TY  - JOUR
AU  - Ćuković, Katarina
AU  - Dragićević, Milan
AU  - Bogdanović, Milica
AU  - Paunović, Danijela
AU  - Giurato, Giorgio
AU  - Filipović, Biljana
AU  - Subotić, Angelina
AU  - Todorović, Slađana
AU  - Simonović, Ana
PY  - 2020
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3686
AB  - Centaurium erythraea Rafn. (common centaury, Gentianaceae) is a medicinal plant with great regeneration potential and developmental plasticity in vitro. Centaury can be regenerated from leaf explants by both somatic embryogenesis (SE) and shoot development (SD). We believe that its regeneration potential and developmental plasticity rest on high activity of certain genes, which may not be active or present in species recalcitrant to in vitro regeneration. However, there are no sequenced Gentianaceae genomes to support investigation of the molecular events during SE or SD. To this end, we have sequenced six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of in vitro grown plants) and de novo assembled centaury referent transcriptome comprising 105.726 genes. The high quality and completeness transcriptome was functionally annotated against NCBI nt, Swissprot and PFAM databases with KOG and GO enrichment. In addition, 11 housekeeping and functional genes were validated for expression stability in 27 tissue samples representing the processes of SE and SD, plants from nature and wounded tissues using GeNorm and NormFinder. The most stable genes that can be used for expression studies during SE, SD and in vitro manipulations are Ribosomal protein L2 (RPL2) and TATA binding protein 1 (TBP1) in combination with RAS (Rat Sarcoma)-related Nuclear protein (RAN) or Adenosine kinase (AK). These results comprise a complete framework for the search for genes involved in SE and SD, but may also be useful in identifying genes involved in biosynthesis of C. erythraea secondary metabolites.
PB  - Springer
T2  - Plant Cell, Tissue and Organ Culture
T1  - Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis
IS  - 2
VL  - 141
DO  - 10.1007/s11240-020-01801-w
SP  - 417
EP  - 433
ER  - 

@article{
author = "Ćuković, Katarina and Dragićević, Milan and Bogdanović, Milica and Paunović, Danijela and Giurato, Giorgio and Filipović, Biljana and Subotić, Angelina and Todorović, Slađana and Simonović, Ana",
year = "2020",
abstract = "Centaurium erythraea Rafn. (common centaury, Gentianaceae) is a medicinal plant with great regeneration potential and developmental plasticity in vitro. Centaury can be regenerated from leaf explants by both somatic embryogenesis (SE) and shoot development (SD). We believe that its regeneration potential and developmental plasticity rest on high activity of certain genes, which may not be active or present in species recalcitrant to in vitro regeneration. However, there are no sequenced Gentianaceae genomes to support investigation of the molecular events during SE or SD. To this end, we have sequenced six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of in vitro grown plants) and de novo assembled centaury referent transcriptome comprising 105.726 genes. The high quality and completeness transcriptome was functionally annotated against NCBI nt, Swissprot and PFAM databases with KOG and GO enrichment. In addition, 11 housekeeping and functional genes were validated for expression stability in 27 tissue samples representing the processes of SE and SD, plants from nature and wounded tissues using GeNorm and NormFinder. The most stable genes that can be used for expression studies during SE, SD and in vitro manipulations are Ribosomal protein L2 (RPL2) and TATA binding protein 1 (TBP1) in combination with RAS (Rat Sarcoma)-related Nuclear protein (RAN) or Adenosine kinase (AK). These results comprise a complete framework for the search for genes involved in SE and SD, but may also be useful in identifying genes involved in biosynthesis of C. erythraea secondary metabolites.",
publisher = "Springer",
journal = "Plant Cell, Tissue and Organ Culture",
title = "Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis",
number = "2",
volume = "141",
doi = "10.1007/s11240-020-01801-w",
pages = "417-433"
}

Ćuković, K., Dragićević, M., Bogdanović, M., Paunović, D., Giurato, G., Filipović, B., Subotić, A., Todorović, S.,& Simonović, A.. (2020). Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis. in Plant Cell, Tissue and Organ Culture
Springer., 141(2), 417-433.
https://doi.org/10.1007/s11240-020-01801-w

Ćuković K, Dragićević M, Bogdanović M, Paunović D, Giurato G, Filipović B, Subotić A, Todorović S, Simonović A. Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis. in Plant Cell, Tissue and Organ Culture. 2020;141(2):417-433.
doi:10.1007/s11240-020-01801-w .

Ćuković, Katarina, Dragićević, Milan, Bogdanović, Milica, Paunović, Danijela, Giurato, Giorgio, Filipović, Biljana, Subotić, Angelina, Todorović, Slađana, Simonović, Ana, "Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis" in Plant Cell, Tissue and Organ Culture, 141, no. 2 (2020):417-433,
https://doi.org/10.1007/s11240-020-01801-w . .

