Genome-wide identification and characterization of SnRK family genes in Brassica napus
Abstract Background Sucrose non-fermenting 1 related protein kinases (SnRK) play crucial roles in responding to biotic and abiotic stresses through activating protein phosphorylation pathways. However, little information of SnRK genes was available in Brassica napus, one of important oil crops. Rece...
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| Format: | Article |
| Language: | English |
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BMC
2020-06-01
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| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12870-020-02484-3 |
| _version_ | 1818275027008618496 |
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| author | Weizhuo Zhu Dezhi Wu Lixi Jiang Lingzhen Ye |
| author_facet | Weizhuo Zhu Dezhi Wu Lixi Jiang Lingzhen Ye |
| author_sort | Weizhuo Zhu |
| collection | DOAJ |
| description | Abstract Background Sucrose non-fermenting 1 related protein kinases (SnRK) play crucial roles in responding to biotic and abiotic stresses through activating protein phosphorylation pathways. However, little information of SnRK genes was available in Brassica napus, one of important oil crops. Recently, the released sequences of the reference genome of B.napus provide a good chance to perform genome-wide identification and characterization of BnSnRK gene family in the rapeseed. Results Totally 114 SnRK genes distributed on 19 chromosomes were identified in the genome of B.napus and classified into three subfamilies on the basis of phylogenetic analysis and the domain types. According to gene structure and motif composition analysis, the BnSnRK sequences showed obvious divergence among three subfamilies. Gene duplication and synteny between the genomes of the rapeseed and Arabidopsis were also analyzed to provide insights into the evolutionary characteristics of BnSnRK family genes. Cis-element analysis revealed that BnSnRKs may response to diverse environmental stresses. Moreover, the expression patterns of BnSnRKs in various tissues and under diverse abiotic stresses were distinct difference. Besides, Single Nucleotide Polymorphisms (SNP) distribution analysis suggests the function disparity of BnSnRK family genes in different genotypes of the rapeseed. Conclusion We examined genomic structures, evolution features, expression patterns and SNP distribution of 114 BnSnRKs. The results provide valuable information for functional characterization of BnSnRK genes in future studies. |
| first_indexed | 2024-12-12T22:23:13Z |
| format | Article |
| id | doaj.art-a02f001fd8bf4c5c99144e555b8fb7a9 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-12T22:23:13Z |
| publishDate | 2020-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-a02f001fd8bf4c5c99144e555b8fb7a92022-12-22T00:09:50ZengBMCBMC Plant Biology1471-22292020-06-0120111410.1186/s12870-020-02484-3Genome-wide identification and characterization of SnRK family genes in Brassica napusWeizhuo Zhu0Dezhi Wu1Lixi Jiang2Lingzhen Ye3Institute of Crop Science, Zhejiang UniversityInstitute of Crop Science, Zhejiang UniversityInstitute of Crop Science, Zhejiang UniversityInstitute of Crop Science, Zhejiang UniversityAbstract Background Sucrose non-fermenting 1 related protein kinases (SnRK) play crucial roles in responding to biotic and abiotic stresses through activating protein phosphorylation pathways. However, little information of SnRK genes was available in Brassica napus, one of important oil crops. Recently, the released sequences of the reference genome of B.napus provide a good chance to perform genome-wide identification and characterization of BnSnRK gene family in the rapeseed. Results Totally 114 SnRK genes distributed on 19 chromosomes were identified in the genome of B.napus and classified into three subfamilies on the basis of phylogenetic analysis and the domain types. According to gene structure and motif composition analysis, the BnSnRK sequences showed obvious divergence among three subfamilies. Gene duplication and synteny between the genomes of the rapeseed and Arabidopsis were also analyzed to provide insights into the evolutionary characteristics of BnSnRK family genes. Cis-element analysis revealed that BnSnRKs may response to diverse environmental stresses. Moreover, the expression patterns of BnSnRKs in various tissues and under diverse abiotic stresses were distinct difference. Besides, Single Nucleotide Polymorphisms (SNP) distribution analysis suggests the function disparity of BnSnRK family genes in different genotypes of the rapeseed. Conclusion We examined genomic structures, evolution features, expression patterns and SNP distribution of 114 BnSnRKs. The results provide valuable information for functional characterization of BnSnRK genes in future studies.http://link.springer.com/article/10.1186/s12870-020-02484-3Brassica napusSnRKGenome-wideAbiotic stressExpression patterns |
| spellingShingle | Weizhuo Zhu Dezhi Wu Lixi Jiang Lingzhen Ye Genome-wide identification and characterization of SnRK family genes in Brassica napus BMC Plant Biology Brassica napus SnRK Genome-wide Abiotic stress Expression patterns |
| title | Genome-wide identification and characterization of SnRK family genes in Brassica napus |
| title_full | Genome-wide identification and characterization of SnRK family genes in Brassica napus |
| title_fullStr | Genome-wide identification and characterization of SnRK family genes in Brassica napus |
| title_full_unstemmed | Genome-wide identification and characterization of SnRK family genes in Brassica napus |
| title_short | Genome-wide identification and characterization of SnRK family genes in Brassica napus |
| title_sort | genome wide identification and characterization of snrk family genes in brassica napus |
| topic | Brassica napus SnRK Genome-wide Abiotic stress Expression patterns |
| url | http://link.springer.com/article/10.1186/s12870-020-02484-3 |
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