Pan-genome wide identification and analysis of the SAMS gene family in sunflowers (Helianthus annuus L.) revealed their intraspecies diversity and potential roles in abiotic stress tolerance
IntroductionS-adenosylmethionine (SAM), a key molecule in plant biology, plays an essential role in stress response and growth regulation. Despite its importance, the SAM synthetase (SAMS) gene family in sunflowers (Helianthus annuus L.) remains poorly understood.MethodsIn this study, the SAMS genes...
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Frontiers Media S.A.
2024-11-01
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1499024/full |
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| author | Chun Zhang Haoyu Li Jiamin Yin Zhibin Han Xinqi Liu Yang Chen |
| author_facet | Chun Zhang Haoyu Li Jiamin Yin Zhibin Han Xinqi Liu Yang Chen |
| author_sort | Chun Zhang |
| collection | DOAJ |
| description | IntroductionS-adenosylmethionine (SAM), a key molecule in plant biology, plays an essential role in stress response and growth regulation. Despite its importance, the SAM synthetase (SAMS) gene family in sunflowers (Helianthus annuus L.) remains poorly understood.MethodsIn this study, the SAMS genes were identified from the sunflower genome. Subsequently, the protein properties, gene structure, chromosomal location, cis-acting elements, collinearity, and phylogeny of the SAMS gene family were analyzed by bioinformatic methods. Finally, the expression patterns of SAMS genes in different tissues, under different hormonal treatment and abiotic stress were analyzed based on transcriptome data and qRT-PCR.ResultsThis study identified 58 SAMS genes across nine cultivated sunflower species, which were phylogenetically classified into seven distinct subgroups. Physicochemical properties and gene structure analysis showed that the SAMS genes are tightly conserved between cultivars. Collinearity analysis revealed segmental duplications as the primary driver of gene family expansion. The codon usage bias analysis suggested that natural selection substantially shapes the codon usage patterns of sunflower SAMS genes, with a bias for G/C-ending high-frequency codons, particularly encoding glycine, leucine, and arginine. Analysis of the cis-regulatory elements in promoter regions, implied their potential roles in stress responsiveness. Differential expression patterns for HanSAMS genes were observed in different tissues as well as under hormone treatment or abiotic stress conditions by analyzing RNA-seq data from previous studies and qRT-PCR data in our current study. The majority of genes demonstrated a robust response to BRA and IAA treatments in leaf tissues, with no significant expression change observed in roots, suggesting the response of HanSAMS genes to hormones is tissue-specific. Expression analyses under abiotic stresses demonstrated diverse expression profiles of HanSAMS genes, with HanSAMS5 showing significant upregulation in response to both drought and salt stresses.DiscussionThis comprehensive genomic and expression analysis provides valuable insights into the SAMS gene family in sunflowers, laying a robust foundation for future functional studies and applications in crop improvement for stress resilience. |
| format | Article |
| id | doaj-art-a613517ffa3e4f6ab4e8f8c95e172027 |
| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj-art-a613517ffa3e4f6ab4e8f8c95e1720272024-11-13T05:03:29ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-11-011510.3389/fpls.2024.14990241499024Pan-genome wide identification and analysis of the SAMS gene family in sunflowers (Helianthus annuus L.) revealed their intraspecies diversity and potential roles in abiotic stress toleranceChun Zhang0Haoyu Li1Jiamin Yin2Zhibin Han3Xinqi Liu4Yang Chen5Department of Agronomy, Hetao College, Bayannur, ChinaBayannur Modern Agriculture and Animal Husbandry Development Center, Bayannur, ChinaDepartment of Agronomy, Hetao College, Bayannur, ChinaDepartment of Agronomy, Hetao College, Bayannur, ChinaDepartment of Agronomy, Hetao College, Bayannur, ChinaDepartment of Agronomy, Hetao College, Bayannur, ChinaIntroductionS-adenosylmethionine (SAM), a key molecule in plant biology, plays an essential role in stress response and growth regulation. Despite its importance, the SAM synthetase (SAMS) gene family in sunflowers (Helianthus annuus L.) remains poorly understood.MethodsIn this study, the SAMS genes were identified from the sunflower genome. Subsequently, the protein properties, gene structure, chromosomal location, cis-acting elements, collinearity, and phylogeny of the SAMS gene family were analyzed by bioinformatic methods. Finally, the expression patterns of SAMS genes in different tissues, under different hormonal treatment and abiotic stress were analyzed based on transcriptome data and qRT-PCR.ResultsThis study identified 58 SAMS genes across nine cultivated sunflower species, which were phylogenetically classified into seven distinct subgroups. Physicochemical properties and gene structure analysis showed that the SAMS genes are tightly conserved between cultivars. Collinearity analysis revealed segmental duplications as the primary driver of gene family expansion. The codon usage bias analysis suggested that natural selection substantially shapes the codon usage patterns of sunflower SAMS genes, with a bias for G/C-ending high-frequency codons, particularly encoding glycine, leucine, and arginine. Analysis of the cis-regulatory elements in promoter regions, implied their potential roles in stress responsiveness. Differential expression patterns for HanSAMS genes were observed in different tissues as well as under hormone treatment or abiotic stress conditions by analyzing RNA-seq data from previous studies and qRT-PCR data in our current study. The majority of genes demonstrated a robust response to BRA and IAA treatments in leaf tissues, with no significant expression change observed in roots, suggesting the response of HanSAMS genes to hormones is tissue-specific. Expression analyses under abiotic stresses demonstrated diverse expression profiles of HanSAMS genes, with HanSAMS5 showing significant upregulation in response to both drought and salt stresses.DiscussionThis comprehensive genomic and expression analysis provides valuable insights into the SAMS gene family in sunflowers, laying a robust foundation for future functional studies and applications in crop improvement for stress resilience.https://www.frontiersin.org/articles/10.3389/fpls.2024.1499024/fullS-adenosylmethionine synthasepan-genomesunflowersabiotic stressesqRT-PCR |
| spellingShingle | Chun Zhang Haoyu Li Jiamin Yin Zhibin Han Xinqi Liu Yang Chen Pan-genome wide identification and analysis of the SAMS gene family in sunflowers (Helianthus annuus L.) revealed their intraspecies diversity and potential roles in abiotic stress tolerance Frontiers in Plant Science S-adenosylmethionine synthase pan-genome sunflowers abiotic stresses qRT-PCR |
| title | Pan-genome wide identification and analysis of the SAMS gene family in sunflowers (Helianthus annuus L.) revealed their intraspecies diversity and potential roles in abiotic stress tolerance |
| title_full | Pan-genome wide identification and analysis of the SAMS gene family in sunflowers (Helianthus annuus L.) revealed their intraspecies diversity and potential roles in abiotic stress tolerance |
| title_fullStr | Pan-genome wide identification and analysis of the SAMS gene family in sunflowers (Helianthus annuus L.) revealed their intraspecies diversity and potential roles in abiotic stress tolerance |
| title_full_unstemmed | Pan-genome wide identification and analysis of the SAMS gene family in sunflowers (Helianthus annuus L.) revealed their intraspecies diversity and potential roles in abiotic stress tolerance |
| title_short | Pan-genome wide identification and analysis of the SAMS gene family in sunflowers (Helianthus annuus L.) revealed their intraspecies diversity and potential roles in abiotic stress tolerance |
| title_sort | pan genome wide identification and analysis of the sams gene family in sunflowers helianthus annuus l revealed their intraspecies diversity and potential roles in abiotic stress tolerance |
| topic | S-adenosylmethionine synthase pan-genome sunflowers abiotic stresses qRT-PCR |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1499024/full |
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