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Transcriptome of weeping pinyon pine, Pinus pinceana, shows differences across heterogeneous habitats

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Abstract

Key message

We reconstructed the needle tissue Transcriptome of P. pinceana for individuals from distinct biogeographic regions across a temperature and precipitation gradient that represents its natural distribution. Gene expression analysis via RNA-Seq identified differential response to biotic stress.

Abstract

Phenotypic plasticity includes physiological traits affected by subtle changes in mRNA expression levels, causing different molecular phenotypes. We assessed the differential response to climate heterogeneity across the geographic range of Pinus pinceana G. Gordon & Glendinning. This pinyon pine shows a fragmented geographic distribution suggesting adaptation to the arid and extreme conditions of the eastern mountain slopes of the Chihuahuan desert. The geographic distribution of P. pinceana spans regions with significant variation in annual temperature and precipitation. We tested whether phenotypic divergence is supported by differences in expression profiles in P. pinceana mature trees along its natural distribution and corresponds to the changes in drought and other environmental stress. The reconstructed Transcriptome included 45,431 high-quality annotations derived from the needles of seven individuals across contrasting biogeographic and climatic localities. Trees from the driest regions shared active responses related to abiotic factors. The differential expression analysis identified intermediates and regulators of abiotic stress response for 26 genes, highlighting families involved in the environmental response to abiotic stress, and proteins linked to up-regulated responses, such as LRR receptor-like serine/threonine-protein kinase and L-type lectin receptor kinases (LecRK), directly related to pathogens. When Chihuahuan desert samples were compared with arboretum samples, we found differential expression of a regulator of root morphogenesis, cysteine-rich receptor-like protein kinase (CRK28), which could relate to differential absorption in drought conditions.

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Availability of data and material

The RNA reads and the de novo Transcriptome assemblies are available in NCBI via Bioproject PRJNA63711. The code used is available at https://gitlab.com/lcorona/transcriptome_of_weeping_pinyon_pine.git.

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Acknowledgements

We thank L. Eguiarte and Jessica Gunoskey for valuable suggestions on data analysis and comments on earlier versions of the manuscript; the staff of the Herbarium of the UACh, especially Dr. E. Guizar Nolazco for permission to collect samples in the Pinetum Maximino Martínez; C. Bautista, E. García-Morales, D. Gernandt, S. Gonzalez, A. Moreno-Letelier, R. Salas-Lizana, A. Vázquez-Lobo, and A. Villarruel for fieldwork assistance; A. Gamboa de Buen, M. Garciadiego, M. López, and S. Shishkova for the RNA extraction training; P. Peláez, A. Trouern-Trend, and S. Zaman for bioinformatic assistance; and the Institute for Systems Genomics, Computational Biology Core, UCONN for access to both software and hardware. This work constitutes a partial fulfillment of the requirements for the Ph.D. degree at the Posgrado de Ciencias Biológicas at the Universidad Nacional Autónoma de México (UNAM) for LFC.

Funding

Fieldwork was supported by PAPIIT-DGAPA UNAM grant IN209816 to David Gernandt. Lab processing and sequencing was financed by Instituto de Ecología (DP) and CONACYT financial scholarship number 449615 to LFC.

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Authors and Affiliations

  1. Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico

    Laura Figueroa-Corona

  2. Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico

    Laura Figueroa-Corona & Daniel Piñero

  3. Facultad de Agrobiología, Universidad Michoacana de San Nicolás de Hidalgo, Uruapan, Mexico

    Patricia Delgado Valerio

  4. Department of Ecology and Evolutionary Biology, University of Connecticut, CT, 06269, Storrs, USA

    Jill Wegrzyn

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  1. Laura Figueroa-Corona
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  4. Daniel Piñero
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Correspondence to Daniel Piñero.

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Figueroa-Corona, L., Delgado Valerio, P., Wegrzyn, J. et al. Transcriptome of weeping pinyon pine, Pinus pinceana, shows differences across heterogeneous habitats. Trees 35, 1351–1365 (2021). https://doi.org/10.1007/s00468-021-02125-8

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