TY  - CONF
AU  - Simonović, Ana
AU  - Dragićević, Milan
AU  - Giurato, Giorgio
AU  - Filipović, Biljana
AU  - Todorović, Slađana
AU  - Bogdanović, Milica
AU  - Ćuković, Katarina
AU  - Subotić, Angelina
PY  - 2016
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/6157
AB  - Centaurium erythraea is a n endangered medicinal plant with great regeneration potential and developmental plasticity in vitro [1]. Identification of genes involved in organogenesis and somatic embryogenesis (SE) is the first step towards elucidation of molecular mechanisms underlying centaurys morphogenic plasticity. RNA from leaves (L), roots (R), embryogenic calii (EC), globular somatic embryos (GSE), cotyledonary somatic embryos (CSE) and adventitious buds (AB) was sequenced, resulting in 29-37 million reads/sample. Sequencing, de novo transcriptome assembly using Trinity and annotation were operated by Genomix4Life. The reference transcriptome (142 Mbp) contained 160,839 Trinity transcripts comprising 105,726 "genes". Of 160,839 transcripts, 44,288 had Blast hits, 26,435 had GO Slim annotation, whereas 9,552 were with GO mapping. The top-hit species was Coffea canephora. Relative expression was computed by aligning high quality reads to the Trinity transcripts and presented as TMM-FPKM. In each sample >=30,000 transcripts were expressed. Transcripts involved in different morphogenetic paths were filtered using R. Potential SE markers (FPKM >=1 in EC or GSE and >=8X higher FPKM in EC or GSE than in L, R and AB) included 1989 sequences, such as LRR receptor-like PK, germin-like proteins, TFs WRKY, AINTEGUMENTA and others. There were 1203 transcripts important for later SE development, including seed storage proteins and expansins. Finally, 727 transcripts with at least 8x higher FPKM in AB than in other samples were considered as important for organogenesis.
PB  - Belgrade: Faculty of Mathematics, University
C3  - Book of Abstracts: Belgrade Bioinformatics Conference: BelBI2016; 2016 Jun 20-24; Belgrade, Serbia
T1  - Identification of genes involved in morphogenesis in vitro in Centaurium erythraea Rafn. as a model organism
SP  - 97
EP  - 98
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_6157
ER  - 

@conference{
author = "Simonović, Ana and Dragićević, Milan and Giurato, Giorgio and Filipović, Biljana and Todorović, Slađana and Bogdanović, Milica and Ćuković, Katarina and Subotić, Angelina",
year = "2016",
abstract = "Centaurium erythraea is a n endangered medicinal plant with great regeneration potential and developmental plasticity in vitro [1]. Identification of genes involved in organogenesis and somatic embryogenesis (SE) is the first step towards elucidation of molecular mechanisms underlying centaurys morphogenic plasticity. RNA from leaves (L), roots (R), embryogenic calii (EC), globular somatic embryos (GSE), cotyledonary somatic embryos (CSE) and adventitious buds (AB) was sequenced, resulting in 29-37 million reads/sample. Sequencing, de novo transcriptome assembly using Trinity and annotation were operated by Genomix4Life. The reference transcriptome (142 Mbp) contained 160,839 Trinity transcripts comprising 105,726 "genes". Of 160,839 transcripts, 44,288 had Blast hits, 26,435 had GO Slim annotation, whereas 9,552 were with GO mapping. The top-hit species was Coffea canephora. Relative expression was computed by aligning high quality reads to the Trinity transcripts and presented as TMM-FPKM. In each sample >=30,000 transcripts were expressed. Transcripts involved in different morphogenetic paths were filtered using R. Potential SE markers (FPKM >=1 in EC or GSE and >=8X higher FPKM in EC or GSE than in L, R and AB) included 1989 sequences, such as LRR receptor-like PK, germin-like proteins, TFs WRKY, AINTEGUMENTA and others. There were 1203 transcripts important for later SE development, including seed storage proteins and expansins. Finally, 727 transcripts with at least 8x higher FPKM in AB than in other samples were considered as important for organogenesis.",
publisher = "Belgrade: Faculty of Mathematics, University",
journal = "Book of Abstracts: Belgrade Bioinformatics Conference: BelBI2016; 2016 Jun 20-24; Belgrade, Serbia",
title = "Identification of genes involved in morphogenesis in vitro in Centaurium erythraea Rafn. as a model organism",
pages = "97-98",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_6157"
}

Simonović, A., Dragićević, M., Giurato, G., Filipović, B., Todorović, S., Bogdanović, M., Ćuković, K.,& Subotić, A.. (2016). Identification of genes involved in morphogenesis in vitro in Centaurium erythraea Rafn. as a model organism. in Book of Abstracts: Belgrade Bioinformatics Conference: BelBI2016; 2016 Jun 20-24; Belgrade, Serbia
Belgrade: Faculty of Mathematics, University., 97-98.
https://hdl.handle.net/21.15107/rcub_ibiss_6157

Simonović A, Dragićević M, Giurato G, Filipović B, Todorović S, Bogdanović M, Ćuković K, Subotić A. Identification of genes involved in morphogenesis in vitro in Centaurium erythraea Rafn. as a model organism. in Book of Abstracts: Belgrade Bioinformatics Conference: BelBI2016; 2016 Jun 20-24; Belgrade, Serbia. 2016;:97-98.
https://hdl.handle.net/21.15107/rcub_ibiss_6157 .

Simonović, Ana, Dragićević, Milan, Giurato, Giorgio, Filipović, Biljana, Todorović, Slađana, Bogdanović, Milica, Ćuković, Katarina, Subotić, Angelina, "Identification of genes involved in morphogenesis in vitro in Centaurium erythraea Rafn. as a model organism" in Book of Abstracts: Belgrade Bioinformatics Conference: BelBI2016; 2016 Jun 20-24; Belgrade, Serbia (2016):97-98,
https://hdl.handle.net/21.15107/rcub_ibiss_6157 .