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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 May 2023) | Viewed by 28990

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Special Issue Editors

Dr. Pedro Martínez-Gómez

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CEBAS-CSIC, Centro de Edafología y Biología Aplicada del Segura, Department of Plant Breeding, 30100 Murcia, Spain
Interests: Prunus breeding; marker-assisted selection; integrating genetic; genomic; transcriptomic; proteomic and epigenetic approaches
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Prof. Dr. Jesus V. Jorrin Novo

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Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
Interests: forest species; biotic and abiotic stresses; molecular markers; omics approaches; systems biology
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Dr. Ricardo Aroca

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Department of Soil and Plant Microbiology, EEZ-CSIC (Estación Experimental del Zaidin-Consejo Superior de Investigaciones Científicas), E-18100 Granada, Spain
Interests: abscisic acid; aquaporins; drought, ethylene; jasmonic acid; mycorrhizal fungi; salinity; soil bacteria; water relations
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Dr. María-Dolores Rey

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Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
Interests: plant breeding; forest species; drought; Phytophthora cinnamomi; molecular markers; cytogenetics; genomics; transcriptomics
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Dr. Veronica Truniger

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CEBAS-CSIC, Centro de Edafología y Biología Aplicada del Segura, 30100 Murcia, Spain
Interests: cap-independent translation; resistance to plant virus; plant virus-host interaction; plant virology
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Special Issue Information

Dear Colleagues,

We are happy to announce the IJMS Special Issue entitled “Plant Molecular Biology Research in Spain”. Spanish groups dealing with plant biology investigations using molecular biology approaches are well known and reputed within the international scenario, which justifies the launching of this Special Issue. This Special Issue aims to provide a comprehensive overview of recent advances in plant molecular science in Spain by inviting contributions from Spanish research institutes/laboratories that consolidate our understanding of this area. In addition, it aims to showcase the quality of the research carried out on different aspects of plant biology (development, response to stresses, etc.) with different species, including models, crops, forest trees, and wild, non-domesticated species, and their translation to biotechnology in the agri-food, environmental, and industrial sectors. In this Special Issue, we welcome submissions in the form of comprehensive reviews or original contributions, in various different areas related to the biological knowledge of plants from a molecular point of view, including classic physiology, genetics, plant–microbe interactions, developmental biology, biochemistry, cell biology and the most recent systems biology, and biotechnology, based on classic biochemical and the more recent -omics approaches, putting together wet and in silico techniques.

Dr. Pedro Martínez-Gómez
Prof. Dr. Jesus V. Jorrin Novo
Prof. Dr. Ricardo Aroca
Dr. María-Dolores Rey
Dr. Veronica Truniger
Guest Editors

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Published Papers (10 papers)

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Editorial

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9 pages, 1556 KiB

Open AccessEditorial

State-of-the-Art Molecular Plant Biology Research in Spain

by Jesús V. Jorrin-Novo, Ricardo Aroca, María-Dolores Rey, Verónica Truniger and Pedro Martínez-Gómez

Int. J. Mol. Sci. 2023, 24(23), 16557; https://doi.org/10.3390/ijms242316557 - 21 Nov 2023

Viewed by 1961

Abstract

Molecular plant biology is the study of the molecular basis of plant life [...] Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Biology Research in Spain)

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Research

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19 pages, 6017 KiB

Open AccessArticle

Olive Polyphenol Oxidase Gene Family

by Rosario Sánchez, Laura Arroyo, Pilar Luaces, Carlos Sanz and Ana G. Pérez

Int. J. Mol. Sci. 2023, 24(4), 3233; https://doi.org/10.3390/ijms24043233 - 6 Feb 2023

