Role of Homeobox Genes in the Development of Pinus Sylvestris

Guseva, Tatiana; Бирюков, В. В.; Sadovsky, Michael G.

doi:10.1007/978-3-030-45385-5_38

Cited by 2 publications

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“…The mapping and bioinformatic analyses of gene expression are based on the most complete and high-quality reference transcriptome of P. sylvestris available to date ( Ojeda et al, 2019 ). Previous transcriptome studies of P. sylvestris have concentrated on a narrow set of tissues in each study such as wood ( Paasela et al, 2017 ), embryo ( Merino et al, 2016 ), and needles ( Wachowiak et al, 2015 ; Duarte, Volkova & Geras’kin, 2019 ) or focused on a limited set of genes ( Guseva, Biriukov & Sadovsky, 2020 ). The present study allows comparison across a wide set of genes expressed in the above-ground parts of adult P. sylvestris trees growing in a natural forest.…”

Section: Discussionmentioning

confidence: 99%

Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris

Cervantes

Vuosku

Pyhäjärvi

2021

PeerJ

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Despite their ecological and economical importance, conifers genomic resources are limited, mainly due to the large size and complexity of their genomes. Additionally, the available genomic resources lack complete structural and functional annotation. Transcriptomic resources have been commonly used to compensate for these deficiencies, though for most conifer species they are limited to a small number of tissues, or capture only a fraction of the genes present in the genome. Here we provide an atlas of gene expression patterns for conifer Pinus sylvestris across five tissues: embryo, megagametophyte, needle, phloem and vegetative bud. We used a wide range of tissues and focused our analyses on the expression profiles of genes at tissue level. We provide comprehensive information of the per-tissue normalized expression level, indication of tissue preferential upregulation and tissue-specificity of expression. We identified a total of 48,001 tissue preferentially upregulated and tissue specifically expressed genes, of which 28% have annotation in the Swiss-Prot database. Even though most of the putative genes identified do not have functional information in current biological databases, the tissue-specific patterns discovered provide valuable information about their potential functions for further studies, as for example in the areas of plant physiology, population genetics and genomics in general. As we provide information on tissue specificity at both diploid and haploid life stages, our data will also contribute to the understanding of evolutionary rates of different tissue types and ploidy levels.

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Section: Discussionmentioning

confidence: 99%

Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris

Cervantes

Vuosku

Pyhäjärvi

2021

PeerJ

View full text Add to dashboard Cite

show abstract

“…The mapping and bioinformatic analyses of gene expression are based on the most complete and high-quality reference transcriptome of P. sylvestris available to date (Ojeda et al 2019). Previous transcriptome studies of P. sylvestris have concentrated on a narrow set of tissues in each study such as wood (Paasela et al 2017), embryo (Merino et al 2016), and needles (Wachowiak et al 2015; Duarte et al 2019) or focused on a limited set of genes (Guseva et al 2020). The present study allows comparison across a wide set of genes expressed in the above-ground parts of adult P. sylvestris trees growing in a natural forest.…”

Section: Resultsmentioning

confidence: 99%

Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant coniferPinus sylvestris

Cervantes

Vuosku

Paczesniak

et al. 2020

Preprint

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Background: Despite their ecological and economical importance, conifers still have limited genomic resources, mainly due to the large size and complexity of their genomes. In addition, several of the available genomic resources lack complete structural and functional annotation. Transcriptomic resources have been commonly used to compensate for these deficiencies, though for most conifer species the currently available transcriptomes are limited to a small number of tissues, or capture only a fraction of the genes present in the genome. Results: Here we provide an atlas of gene expression patterns for conifer Pinus sylvestris grown under natural conditions across five tissues: embryo, megagametophyte, needle, phloem, and vegetative bud. Compared to previous studies, we used a wider range of tissues and focused our analyses on the expression profiles of genes at tissue level. We provide comprehensive information of the per-tissue normalized expression level, and indication of tissue preferential upregulation or tissue preferential expression. We identified a total of 48,001 tissue preferentially upregulated and tissue specifically expressed genes, of which 28% have annotation in the Swiss-Prot database. The annotated genes were associated with a total of 84,498 GO terms, of which 1,834 had significant enrichment in different processes and functions, for example glyoxylate cycle in megagametophyte and defense response in needle. Even though most of the genes originating from the transcriptome do not have functional information in current biological databases, the tissue-specific patterns identified here provide valuable information about their potential functions for further studies. Conclusions: The genes identified in this study will contribute to improve the annotation of the already available and forthcoming conifer genomes. This atlas of gene expression also provides ground to further the research in the areas of plant physiology, population genetics, and genomics in general. As we provide information on tissue specificity at both diploid and haploid life stages, our data will also contribute to the understanding of evolutionary rates of different tissue types and ploidy levels.

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Role of Homeobox Genes in the Development of Pinus Sylvestris

Cited by 2 publications

References 28 publications

Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris

Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris

Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant coniferPinus sylvestris

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