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Pagana I, Nava V, Puglia GD, Genovese C, Emma G, Salonia C, Cicero N, Alongi G. Cystoseira compressa and Ericaria mediterranea: Effective Bioindicators for Heavy- and Semi-Metal Monitoring in Marine Environments with Rocky Substrates. Plants (Basel) 2024; 13:530. [PMID: 38498557 PMCID: PMC10893443 DOI: 10.3390/plants13040530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/05/2024] [Accepted: 02/13/2024] [Indexed: 03/20/2024]
Abstract
Marine environmental monitoring is essential to ensure that heavy-metal (HM) concentrations remain within safe limits. Most seawater analyses currently consider sediment or water samples, but this approach does not apply to rocky substrates, where water samples can only indicate immediate contamination. We used two common Mediterranean algae species, Cystoseira compressa and Ericaria mediterranea, as bioindicators living in the intertidal zone on rocky substrates along the seacoast. HM concentrations were assessed over a one-year period in the perennial base crust and in the seasonal frond, considering marine sites characterised by different contamination risks. Both algae showed that HMs accumulate mainly in the perennial base rather than in the seasonal frond. Furthermore, the algae species always showed a different order of bioaccumulation factors: Cd > Ni > Pb > Cr > Cu > Mn > Zn for the frond and Pb > Cr > Ni > Cd > Mn > Cu > Zn for the base. Our study shows that C. compressa and E. mediterranea accumulate HM consistently with the types of sites analysed and differentially with respect to the part of the thallus. These results demonstrate that these algae can be effectively used as reliable bioindicators to assess the presence of HM in marine environments with rocky substrates, providing both short- and long-term monitoring.
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Affiliation(s)
- Ilaria Pagana
- Department of Biological, Geological and Environmental Sciences, University of Catania, 95128 Catania, Italy; (I.P.); (G.E.); (C.S.); (G.A.)
- Consorzio Nazionale Interuniversitario per le Scienze Del Mare, 00196 Rome, Italy
| | - Vincenzo Nava
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98168 Messina, Italy; (V.N.)
| | - Giuseppe D. Puglia
- Institute for Agriculture and Forestry Systems in the Mediterranean, National Research Council of Italy, Via Empedocle, 58, 95128 Catania, Italy
| | - Claudia Genovese
- Institute for Agriculture and Forestry Systems in the Mediterranean, National Research Council of Italy, Via Empedocle, 58, 95128 Catania, Italy
| | - Giuseppe Emma
- Department of Biological, Geological and Environmental Sciences, University of Catania, 95128 Catania, Italy; (I.P.); (G.E.); (C.S.); (G.A.)
| | - Carla Salonia
- Department of Biological, Geological and Environmental Sciences, University of Catania, 95128 Catania, Italy; (I.P.); (G.E.); (C.S.); (G.A.)
| | - Nicola Cicero
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98168 Messina, Italy; (V.N.)
| | - Giuseppina Alongi
- Department of Biological, Geological and Environmental Sciences, University of Catania, 95128 Catania, Italy; (I.P.); (G.E.); (C.S.); (G.A.)
- Consorzio Nazionale Interuniversitario per le Scienze Del Mare, 00196 Rome, Italy
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Arlotta C, Puglia GD, Genovese C, Toscano V, Karlova R, Beekwilder J, De Vos RCH, Raccuia SA. MYB5-like and bHLH influence flavonoid composition in pomegranate. Plant Sci 2020; 298:110563. [PMID: 32771164 DOI: 10.1016/j.plantsci.2020.110563] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/25/2020] [Accepted: 06/11/2020] [Indexed: 05/28/2023]
Abstract
The fruit of the pomegranate (Punica granatum L.) is an important nutraceutical food rich in polyphenolic compounds, including hydrolysable tannins, anthocyanins and flavonols. Their composition varies according to cultivar, tissue and fruit development stage and is probably regulated by a combination of MYB and bHLH type transcription factors (TFs). In this study, metabolomics analysis during fruit developmental stages in the main pomegranate cultivars, Wonderful and Valenciana with contrasting colour of their ripe fruits, showed that flavonols were mostly present in flowers while catechins were highest in unripe fruits and anthocyanins in late fruit maturation stages. A novel MYB TF, PgMYB5-like, was identified, which differs from previously isolated pomegranate TFs by unique C-terminal protein motifs and lack of the amino-acid residues conserved among anthocyanins promoting MYBs. In both pomegranate cultivars the expression of PgMYB5-like was high at flowering stage, while it decreased during fruit ripening. A previously identified bHLH-type TF, PgbHLH, also showed high transcript levels at flowering stage in both cultivars, while it showed a decrease in expression during fruit ripening in cv. Valenciana, but not in cv. Wonderful. Functional analysis of both TFs was performed by agro-infiltration into Nicotiana benthamiana leaves. Plants infiltrated with the PgMYB5-like+PgbHLH combined construct showed a specific and significant accumulation of intermediates of the flavonoid pathway, especially dihydroflavonols, while anthocyanins were not produced. Thus, we propose a role for PgMYB5-like and PgbHLH in the first steps of flavonoid production in flowers and in unripe fruits. The expression patterns of these two TFs may be key in determining the differential flavonoid composition in both flowers and fruits of the pomegranate varieties Wonderful and Valenciana.