Cited by 8 | Viewed by 2490

Abstract

The phenolic compounds containing hydroxytyrosol are the minor components of virgin olive oil (VOO) with the greatest impact on its functional properties and health benefits. Olive breeding for improving the phenolic composition of VOO is strongly dependent on the identification of the key genes determining the biosynthesis of these compounds in the olive fruit and also their transformation during the oil extraction process. In this work, olive polyphenol oxidase (PPO) genes have been identified and fully characterized in order to evaluate their specific role in the metabolism of hydroxytyrosol-derived compounds by combining gene expression analysis and metabolomics data. Four PPO genes have been identified, synthesized, cloned and expressed in Escherichia coli, and the functional identity of the recombinant proteins has been verified using olive phenolic substrates. Among the characterized genes, two stand out: (i) OePPO2 with its diphenolase activity, which is very active in the oxidative degradation of phenols during oil extraction and also seems to be highly involved in the natural defense mechanism in response to biotic stress, and (ii) OePPO3, which codes for a tyrosinase protein, having diphenolase but also monophenolase activity, which catalyzes the hydroxylation of tyrosol to form hydroxytyrosol. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Biology Research in Spain)

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13 pages, 1661 KiB

Open AccessArticle

Giant Fern Genomes Show Complex Evolution Patterns: A Comparative Analysis in Two Species of Tmesipteris (Psilotaceae)

by Pol Fernández, Ilia J. Leitch, Andrew R. Leitch, Oriane Hidalgo, Maarten J. M. Christenhusz, Lisa Pokorny and Jaume Pellicer

Int. J. Mol. Sci. 2023, 24(3), 2708; https://doi.org/10.3390/ijms24032708 - 31 Jan 2023

Cited by 5 | Viewed by 2708

Abstract

Giant genomes are rare across the plant kingdom and their study has focused almost exclusively on angiosperms and gymnosperms. The scarce genetic data that are available for ferns, however, indicate differences in their genome organization and a lower dynamism compared to other plant groups. Tmesipteris is a small genus of mainly epiphytic ferns that occur in Oceania and several Pacific Islands. So far, only two species with giant genomes have been reported in the genus, T. tannensis (1C = 73.19 Gbp) and T. obliqua (1C = 147.29 Gbp). Low-coverage genome skimming sequence data were generated in these two species and analyzed using the RepeatExplorer2 pipeline to identify and quantify the repetitive DNA fraction of these genomes. We found that both species share a similar genomic composition, with high repeat diversity compared to taxa with small (1C < 10 Gbp) genomes. We also found that, in general, characterized repetitive elements have relatively high heterogeneity scores, indicating ancient diverging evolutionary trajectories. Our results suggest that a whole genome multiplication event, accumulation of repetitive elements, and recent activation of those repeats have all played a role in shaping these genomes. It will be informative to compare these data in the future with data from the giant genome of the angiosperm Paris japonica, to determine if the structures observed here are an emergent property of massive genomic inflation or derived from lineage specific processes. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Biology Research in Spain)

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25 pages, 2807 KiB

Open AccessArticle

Brassica napus Roots Use Different Strategies to Respond to Warm Temperatures

by Marta Boter, Jenifer Pozas, Jose A. Jarillo, Manuel Piñeiro and Mónica Pernas

Int. J. Mol. Sci. 2023, 24(2), 1143; https://doi.org/10.3390/ijms24021143 - 6 Jan 2023

Cited by 4 | Viewed by 3081

Abstract

Elevated growth temperatures are negatively affecting crop productivity by increasing yield losses. The modulation of root traits associated with improved response to rising temperatures is a promising approach to generate new varieties better suited to face the environmental constraints caused by climate change. In this study, we identified several Brassica napus root traits altered in response to warm ambient temperatures. Different combinations of changes in specific root traits result in an extended and deeper root system. This overall root growth expansion facilitates root response by maximizing root–soil surface interaction and increasing roots’ ability to explore extended soil areas. We associated these traits with coordinated cellular events, including changes in cell division and elongation rates that drive root growth increases triggered by warm temperatures. Comparative transcriptomic analysis revealed the main genetic determinants of these root system architecture (RSA) changes and uncovered the necessity of a tight regulation of the heat-shock stress response to adjusting root growth to warm temperatures. Our work provides a phenotypic, cellular, and genetic framework of root response to warming temperatures that will help to harness root response mechanisms for crop yield improvement under the future climatic scenario. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Biology Research in Spain)

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12 pages, 2235 KiB

Open AccessArticle

Transcriptome Analysis of Two Tetraploid Potato Varieties under Water-Stress Conditions

by Alba Alvarez-Morezuelas, Leire Barandalla, Enrique Ritter and Jose Ignacio Ruiz de Galarreta

