The Chloroplast Genome of Endive (<i>Cichorium endivia</i> L.): Cultivar Structural Variants and Transcriptome Responses to Stress Due to Rain Extreme Events
The chloroplast (cp) genome diversity has been used in phylogeny studies, breeding, and variety protection, and its expression has been shown to play a role in stress response. Smooth- and curly-leafed endives (<i>Cichorium endivia</i> var. <i>latifolium</i> and var. <i>...
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MDPI AG
2023-09-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/9/1829 |
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| author | Giulio Testone Michele Lamprillo Maria Gonnella Giuseppe Arnesi Anatoly Petrovich Sobolev Riccardo Aiese Cigliano Donato Giannino |
| author_facet | Giulio Testone Michele Lamprillo Maria Gonnella Giuseppe Arnesi Anatoly Petrovich Sobolev Riccardo Aiese Cigliano Donato Giannino |
| author_sort | Giulio Testone |
| collection | DOAJ |
| description | The chloroplast (cp) genome diversity has been used in phylogeny studies, breeding, and variety protection, and its expression has been shown to play a role in stress response. Smooth- and curly-leafed endives (<i>Cichorium endivia</i> var. <i>latifolium</i> and var. <i>crispum</i>) are of nutritional and economic importance and are the target of ever-changing breeding programmes. A reference cp genome sequence was assembled and annotated (cultivar ‘Confiance’), which was 152,809 base pairs long, organized into the angiosperm-typical quadripartite structure, harboring two inverted repeats separated by the large- and short- single copy regions. The annotation included 136 genes, 90 protein-coding genes, 38 transfer, and 8 ribosomal RNAs and the sequence generated a distinct phyletic group within <i>Asteraceae</i> with the well-separated <i>C. endivia</i> and <i>intybus</i> species. SSR variants within the reference genome were mostly of tri-nucleotide type, and the cytosine to uracil (C/U) RNA editing recurred. The cp genome was nearly fully transcribed, hence sequence polymorphism was investigated by RNA-Seq of seven cultivars, and the SNP number was higher in smooth- than curly-leafed ones. All cultivars maintained C/U changes in identical positions, suggesting that RNA editing patterns were conserved; most cultivars shared SNPs of moderate impact on protein changes in the <i>ndhD</i>, <i>ndhA</i>, and <i>psbF</i> genes, suggesting that their variability may have a potential role in adaptive response. The cp transcriptome expression was investigated in leaves of plants affected by pre-harvest rainfall and rainfall excess plus waterlogging events characterized by production loss, compared to those of a cycle not affected by extreme rainfall. Overall, the analyses evidenced stress- and cultivar-specific responses, and further revealed that genes of the Cytochrome b6/f, and PSI-PSII systems were commonly affected and likely to be among major targets of extreme rain-related stress. |
| first_indexed | 2024-03-10T22:43:01Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T22:43:01Z |
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| spelling | doaj.art-10840476e8194137bd42a05acd8f69d22023-11-19T10:54:17ZengMDPI AGGenes2073-44252023-09-01149182910.3390/genes14091829The Chloroplast Genome of Endive (<i>Cichorium endivia</i> L.): Cultivar Structural Variants and Transcriptome Responses to Stress Due to Rain Extreme EventsGiulio Testone0Michele Lamprillo1Maria Gonnella2Giuseppe Arnesi3Anatoly Petrovich Sobolev4Riccardo Aiese Cigliano5Donato Giannino6Institute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300, Monterotondo, 00015 Rome, ItalyInstitute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300, Monterotondo, 00015 Rome, ItalyInstitute of Sciences of Food Production, National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, ItalyEnza Zaden Italia, Strada Statale Aurelia Km 96.400, Tarquinia, 01016 Viterbo, ItalyInstitute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300, Monterotondo, 