University of Oulu

Cervantes S, Vuosku J, Pyhäjärvi T. 2021. Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris. PeerJ 9:e11781 https://doi.org/10.7717/peerj.11781

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

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Author: Cervantes, Sandra1,2; Vuosku, Jaana1; Pyhäjärvi, Tanja1,3
Organizations: 1Department of Ecology and Genetics, University of Oulu, Oulu, Finland
2Biocenter Oulu, University of Oulu, Oulu, Finland
3Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 4.1 MB)
Persistent link: http://urn.fi/urn:nbn:fi-fe2021102151925
Language: English
Published: PeerJ, 2021
Publish Date: 2021-10-21
Description:

Abstract

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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Series: PeerJ
ISSN: 2167-8359
ISSN-E: 2167-8359
ISSN-L: 2167-8359
Volume: 9
Article number: e11781
DOI: 10.7717/peerj.11781
OADOI: https://oadoi.org/10.7717/peerj.11781
Type of Publication: A1 Journal article – refereed
Field of Science: 1181 Ecology, evolutionary biology
Subjects:
Bud
Funding: This work was supported by the Academy of Finland (grants 287431, 293819, 319313 and 329438) and Biocenter Oulu. This publication is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 676876 (GenTree). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Academy of Finland Grant Number: 287431
293819
319313
329438
Detailed Information: 287431 (Academy of Finland Funding decision)
293819 (Academy of Finland Funding decision)
319313 (Academy of Finland Funding decision)
329438 (Academy of Finland Funding decision)
Copyright information: Copyright 2021 Cervantes et al. Distributed under Creative Commons CC-BY 4.0
  https://creativecommons.org/licenses/by/4.0/