Int. J. Mol. Sci. 2022, 23(22), 13905; https://doi.org/10.3390/ijms232213905 - 11 Nov 2022

Cited by 6 | Viewed by 2190

Abstract

Potato (Solanum tuberosum L.) is one of the most important crops worldwide, but due to its sensitivity to drought, its production can be affected by water availability. In this study, the varieties Agria and Zorba were used to determine the expression differences between control and water-stressed plants. For this purpose, they were sequenced by RNAseq, obtaining around 50 million transcripts for each variety and treatment. When comparing the significant transcripts obtained from control and drought-stressed plants of the Agria variety, we detected 931 genes that were upregulated and 2077 genes that were downregulated under stress conditions. When both treatments were compared in Zorba plants, 735 genes were found to be upregulated and 923 genes were found to be downregulated. Significantly more DEGs were found in the Agria variety, indicating a good stress response of this variety. “Abscisic acid and environmental stress-inducible protein TAS14-like” was the most overexpressed gene under drought conditions in both varieties, but expression differences were also found in numerous transcription factors and heat shock proteins. The principal GO term found was “cellular components”, more specifically related to the cell membrane and the cell wall, but other metabolic pathways such as carbohydrate metabolism and osmotic adjustment were also identified. These results provide valuable information related to the molecular mechanisms of tolerance to water stress in order to establish the basis for breeding new, more tolerant varieties. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Biology Research in Spain)

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17 pages, 2686 KiB

Open AccessArticle

Different RNA Elements Control Viral Protein Synthesis in Polerovirus Isolates Evolved in Separate Geographical Regions

by Manuel Miras, Miguel A. Aranda and Verónica Truniger

Int. J. Mol. Sci. 2022, 23(20), 12503; https://doi.org/10.3390/ijms232012503 - 19 Oct 2022

Cited by 3 | Viewed by 1916

Abstract

Most plant viruses lack the 5′-cap and 3′-poly(A) structures, which are common in their host mRNAs, and are crucial for translation initiation. Thus, alternative translation initiation mechanisms were identified for viral mRNAs, one of these being controlled by an RNA element in their 3′-ends that is able to enhance mRNA cap-independent translation (3′-CITE). The 3′-CITEs are modular and transferable RNA elements. In the case of poleroviruses, the mechanism of translation initiation of their RNAs in the host cell is still unclear; thus, it was studied for one of its members, cucurbit aphid-borne yellows virus (CABYV). We determined that efficient CABYV RNA translation requires the presence of a 3′-CITE in its 3′-UTR. We showed that this 3′-CITE requires the presence of the 5′-UTR in cis for its eIF4E-independent activity. Efficient virus multiplication depended on 3′-CITE activity. In CABYV isolates belonging to the three phylogenetic groups identified so far, the 3′-CITEs differ, and recombination prediction analyses suggest that these 3′-CITEs have been acquired through recombination with an unknown donor. Since these isolates have evolved in different geographical regions, this may suggest that their respective 3′-CITEs are possibly better adapted to each region. We propose that translation of other polerovirus genomes may also be 3′-CITE-dependent. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Biology Research in Spain)

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18 pages, 3156 KiB

Open AccessArticle

Transcriptome Analysis and Intraspecific Variation in Spanish Fir (Abies pinsapo Boiss.)

by Francisco Ortigosa, Concepción Ávila, Lourdes Rubio, Lucía Álvarez-Garrido, José A. Carreira, Rafael A. Cañas and Francisco M. Cánovas

Int. J. Mol. Sci. 2022, 23(16), 9351; https://doi.org/10.3390/ijms23169351 - 19 Aug 2022

