strategies for improvement of ornamental plants and their properties relay on miRNA control of differential plant gene expression modulation. Still, in response to the same abiotic stresses, some conserved miRNA families show different expression patterns in different plant species. In parallel, the use of deep sequencing technologies reveals new levels of complexity of regulatory networks in plants through identification of new miRNAs. Methods and results Fritillaria imperialis plants were collected from their natural habitats in Koohrang, Chaharmahal va Bakhtiari, Iran. Several tissues including stamen, pistil, petal, sepal, leaf, stem, bulb and fruit were collected during three developmental stages (stem elongation, flower development and seed head stages). Using RNAseq and qRT-PCR approach, this research revealed 21 conserved miRNAs, matching 15 miRNA families, in Fritilaria imperialis. Conclusions The expression of seven conserved miRNAs (Fim-miR156b, Fim-miR159, Fim-miR166a-5p, Fim-miR169d-5p, Fim-miR171c, Fim-miR393 and Fim-miR396e-3p) was further investigated in different tissues and three developmental stages, suggesting different roles for these miRNAs during growth and development of crown imperial. Gained knowledge from this research can open the door to find efficient ways to secure crown imperial survival, preservation and utilization and if proven useful may be applied in other plant species as well.",
publisher = "Springer, Dordrecht",
journal = "Molecular Biology Reports",
title = "Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing",
pages = "1132-1121",
number = "2",
volume = "49",
doi = "10.1007/s11033-021-06938-1"
}

Ahmadi-Teshniz, F., Shiran, B., Mousavi-Fard, S., Fallahi, H.,& Banović Đeri, B.. (2022). Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing. in Molecular Biology Reports
Springer, Dordrecht., 49(2), 1121-1132.
https://doi.org/10.1007/s11033-021-06938-1

Ahmadi-Teshniz F, Shiran B, Mousavi-Fard S, Fallahi H, Banović Đeri B. Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing. in Molecular Biology Reports. 2022;49(2):1121-1132.
doi:10.1007/s11033-021-06938-1 .

Ahmadi-Teshniz, Fereshteh, Shiran, Behrouz, Mousavi-Fard, Sadegh, Fallahi, Hossein, Banović Đeri, Bojana, "Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing" in Molecular Biology Reports, 49, no. 2 (2022):1121-1132,
https://doi.org/10.1007/s11033-021-06938-1 . .

TY  - JOUR
AU  - Shahvali, Roohollah
AU  - Shiran, Behrouz
AU  - Ravash, Rudabeh
AU  - Fallahi, Hossein
AU  - Banović Đeri, Bojana
PY  - 2020
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1308
AB  - Genus Prunus is of great importance for cultivation, mainly because its main species provide fruits and seeds, valuable ornamental qualifies and timber. However, stone fruit trees and almonds, major cultivars of genus Prunus, are sensitive to salt stress. Such sensitivity causes losses in stone fruit and almond production (ca. 50% of regular yield at high salinity grounds). Having in mind that symbiosis with arbuscular mycorrhiza fungi (AMF) may improve plant tolerance to salt stress and that symbiosis effect should be tested in case-by-case approach, we tested salt stress response of AMF inoculated GF677 rootstock (Prunus dulcis x Prunus persica hybrid) in this study. Adding to that, we tested GF677 symbiosis with two AMF species R. intraradices and F. mosseae. Results showed that under salinity stress AMF inoculated GF677 plants displayed improved physiological parameters (chlorophyll, soluble sugars and proline content) and increased antioxidant enzymes activity in comparison to non-inoculated control plants. Comparison of two AMF species beneficial effects on tested parameters revealed that for total chlorophyll content inoculation with F. mosseae has prevailed, while for total soluble sugars and proline content R. intraradices has prevailed. Finally, GF677 in symbiosis with F. mosseae was selected for molecular studies of salinity response. Since many of plants' genes involved in simultaneous response to salt stress and AMF colonization remained unidentified so far, we performed bioinformatics analysis of freely online available data to find differentially expressed genes common to these two responses. Upon GO classification and networking analysis of genes identified as common to both responses, we selected two most prominent ones (UDPGT73C6 and CYP707A3) and tested their expression profile in leaves and roots of F. mosseae inoculated GF677 rootstocks under salt stress. Even though specific roles of UDPGT73C6 and CYP707A3 are un-characterized in Prunus tree species, results suggested their involvement in response to salt stress and AMF inoculation of GF677 plants, which is in concordance with a scarce knowledge on their roles in other plant species. Based on this study finding we may conclude that symbiosis of GF677 rootstocks with AMF increases plants tolerance to salinity stress, which should be considered in other Prunus tree species as well.
PB  - Elsevier, Amsterdam
T2  - Scientia Horticulturae
T1  - Effect of symbiosis with arbuscular mycorrhizal fungi on salt stress tolerance in GF677 (peach x almond) rootstock
VL  - 272
DO  - 10.1016/j.scienta.2020.109535
ER  - 

