Identification and Bioinformatics Analysis of SnRK2 and CIPK Family Genes in Sorghum

Through bioinformatic data mining, 10 SnRK2 and 31 CIPK genes were identified from sorghum genome. They are unevenly distributed in the sorghum chromosomes. Most SnRK2 genes have 8 introns, while the CIPK genes have a few (no intron or less than 3 introns) or more than I0 introns. Phylogenetic analy...

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Veröffentlicht in:Agricultural sciences in China 2010-01, Vol.9 (1), p.19-30
Hauptverfasser: LI, Li-bin, ZHANG, Yi-rong, LIU, Kai-chang, NI, Zhong-fu, FANG, Zhi-jun, SUN, Qi-xin, GAO, Jian-wei
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container_title Agricultural sciences in China
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ZHANG, Yi-rong
LIU, Kai-chang
NI, Zhong-fu
FANG, Zhi-jun
SUN, Qi-xin
GAO, Jian-wei
description Through bioinformatic data mining, 10 SnRK2 and 31 CIPK genes were identified from sorghum genome. They are unevenly distributed in the sorghum chromosomes. Most SnRK2 genes have 8 introns, while the CIPK genes have a few (no intron or less than 3 introns) or more than I0 introns. Phylogenetic analysis revealed that SnRK2 genes belong to one cluster and CIPK genes form the other independent cluster. The sorghum SnRK2s are subgrouped into three parts, and CIPK into five parts. More than half SnRK2 and CIPK genes present in homologous pairs, suggesting gene duplication may be due to the amplification of SnRK family genes. The kinase domains of SnRK2 family are highly conserved with 88.40% identity, but those of the CIPK family are less conserved with 63.72% identity. And the identity of sorghum CBLinteracting NAF domains of CIPKs is 61.66%. What's more, regarding to the sorghum SnRK2 and CIPK kinases, they are characterized with distinct motifs and their subcellular localization is not necessarily the same, which suggests they may be divergent in functions. Due to less conserved sequences, complex subcellular localization, and more family members, sorghum CIPK genes may play more flexible and multiple biological functions. According to the phylogenetic analysis of SnRK genes and SnRK functional studies in other plants, it is speculated that sorghum SnRK2 and CIPK genes may play important roles in stress response, growth and development.
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They are unevenly distributed in the sorghum chromosomes. Most SnRK2 genes have 8 introns, while the CIPK genes have a few (no intron or less than 3 introns) or more than I0 introns. Phylogenetic analysis revealed that SnRK2 genes belong to one cluster and CIPK genes form the other independent cluster. The sorghum SnRK2s are subgrouped into three parts, and CIPK into five parts. More than half SnRK2 and CIPK genes present in homologous pairs, suggesting gene duplication may be due to the amplification of SnRK family genes. The kinase domains of SnRK2 family are highly conserved with 88.40% identity, but those of the CIPK family are less conserved with 63.72% identity. And the identity of sorghum CBLinteracting NAF domains of CIPKs is 61.66%. What's more, regarding to the sorghum SnRK2 and CIPK kinases, they are characterized with distinct motifs and their subcellular localization is not necessarily the same, which suggests they may be divergent in functions. Due to less conserved sequences, complex subcellular localization, and more family members, sorghum CIPK genes may play more flexible and multiple biological functions. According to the phylogenetic analysis of SnRK genes and SnRK functional studies in other plants, it is speculated that sorghum SnRK2 and CIPK genes may play important roles in stress response, growth and development.</description><identifier>ISSN: 1671-2927</identifier><identifier>DOI: 10.1016/S1671-2927(09)60063-8</identifier><language>eng</language><publisher>Vegetable Research Institute,Shandong Academy of Agricultural Sciences,Jinan 250100,P.R.China%Department of Plant Genetics &amp; Breeding,China Agricultural University/National Center of Maize Improvement,Beijing 100193,P.R.China%Department of Scientific Research Administration,Shandong Academy of Agricultural Sciences,Jinan 250100,P.R.China%Department of Plant Genetics &amp; Breeding,China Agricultural University/State Key Laboratory for Agrobiotechnology,Beijing 100193,P.R.China%Experimental Farm,Shandong Academy of Agricultural Sciences,Jinan 250100,P.R.China</publisher><subject>PK基因 ; 亚细胞定位 ; 基因分析 ; 生物信息学 ; 系统发育分析</subject><ispartof>Agricultural sciences in China, 2010-01, Vol.9 (1), p.19-30</ispartof><rights>Copyright © Wanfang Data Co. 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Due to less conserved sequences, complex subcellular localization, and more family members, sorghum CIPK genes may play more flexible and multiple biological functions. 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They are unevenly distributed in the sorghum chromosomes. Most SnRK2 genes have 8 introns, while the CIPK genes have a few (no intron or less than 3 introns) or more than I0 introns. Phylogenetic analysis revealed that SnRK2 genes belong to one cluster and CIPK genes form the other independent cluster. The sorghum SnRK2s are subgrouped into three parts, and CIPK into five parts. More than half SnRK2 and CIPK genes present in homologous pairs, suggesting gene duplication may be due to the amplification of SnRK family genes. The kinase domains of SnRK2 family are highly conserved with 88.40% identity, but those of the CIPK family are less conserved with 63.72% identity. And the identity of sorghum CBLinteracting NAF domains of CIPKs is 61.66%. What's more, regarding to the sorghum SnRK2 and CIPK kinases, they are characterized with distinct motifs and their subcellular localization is not necessarily the same, which suggests they may be divergent in functions. Due to less conserved sequences, complex subcellular localization, and more family members, sorghum CIPK genes may play more flexible and multiple biological functions. 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subjects PK基因
亚细胞定位
基因分析
生物信息学
系统发育分析
title Identification and Bioinformatics Analysis of SnRK2 and CIPK Family Genes in Sorghum
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