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Affiliation(s)
- Carmen Arlotta
- Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy
| | - Giuseppe D Puglia
- Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy.
| | - Claudia Genovese
- Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy
| | - Valeria Toscano
- Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy
| | - Rumyana Karlova
- Wageningen Plant Research, Bioscience, 6700 AA, Wageningen, the Netherlands
| | - Jules Beekwilder
- Wageningen Plant Research, Bioscience, 6700 AA, Wageningen, the Netherlands
| | - Ric C H De Vos
- Wageningen Plant Research, Bioscience, 6700 AA, Wageningen, the Netherlands
| | - Salvatore A Raccuia
- Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy
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Puglia GD, Prjibelski AD, Vitale D, Bushmanova E, Schmid KJ, Raccuia SA. Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.). BMC Genomics 2020; 21:317. [PMID: 32819282 PMCID: PMC7441626 DOI: 10.1186/s12864-020-6670-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 03/13/2020] [Indexed: 12/11/2022] Open
Abstract
Background The investigation of transcriptome profiles using short reads in non-model organisms, which lack of well-annotated genomes, is limited by partial gene reconstruction and isoform detection. In contrast, long-reads sequencing techniques revealed their potential to generate complete transcript assemblies even when a reference genome is lacking. Cynara cardunculus var. altilis (DC) (cultivated cardoon) is a perennial hardy crop adapted to dry environments with many industrial and nutraceutical applications due to the richness of secondary metabolites mostly produced in flower heads. The investigation of this species benefited from the recent release of a draft genome, but the transcriptome profile during the capitula formation still remains unexplored. In the present study we show a transcriptome analysis of vegetative and inflorescence organs of cultivated cardoon through a novel hybrid RNA-seq assembly approach utilizing both long and short RNA-seq reads. Results The inclusion of a single Nanopore flow-cell output in a hybrid sequencing approach determined an increase of 15% complete assembled genes and 18% transcript isoforms respect to short reads alone. Among 25,463 assembled unigenes, we identified 578 new genes and updated 13,039 gene models, 11,169 of which were alternatively spliced isoforms. During capitulum development, 3424 genes were differentially expressed and approximately two-thirds were identified as transcription factors including bHLH, MYB, NAC, C2H2 and MADS-box which were highly expressed especially after capitulum opening. We also show the expression dynamics of key genes involved in the production of valuable secondary metabolites of which capitulum is rich such as phenylpropanoids, flavonoids and sesquiterpene lactones. Most of their biosynthetic genes were strongly transcribed in the flower heads with alternative isoforms exhibiting differentially expression levels across the tissues. Conclusions This novel hybrid sequencing approach allowed to improve the transcriptome assembly, to update more than half of annotated genes and to identify many novel genes and different alternatively spliced isoforms. This study provides new insights on the flowering cycle in an Asteraceae plant, a valuable resource for plant biology and breeding in Cynara and an effective method for improving gene annotation.
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Affiliation(s)
- Giuseppe D Puglia
- Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstrasse 21, 70599, Stuttgart, Germany. .,Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy.
| | - Andrey D Prjibelski
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Domenico Vitale
- Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy
| | - Elena Bushmanova
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Karl J Schmid
- Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstrasse 21, 70599, Stuttgart, Germany.
| | - Salvatore A Raccuia
- Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy
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Prjibelski AD, Puglia GD, Antipov D, Bushmanova E, Giordano D, Mikheenko A, Vitale D, Lapidus A. Extending rnaSPAdes functionality for hybrid transcriptome assembly. BMC Bioinformatics 2020; 21:302. [PMID: 32703149 PMCID: PMC7379828 DOI: 10.1186/s12859-020-03614-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 06/18/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND De novo RNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impossible to reconstruct complete sequences of complex genes and alternative isoforms. Recently emerged possibility to generate long RNA reads, such as PacBio and Oxford Nanopores, may dramatically improve the assembly quality, and thus the consecutive analysis. While reference-based tools for analysing long RNA reads were recently developed, there is no established pipeline for de novo assembly of such data. RESULTS In this work we present a novel method that allows to perform high-quality de novo transcriptome assemblies by combining accuracy and reliability of short reads with exon structure information carried out from long error-prone reads. The algorithm is designed by incorporating existing hybridSPAdes approach into rnaSPAdes pipeline and adapting it for transcriptomic data. CONCLUSION To evaluate the benefit of using long RNA reads we selected several datasets containing both Illumina and Iso-seq or Oxford Nanopore Technologies (ONT) reads. Using an existing quality assessment software, we show that hybrid assemblies performed with rnaSPAdes contain more full-length genes and alternative isoforms comparing to the case when only short-read data is used.
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Affiliation(s)
- Andrey D Prjibelski
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
| | - Giuseppe D Puglia
- Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo, Catania, Italy
| | - Dmitry Antipov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Elena Bushmanova
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Daniela Giordano
- Department of Electrical, Electronics and Computer Engineering, University of Catania, Catania, Italy
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Domenico Vitale
- Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo, Catania, Italy
| | - Alla Lapidus
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
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