@article{
author = "Shahvali, Roohollah and Shiran, Behrouz and Ravash, Rudabeh and Fallahi, Hossein and Banović Đeri, Bojana",
year = "2020",
abstract = "Genus Prunus is of great importance for cultivation, mainly because its main species provide fruits and seeds, valuable ornamental qualifies and timber. However, stone fruit trees and almonds, major cultivars of genus Prunus, are sensitive to salt stress. Such sensitivity causes losses in stone fruit and almond production (ca. 50% of regular yield at high salinity grounds). Having in mind that symbiosis with arbuscular mycorrhiza fungi (AMF) may improve plant tolerance to salt stress and that symbiosis effect should be tested in case-by-case approach, we tested salt stress response of AMF inoculated GF677 rootstock (Prunus dulcis x Prunus persica hybrid) in this study. Adding to that, we tested GF677 symbiosis with two AMF species R. intraradices and F. mosseae. Results showed that under salinity stress AMF inoculated GF677 plants displayed improved physiological parameters (chlorophyll, soluble sugars and proline content) and increased antioxidant enzymes activity in comparison to non-inoculated control plants. Comparison of two AMF species beneficial effects on tested parameters revealed that for total chlorophyll content inoculation with F. mosseae has prevailed, while for total soluble sugars and proline content R. intraradices has prevailed. Finally, GF677 in symbiosis with F. mosseae was selected for molecular studies of salinity response. Since many of plants' genes involved in simultaneous response to salt stress and AMF colonization remained unidentified so far, we performed bioinformatics analysis of freely online available data to find differentially expressed genes common to these two responses. Upon GO classification and networking analysis of genes identified as common to both responses, we selected two most prominent ones (UDPGT73C6 and CYP707A3) and tested their expression profile in leaves and roots of F. mosseae inoculated GF677 rootstocks under salt stress. Even though specific roles of UDPGT73C6 and CYP707A3 are un-characterized in Prunus tree species, results suggested their involvement in response to salt stress and AMF inoculation of GF677 plants, which is in concordance with a scarce knowledge on their roles in other plant species. Based on this study finding we may conclude that symbiosis of GF677 rootstocks with AMF increases plants tolerance to salinity stress, which should be considered in other Prunus tree species as well.",
publisher = "Elsevier, Amsterdam",
journal = "Scientia Horticulturae",
title = "Effect of symbiosis with arbuscular mycorrhizal fungi on salt stress tolerance in GF677 (peach x almond) rootstock",
volume = "272",
doi = "10.1016/j.scienta.2020.109535"
}

Shahvali, R., Shiran, B., Ravash, R., Fallahi, H.,& Banović Đeri, B.. (2020). Effect of symbiosis with arbuscular mycorrhizal fungi on salt stress tolerance in GF677 (peach x almond) rootstock. in Scientia Horticulturae
Elsevier, Amsterdam., 272.
https://doi.org/10.1016/j.scienta.2020.109535

Shahvali R, Shiran B, Ravash R, Fallahi H, Banović Đeri B. Effect of symbiosis with arbuscular mycorrhizal fungi on salt stress tolerance in GF677 (peach x almond) rootstock. in Scientia Horticulturae. 2020;272.
doi:10.1016/j.scienta.2020.109535 .

