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甘蓝型油菜中 SnRK 家族基因的全基因组鉴定和特征分析。

Genome-wide identification and characterization of SnRK family genes in Brassica napus.

机构信息

Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.

出版信息

BMC Plant Biol. 2020 Jun 22;20(1):287. doi: 10.1186/s12870-020-02484-3.

DOI:10.1186/s12870-020-02484-3
PMID:32571241
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7310057/
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.

摘要

背景

蔗糖非发酵 1 相关蛋白激酶（SnRK）通过激活蛋白磷酸化途径，在应对生物和非生物胁迫方面发挥着重要作用。然而，在一种重要的油料作物油菜中，有关 SnRK 基因的信息却很少。最近，油菜参考基因组的发布序列为油菜中 BnSnRK 基因家族的全基因组鉴定和特征分析提供了一个很好的机会。

结果

在油菜基因组中鉴定出 114 个 SnRK 基因，分布在 19 条染色体上，根据系统发育分析和结构域类型将其分为三个亚家族。根据基因结构和基序组成分析，BnSnRK 序列在三个亚家族之间表现出明显的差异。还分析了油菜和拟南芥基因组之间的基因复制和基因同线性，以深入了解 BnSnRK 家族基因的进化特征。顺式作用元件分析表明，BnSnRK 可能对多种环境胁迫做出反应。此外，BnSnRKs 在不同组织和各种非生物胁迫下的表达模式也存在明显差异。此外，单核苷酸多态性（SNP）分布分析表明，BnSnRK 家族基因在油菜不同基因型中的功能存在差异。

结论

我们研究了 114 个 BnSnRK 的基因组结构、进化特征、表达模式和 SNP 分布。研究结果为今后研究油菜 BnSnRK 基因的功能特征提供了有价值的信息。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/f5e42594b3d3/12870_2020_2484_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/a95de4ab123c/12870_2020_2484_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/3a057c654d9d/12870_2020_2484_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/afec4cd68b0d/12870_2020_2484_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/f94c5ceb01f9/12870_2020_2484_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/9638d74774f0/12870_2020_2484_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/3f7148c3f5f1/12870_2020_2484_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/4cf73d1304d9/12870_2020_2484_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/94f77cb76c30/12870_2020_2484_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/f5e42594b3d3/12870_2020_2484_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/a95de4ab123c/12870_2020_2484_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/3a057c654d9d/12870_2020_2484_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/afec4cd68b0d/12870_2020_2484_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/f94c5ceb01f9/12870_2020_2484_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/9638d74774f0/12870_2020_2484_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/3f7148c3f5f1/12870_2020_2484_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/4cf73d1304d9/12870_2020_2484_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/94f77cb76c30/12870_2020_2484_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3f28/7310057/f5e42594b3d3/12870_2020_2484_Fig9_HTML.jpg

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