Cited by 2 | Viewed by 2385

Abstract

Spanish fir (Abies pinsapo Boiss.) is an endemic, endangered tree that has been scarcely investigated at the molecular level. In this work, the transcriptome of Spanish fir was assembled, providing a large catalog of expressed genes (22,769), within which a high proportion were full-length transcripts (12,545). This resource is valuable for functional genomics studies and genome annotation in this relict conifer species. Two intraspecific variations of A. pinsapo can be found within its largest population at the Sierra de las Nieves National Park: one with standard green needles and another with bluish-green needles. To elucidate the causes of both phenotypes, we studied different physiological and molecular markers and transcriptome profiles in the needles. “Green” trees showed higher electron transport efficiency and enhanced levels of chlorophyll, protein, and total nitrogen in the needles. In contrast, needles from “bluish” trees exhibited higher contents of carotenoids and cellulose. These results agreed with the differential transcriptomic profiles, suggesting an imbalance in the nitrogen status of “bluish” trees. Additionally, gene expression analyses suggested that these differences could be associated with different epigenomic profiles. Taken together, the reported data provide new transcriptome resources and a better understanding of the natural variation in this tree species, which can help improve guidelines for its conservation and the implementation of adaptive management strategies under climatic change. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Biology Research in Spain)

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28 pages, 6245 KiB

Open AccessArticle

Monitoring Apricot (Prunus armeniaca L.) Ripening Progression through Candidate Gene Expression Analysis

by Beatriz E. García-Gómez, Juan A. Salazar, Jose A. Egea, Manuel Rubio, Pedro Martínez-Gómez and David Ruiz

Int. J. Mol. Sci. 2022, 23(9), 4575; https://doi.org/10.3390/ijms23094575 - 20 Apr 2022

Cited by 8 | Viewed by 2932

Abstract

This study aimed at the monitoring of the apricot (Prunus armeniaca L.) ripening progression through the expression analysis of 25 genes related to fruit quality traits in nine cultivars with great differences in fruit color and ripening date. The level of pigment compounds, such as anthocyanins and carotenoids, is a key factor in food taste, and is responsible for the reddish blush color or orange skin and flesh color in apricot fruit, which are desirable quality traits in apricot breeding programs. The construction of multiple linear regression models to predict anthocyanins and carotenoids content from gene expression allows us to evaluate which genes have the strongest influence over fruit color, as these candidate genes are key during biosynthetic pathways or gene expression regulation, and are responsible for the final fruit phenotype. We propose the gene CHS as the main predictor for anthocyanins content, CCD4 and ZDS for carotenoids content, and LOX2 and MADS-box for the beginning and end of the ripening process in apricot fruit. All these genes could be applied as RNA markers to monitoring the ripening stage and estimate the anthocyanins and carotenoids content in apricot fruit during the ripening process. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Biology Research in Spain)

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Review

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26 pages, 3852 KiB

Open AccessReview

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

by Ana María Maldonado-Alconada, María Ángeles Castillejo, María-Dolores Rey, Mónica Labella-Ortega, Marta Tienda-Parrilla, Tamara Hernández-Lao, Irene Honrubia-Gómez, Javier Ramírez-García, Víctor M. Guerrero-Sanchez, Cristina López-Hidalgo, Luis Valledor, Rafael M. Navarro-Cerrillo and Jesús V. Jorrin-Novo

Int. J. Mol. Sci. 2022, 23(17), 9980; https://doi.org/10.3390/ijms23179980 - 1 Sep 2022

Cited by 14 | Viewed by 3488

Abstract

The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors’ group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Biology Research in Spain)

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15 pages, 486 KiB

Open AccessReview

A Journey to the Core of the Plant Cell Cycle

by Crisanto Gutierrez

Int. J. Mol. Sci. 2022, 23(15), 8154; https://doi.org/10.3390/ijms23158154 - 24 Jul 2022

Cited by 7 | Viewed by 4078

Abstract

Production of new cells as a result of progression through the cell division cycle is a fundamental biological process for the perpetuation of both unicellular and multicellular organisms. In the case of plants, their developmental strategies and their largely sessile nature has imposed a series of evolutionary trends. Studies of the plant cell division cycle began with cytological and physiological approaches in the 1950s and 1960s. The decade of 1990 marked a turn point with the increasing development of novel cellular and molecular protocols combined with advances in genetics and, later, genomics, leading to an exponential growth of the field. In this article, I review the current status of plant cell cycle studies but also discuss early studies and the relevance of a multidisciplinary background as a source of innovative questions and answers. In addition to advances in a deeper understanding of the plant cell cycle machinery, current studies focus on the intimate interaction of cell cycle components with almost every aspect of plant biology. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Biology Research in Spain)

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