Events The 2nd International Electronic Conference on Plant Sciences—10th Anniversary of Journal Plants

Event submissions

Published

10.3390/IECPS2021-11937

This submission belongs to the session B. Plant Ecology, Biodiversity and Developmental Biology of the event The 2nd International Electronic Conference on Plant Sciences—10th Anniversary of Journal Plants

Published date

30 Nov, 2021

Academic Editor

Carmen Arena

Citation

Ana Usié, Bruna Mendes, Marta Antunes, Célia Leão, Liliana Marum, António Marcos Ramos, Transcriptome Characterization of Different Tissues of Stone Pine (Pinus pinea L.): de novo Assembly, in Proceedings of The 2nd International Electronic Conference on Plant Sciences—10th Anniversary of Journal Plants, 1 December–15 December 2021, MDPI: Basel, Switzerland, doi: 10.3390/IECPS2021-11937

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Transcriptome Characterization of Different Tissues of Stone Pine (Pinus pinea L.): de novo Assembly

Ana Usié ^1,2

Bruna Mendes ³

Marta Antunes ^3,4

Célia Leão ^2,3,5

Liliana Marum ^2,3

António Marcos Ramos ^2,3

1. CEBAL - Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo / IPBeja - Instituto Politécnico de Beja, 7801-908 Beja, Portugal, Portugal

2. MED-Mediterranean Institute for Agriculture, Environment and Development, Évora, Portugal

3. CEBAL - Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo / IPBeja - Instituto Politécnico de Beja, 7801-908 Beja, Portugal

4. 3cE3c – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Portugal

5. INIAV Instituto Nacional de Investigação Agrária e Veterinária, I.P. Laboratório Nacional de Referência de Saúde Animal. 2780-157 Oeiras, Portugal

Abstract

Stone pine (Pinus Pinea L.) is an emblematic tree currently distributed around the whole Mediterranean basin. The species is well known for the economics of its timber and its seeds, the pine nuts, which are commercialized in food industry. The Iberian Peninsula accounts for the 75% of the world stone pine distribution, being Portugal the second country with the largest area of stone pine, after Spain.

Despite its relevance, the genomic information available for the species is scarce due to the limited studies and data available. Until now no reference genome available. However, advances in sequencing technologies, such as RNAseq, have allowed the characterization of the transcriptome even for species with no reference genome available. The main purpose of this study was to characterize the stone pine transcriptome of seven tissues (needles, xylem, stem bark, terminal bud, first and second year pine cone and pine nuts) by performing a de novo transcriptome assembly. A transcriptome comprising 165,179 contigs with an accumulative size of 81,31 Mbps was generated. A total of 55,328 genes were predicted, which from 50,161 (90.66%) genes had at least one homologous hit against the SWISS-PROT and/or non-redundant NCBI databases. Additionally, InterPro signatures were assigned identifying protein domains and associating GO terms and KEGG pathways. Together, these results represent the first transcriptome characterization of multiple tissues of stone pine. The assembled and annotated sequences will be deposited in a public repository.

Further analysis are ongoing to identify differences in gene expression between tissues.

Acknowledgements: This work was co-financed by Program Alentejo 2020, through the European Fund for Regional Development under the scope SelectPinea- Development of genetic markers for relevant traits in stone pine (ALT20-03-0145-FEDER-000041). Authors also acknowledge FCT for Contrato – Programa to L. Marum (CEECINST/00131/2018) and FCT for UIDB/05183/2020

Keywords

transcriptome assembly

RNA-Seq

pinus pinea

Manuscript

sciforum-052493-done.pdf

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