Shahvali, Roohollah, Shiran, Behrouz, Ravash, Rudabeh, Fallahi, Hossein, Banović Đeri, Bojana, "Effect of symbiosis with arbuscular mycorrhizal fungi on salt stress tolerance in GF677 (peach x almond) rootstock" in Scientia Horticulturae, 272 (2020),
https://doi.org/10.1016/j.scienta.2020.109535 . .

TY  - JOUR
AU  - Eshaghi, Mahsa
AU  - Shiran, Behrouz
AU  - Fallahi, Hossein
AU  - Ravash, Rudabeh
AU  - Banović Đeri, Bojana
PY  - 2019
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1218
AB  - Crown imperial (CI) has been used in traditional medicine. Today it is known that such beneficial effects are due to its richness in steroidal alkaloids (SA). Using de novo transcriptomics, orthologues/paralogues finder, phylogenetic analysis and tissue- and developmental stage-specific expression analysis, we identified ten genes and several TFs involved in the biosynthesis of SA in CI. The comparative analysis of ten genes expression profiles revealed the possibility of their co-regulation, which may imply the possibility of their organization in metabolic gene clusters. Having in mind convergent evolution of steroidal biosynthetic pathways in flowering plants and records of convergent evolution of specific proteins, observed expression patterns open a reasonable interest to investigate the possibility of the existence of genes cluster organization in SA pathway in the family Liliaceae or at least in some species of genus Fritillaria. Obtained results support transcriptomics as useful approach in elucidating genes underlying complex biochemical pathways.
PB  - Academic Press Inc Elsevier Science, San Diego
T2  - Genomics
T1  - Identification of genes involved in steroid alkaloid biosynthesis in Fritillaria imperialis via de novo transcriptomics
EP  - 1372
IS  - 6
SP  - 1360
VL  - 111
DO  - 10.1016/j.ygeno.2018.09.008
ER  - 

@article{
author = "Eshaghi, Mahsa and Shiran, Behrouz and Fallahi, Hossein and Ravash, Rudabeh and Banović Đeri, Bojana",
year = "2019",
abstract = "Crown imperial (CI) has been used in traditional medicine. Today it is known that such beneficial effects are due to its richness in steroidal alkaloids (SA). Using de novo transcriptomics, orthologues/paralogues finder, phylogenetic analysis and tissue- and developmental stage-specific expression analysis, we identified ten genes and several TFs involved in the biosynthesis of SA in CI. The comparative analysis of ten genes expression profiles revealed the possibility of their co-regulation, which may imply the possibility of their organization in metabolic gene clusters. Having in mind convergent evolution of steroidal biosynthetic pathways in flowering plants and records of convergent evolution of specific proteins, observed expression patterns open a reasonable interest to investigate the possibility of the existence of genes cluster organization in SA pathway in the family Liliaceae or at least in some species of genus Fritillaria. Obtained results support transcriptomics as useful approach in elucidating genes underlying complex biochemical pathways.",
publisher = "Academic Press Inc Elsevier Science, San Diego",
journal = "Genomics",
title = "Identification of genes involved in steroid alkaloid biosynthesis in Fritillaria imperialis via de novo transcriptomics",
pages = "1372-1360",
number = "6",
volume = "111",
doi = "10.1016/j.ygeno.2018.09.008"
}

Eshaghi, M., Shiran, B., Fallahi, H., Ravash, R.,& Banović Đeri, B.. (2019). Identification of genes involved in steroid alkaloid biosynthesis in Fritillaria imperialis via de novo transcriptomics. in Genomics
Academic Press Inc Elsevier Science, San Diego., 111(6), 1360-1372.
https://doi.org/10.1016/j.ygeno.2018.09.008

Eshaghi M, Shiran B, Fallahi H, Ravash R, Banović Đeri B. Identification of genes involved in steroid alkaloid biosynthesis in Fritillaria imperialis via de novo transcriptomics. in Genomics. 2019;111(6):1360-1372.
doi:10.1016/j.ygeno.2018.09.008 .

Eshaghi, Mahsa, Shiran, Behrouz, Fallahi, Hossein, Ravash, Rudabeh, Banović Đeri, Bojana, "Identification of genes involved in steroid alkaloid biosynthesis in Fritillaria imperialis via de novo transcriptomics" in Genomics, 111, no. 6 (2019):1360-1372,
https://doi.org/10.1016/j.ygeno.2018.09.008 . .