00015 Rome, ItalySequentia Biotech SL, C/ del Dr. Trueta 179, 08005 Barcelona, SpainInstitute for Biological Systems, National Research Council (CNR), Via Salaria Km 29,300, Monterotondo, 00015 Rome, ItalyThe chloroplast (cp) genome diversity has been used in phylogeny studies, breeding, and variety protection, and its expression has been shown to play a role in stress response. Smooth- and curly-leafed endives (<i>Cichorium endivia</i> var. <i>latifolium</i> and var. <i>crispum</i>) are of nutritional and economic importance and are the target of ever-changing breeding programmes. A reference cp genome sequence was assembled and annotated (cultivar ‘Confiance’), which was 152,809 base pairs long, organized into the angiosperm-typical quadripartite structure, harboring two inverted repeats separated by the large- and short- single copy regions. The annotation included 136 genes, 90 protein-coding genes, 38 transfer, and 8 ribosomal RNAs and the sequence generated a distinct phyletic group within <i>Asteraceae</i> with the well-separated <i>C. endivia</i> and <i>intybus</i> species. SSR variants within the reference genome were mostly of tri-nucleotide type, and the cytosine to uracil (C/U) RNA editing recurred. The cp genome was nearly fully transcribed, hence sequence polymorphism was investigated by RNA-Seq of seven cultivars, and the SNP number was higher in smooth- than curly-leafed ones. All cultivars maintained C/U changes in identical positions, suggesting that RNA editing patterns were conserved; most cultivars shared SNPs of moderate impact on protein changes in the <i>ndhD</i>, <i>ndhA</i>, and <i>psbF</i> genes, suggesting that their variability may have a potential role in adaptive response. The cp transcriptome expression was investigated in leaves of plants affected by pre-harvest rainfall and rainfall excess plus waterlogging events characterized by production loss, compared to those of a cycle not affected by extreme rainfall. Overall, the analyses evidenced stress- and cultivar-specific responses, and further revealed that genes of the Cytochrome b6/f, and PSI-PSII systems were commonly affected and likely to be among major targets of extreme rain-related stress.https://www.mdpi.com/2073-4425/14/9/1829endivecp genome sequenceDNA and RNA variantscp transcriptome responseextreme rain stress |
| spellingShingle | Giulio Testone Michele Lamprillo Maria Gonnella Giuseppe Arnesi Anatoly Petrovich Sobolev Riccardo Aiese Cigliano Donato Giannino The Chloroplast Genome of Endive (<i>Cichorium endivia</i> L.): Cultivar Structural Variants and Transcriptome Responses to Stress Due to Rain Extreme Events Genes endive cp genome sequence DNA and RNA variants cp transcriptome response extreme rain stress |
| title | The Chloroplast Genome of Endive (<i>Cichorium endivia</i> L.): Cultivar Structural Variants and Transcriptome Responses to Stress Due to Rain Extreme Events |
| title_full | The Chloroplast Genome of Endive (<i>Cichorium endivia</i> L.): Cultivar Structural Variants and Transcriptome Responses to Stress Due to Rain Extreme Events |
| title_fullStr | The Chloroplast Genome of Endive (<i>Cichorium endivia</i> L.): Cultivar Structural Variants and Transcriptome Responses to Stress Due to Rain Extreme Events |
| title_full_unstemmed | The Chloroplast Genome of Endive (<i>Cichorium endivia</i> L.): Cultivar Structural Variants and Transcriptome Responses to Stress Due to Rain Extreme Events |
| title_short | The Chloroplast Genome of Endive (<i>Cichorium endivia</i> L.): Cultivar Structural Variants and Transcriptome Responses to Stress Due to Rain Extreme Events |
| title_sort | chloroplast genome of endive i cichorium endivia i l cultivar structural variants and transcriptome responses to stress due to rain extreme events |
| topic | endive cp genome sequence DNA and RNA variants cp transcriptome response extreme rain stress |
| url | https://www.mdpi.com/2073-4425/14/9/1829 |
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