Genome-wide identification and bioinformatics analysis of the oil palm SAUR gene family
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摘要: 【目的】挖掘并鉴定油棕生长素上调小RNA(SAUR)基因家族成员,并对其进行生物信息学分析,为油棕生长素信号转导机制的研究提供参考。【方法】根据拟南芥SAUR基因序列,在油棕全基因组数据库中同源序列搜索,并利用CDD和Pfam数据库进行SAUR蛋白结构域分析,剔除无保守结构域的序列,最后利用生物信息学软件对油棕SAUR基因家族成员进行可视化分析。【结果】从油棕全基因组中共鉴定出40个SAUR基因家族成员(EgSAUR1~EgSAUR40),有31个基因在油棕14条染色体上呈不均匀分布,其中4号染色体上分布的基因最多为7个;除EgSAUR14和EgSAUR24基因含有2个外显子外,其余38个基因均仅含1个外显子,无内含子。40个EgSAURs蛋白亚细胞定位于细胞核,其二级结构均由α-螺旋、β-转角、无规卷曲和延伸链组成,以无规卷曲和α-螺旋所占比例较高,其中有11个EgSAURs蛋白呈酸性,29个EgSAURs蛋白呈碱性。40个油棕SAUR蛋白被划分为四大类,其中第Ⅰ(除EgSAUR27蛋白外)、Ⅱ(除EgSAUR3和EgSAUR22外)、Ⅲ、Ⅳ类蛋白均有Auxin_inducible保守结构域。40个EgSAURs蛋白共含10种保守基序(Motif),其中Motif 2存在于所有基因成员中。在花中特异表达的EgSAURs基因(EgSAUR4、EgSAUR9、EgSAUR10、EgSAUR24、EgSAUR29、EgSAUR30、EgSAUR32和EgSAUR33)数量最多,其次为根、茎和叶,在中果皮中特异表达的基因数最少。【结论】基因重复和组织表达特异性是油棕SAUR家族基因的两大特点,推测该家族基因对油棕花的生长发育及授粉受精过程发挥调控作用。Abstract: 【Objective】To identify members of the small auxin-up RNA(SAUR)gene family in oil palm and analyze them by bioinformatics,so as to provide a foundation for the study of auxin the signal transduction mechanism in oil palm. 【Method】Homologs of Arabidopsis thaliana SAUR genes were identified in the whole genome database of oil palm,their protein sequences analyzed by CDD and Pfam database and sequences without conserved SAUR sequence motifs were eliminated. The SAUR gene family of oil palm was then analyzed by bioinformatics.【Result】A total of 40 oil palm SAUR genes(EgSAUR1-EgSAUR40) were obtained from the whole genome database,and 31 genes were unevenly distributed on the 14 chromosomes of oil palm,with 7 genes on chromosome 4,which contained the most number of genes. The two EgSAURs genes,EgSAUR14 and EgSAUR24,contained two exons,while the other 38 genes contained only one exon without an intron. 40 EgSAURs proteins were all localized in the nucleus. From predictions of the secondary structure of EgSAURs proteins,it was found that 40 EgSAUR proteins had four structural characteristics:α-helix,β-turn,random coil and extended chain. The proportions of random coil and α-helix were higher. 11 EgSAURs proteins were acidic and 29 EgSAURs proteins were alkaline. The 40 EgSAURs proteins were divided into four categories,of which the Ⅰ(except for EgSAUR27 protein),Ⅱ(except for EgSAUR3 and EgSAUR22),Ⅲ and Ⅳ proteins all have Auxin_inducible conservative domain. The oil palm SAUR gene family contained 10 conserved Motifs and Motif 2 existed in all gene members. The number of EgSAUR genes specifically expressed in flowers was the most(EgSAUR4,EgSAUR9,EgSAUR10,EgSAUR24,EgSAUR29,EgSAUR30,EgSAUR32 and EgSAUR33),followed by roots,stems and leaves. The number of genes specifically expressed in the mesocarp was the least.【Conclusion】Gene duplication and tissue expression specificity are the two characteristics of oil palm SAUR gene family members. It is speculated that SAUR gene plays a regulatory role in flower growth and development as well as pollination and fertilization in oil palm.
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Keywords:
- oil palm /
- SAUR /
- genome-wide /
- auxin /
- bioinformatics analysis /
- identifacation
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