TY  - JOUR
AU  - Hafizi, Akram
AU  - Shiran, Behrouz
AU  - Maleki, Bahram
AU  - Imani, Ali
AU  - Banović Đeri, Bojana
PY  - 2013
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/643
AB  - The two main objectives of this research were to identify new S-RNase alleles in Iranian almond cultivars and to characterize naturally occurring mutations in these alleles that may cause self-compatibility. We investigated S genotypes of 22 Iranian almond cultivars using stylar RNase electrophoresis, PCR and DNA sequencing. We report six previously unidentified P. dulcis S-RNase alleles (S (45) , S (46) , S (47) , S (48) , S (49) and S (50) ). Four of 12 tested S-RNases were found to be non-functional in vitro: S (49) , S (50) , S (24) /S (na) and S (25) /S (47) . Detected point mutations in the C3 coding region of S (49) - and S (50) -RNase, leading to the replacement of a highly conserved cysteine and histidine residues, are with the highest probability the reason of these S-RNases inactivity. Results also suggested that ten Iranian almond cultivars display unique S genotype. All presented data confirm Iranian cultivars as valuable almond sources which are of interest to almond breeding and conservation programs.
PB  - Springer Heidelberg, Heidelberg
T2  - Trees-Structure and Function
T1  - Identification of new S-RNase self-incompatibility alleles and characterization of natural mutations in Iranian almond cultivars
EP  - 510
IS  - 3
SP  - 497
VL  - 27
DO  - 10.1007/s00468-012-0803-7
ER  - 

@article{
author = "Hafizi, Akram and Shiran, Behrouz and Maleki, Bahram and Imani, Ali and Banović Đeri, Bojana",
year = "2013",
abstract = "The two main objectives of this research were to identify new S-RNase alleles in Iranian almond cultivars and to characterize naturally occurring mutations in these alleles that may cause self-compatibility. We investigated S genotypes of 22 Iranian almond cultivars using stylar RNase electrophoresis, PCR and DNA sequencing. We report six previously unidentified P. dulcis S-RNase alleles (S (45) , S (46) , S (47) , S (48) , S (49) and S (50) ). Four of 12 tested S-RNases were found to be non-functional in vitro: S (49) , S (50) , S (24) /S (na) and S (25) /S (47) . Detected point mutations in the C3 coding region of S (49) - and S (50) -RNase, leading to the replacement of a highly conserved cysteine and histidine residues, are with the highest probability the reason of these S-RNases inactivity. Results also suggested that ten Iranian almond cultivars display unique S genotype. All presented data confirm Iranian cultivars as valuable almond sources which are of interest to almond breeding and conservation programs.",
publisher = "Springer Heidelberg, Heidelberg",
journal = "Trees-Structure and Function",
title = "Identification of new S-RNase self-incompatibility alleles and characterization of natural mutations in Iranian almond cultivars",
pages = "510-497",
number = "3",
volume = "27",
doi = "10.1007/s00468-012-0803-7"
}

Hafizi, A., Shiran, B., Maleki, B., Imani, A.,& Banović Đeri, B.. (2013). Identification of new S-RNase self-incompatibility alleles and characterization of natural mutations in Iranian almond cultivars. in Trees-Structure and Function
Springer Heidelberg, Heidelberg., 27(3), 497-510.
https://doi.org/10.1007/s00468-012-0803-7

Hafizi A, Shiran B, Maleki B, Imani A, Banović Đeri B. Identification of new S-RNase self-incompatibility alleles and characterization of natural mutations in Iranian almond cultivars. in Trees-Structure and Function. 2013;27(3):497-510.
doi:10.1007/s00468-012-0803-7 .

Hafizi, Akram, Shiran, Behrouz, Maleki, Bahram, Imani, Ali, Banović Đeri, Bojana, "Identification of new S-RNase self-incompatibility alleles and characterization of natural mutations in Iranian almond cultivars" in Trees-Structure and Function, 27, no. 3 (2013):497-510,
https://doi.org/10.1007/s00468-012-0803-7 . .