In silico characterization of putative gene homologues involved in somatic embryogenesis suggests that some conifer species may lack LEC2, one of the key regulators of initiation of the process. Ranade, S. S. & Egertsdotter, U. BMC Genomics, 22(1):392, December, 2021. ![In silico characterization of putative gene homologues involved in somatic embryogenesis suggests that some conifer species may lack LEC2, one of the key regulators of initiation of the process [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex 9 downloads Abstract Background Somatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of initiation and of development of somatic embryos is crucial for application of SE as an efficient tool to enable genetic improvement across genotypes by clonal propagation. Results Current work presents in silico identification of putative homologues of central regulators of SE initiation and development in conifers focusing mainly on key transcription factors (TFs) e.g. BBM , LEC1 , LEC1-LIKE, LEC2 and FUSCA3 , based on sequence similarity using BLASTP. Protein sequences of well-characterised candidates genes from Arabidopsis thaliana were used to query the databases (Gymno PLAZA, Congenie, GenBank) including whole-genome sequence data from two representative species from the genus Picea ( Picea abies ) and Pinus ( Pinus taeda ), for finding putative conifer homologues, using BLASTP. Identification of corresponding conifer proteins was further confirmed by domain search (Conserved Domain Database), alignment (MUSCLE) with respective sequences of Arabidopsis thaliana proteins and phylogenetic analysis (Phylogeny.fr). Conclusions This in silico analysis suggests absence of LEC2 in Picea abies and Pinus taeda , the conifer species whose genomes have been sequenced. Based on available sequence data to date, LEC2 was also not detected in the other conifer species included in the study. LEC2 is one of the key TFs associated with initiation and regulation of the process of SE in angiosperms. Potential alternative mechanisms that might be functional in conifers to compensate the lack of LEC2 are discussed.
@article{ranade_silico_2021,
title = {In silico characterization of putative gene homologues involved in somatic embryogenesis suggests that some conifer species may lack {LEC2}, one of the key regulators of initiation of the process},
volume = {22},
issn = {1471-2164},
url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07718-8},
doi = {10/gkbhh3},
abstract = {Abstract
Background
Somatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of initiation and of development of somatic embryos is crucial for application of SE as an efficient tool to enable genetic improvement across genotypes by clonal propagation.
Results
Current work presents in silico identification of putative homologues of central regulators of SE initiation and development in conifers focusing mainly on key transcription factors (TFs) e.g.
BBM
,
LEC1
,
LEC1-LIKE, LEC2
and
FUSCA3
, based on sequence similarity using BLASTP. Protein sequences of well-characterised candidates genes from
Arabidopsis thaliana
were used to query the databases (Gymno PLAZA, Congenie, GenBank) including whole-genome sequence data from two representative species from the genus
Picea
(
Picea abies
) and
Pinus
(
Pinus taeda
), for finding putative conifer homologues, using BLASTP. Identification of corresponding conifer proteins was further confirmed by domain search (Conserved Domain Database), alignment (MUSCLE) with respective sequences of
Arabidopsis thaliana
proteins and phylogenetic analysis (Phylogeny.fr).
Conclusions
This in silico analysis suggests absence of
LEC2
in
Picea abies
and
Pinus taeda
, the conifer species whose genomes have been sequenced. Based on available sequence data to date,
LEC2
was also not detected in the other conifer species included in the study.
LEC2
is one of the key TFs associated with initiation and regulation of the process of SE in angiosperms. Potential alternative mechanisms that might be functional in conifers to compensate the lack of
LEC2
are discussed.},
language = {en},
number = {1},
urldate = {2021-06-03},
journal = {BMC Genomics},
author = {Ranade, Sonali Sachin and Egertsdotter, Ulrika},
month = dec,
year = {2021},
pages = {392},
}
Downloads: 9
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Knowledge of genes involved in regulation of initiation and of development of somatic embryos is crucial for application of SE as an efficient tool to enable genetic improvement across genotypes by clonal propagation. Results Current work presents in silico identification of putative homologues of central regulators of SE initiation and development in conifers focusing mainly on key transcription factors (TFs) e.g. BBM , LEC1 , LEC1-LIKE, LEC2 and FUSCA3 , based on sequence similarity using BLASTP. Protein sequences of well-characterised candidates genes from Arabidopsis thaliana were used to query the databases (Gymno PLAZA, Congenie, GenBank) including whole-genome sequence data from two representative species from the genus Picea ( Picea abies ) and Pinus ( Pinus taeda ), for finding putative conifer homologues, using BLASTP. Identification of corresponding conifer proteins was further confirmed by domain search (Conserved Domain Database), alignment (MUSCLE) with respective sequences of Arabidopsis thaliana proteins and phylogenetic analysis (Phylogeny.fr). Conclusions This in silico analysis suggests absence of LEC2 in Picea abies and Pinus taeda , the conifer species whose genomes have been sequenced. Based on available sequence data to date, LEC2 was also not detected in the other conifer species included in the study. LEC2 is one of the key TFs associated with initiation and regulation of the process of SE in angiosperms. Potential alternative mechanisms that might be functional in conifers to compensate the lack of LEC2 are discussed.","language":"en","number":"1","urldate":"2021-06-03","journal":"BMC Genomics","author":[{"propositions":[],"lastnames":["Ranade"],"firstnames":["Sonali","Sachin"],"suffixes":[]},{"propositions":[],"lastnames":["Egertsdotter"],"firstnames":["Ulrika"],"suffixes":[]}],"month":"December","year":"2021","pages":"392","bibtex":"@article{ranade_silico_2021,\n\ttitle = {In silico characterization of putative gene homologues involved in somatic embryogenesis suggests that some conifer species may lack {LEC2}, one of the key regulators of initiation of the process},\n\tvolume = {22},\n\tissn = {1471-2164},\n\turl = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07718-8},\n\tdoi = {10/gkbhh3},\n\tabstract = {Abstract\n \n Background\n Somatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of initiation and of development of somatic embryos is crucial for application of SE as an efficient tool to enable genetic improvement across genotypes by clonal propagation.\n \n \n Results\n \n Current work presents in silico identification of putative homologues of central regulators of SE initiation and development in conifers focusing mainly on key transcription factors (TFs) e.g.\n BBM\n ,\n LEC1\n ,\n LEC1-LIKE, LEC2\n and\n FUSCA3\n , based on sequence similarity using BLASTP. Protein sequences of well-characterised candidates genes from\n Arabidopsis thaliana\n were used to query the databases (Gymno PLAZA, Congenie, GenBank) including whole-genome sequence data from two representative species from the genus\n Picea\n (\n Picea abies\n ) and\n Pinus\n (\n Pinus taeda\n ), for finding putative conifer homologues, using BLASTP. Identification of corresponding conifer proteins was further confirmed by domain search (Conserved Domain Database), alignment (MUSCLE) with respective sequences of\n Arabidopsis thaliana\n proteins and phylogenetic analysis (Phylogeny.fr).\n \n \n \n Conclusions\n \n This in silico analysis suggests absence of\n LEC2\n in\n Picea abies\n and\n Pinus taeda\n , the conifer species whose genomes have been sequenced. Based on available sequence data to date,\n LEC2\n was also not detected in the other conifer species included in the study.\n LEC2\n is one of the key TFs associated with initiation and regulation of the process of SE in angiosperms. 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