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 FENG Kai,HOU Jing,DAI Xiaogang,et al.Analyzing the SPL gene family in Salix suchowensis[J].Journal of Nanjing Forestry University(Natural Science Edition),2017,41(02):055-62.[doi:10.3969/j.issn.1000-2006.2017.02.009]





Analyzing the SPL gene family in Salix suchowensis
冯 凯 侯 静 戴晓港 李淑娴*
南方现代林业协同创新中心,南京林业大学林学院,江苏 南京 210037
FENG Kai HOU Jing DAI Xiaogang LI Shuxian*
Co-Innovation Center for the Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
簸箕柳 花发育 SPL基因家族 基因复制
Salix suchowensis flower development SPL gene family gene duplication
S718; Q811.4
【目的】确定SPL基因家族在不同物种之间的选择性保留和丢失情况,为后续研究被子植物花发育提供参考。【方法】通过在拟南芥(Arabidopsis thaliana)、毛果杨(Populus trichocarpa)、簸箕柳(Salix suchowensis)、葡萄(Vitis vinifera)、番木瓜(Carica papaya)、水稻(Oryza sativa)6种被子植物基因组中查找SPL结构域,寻找6个物种的SPL同源序列。对所找到的SPL序列进行BLASTN比对鉴定同源基因类型。使用自编Perl脚本结合KaKs_Calculator计算SPL同源基因的非同义突变(Ka)以及同义突变(Ks)值,采用共线性分析确定该基因家族的复制和扩张方式。【结果】在6种被子植物基因组中,共发现120个SPL基因。根据种内和种间旁系同源、直系同源基因以及这些同源基因选择压的计算显示:杨柳科SPL同源基因最多,共有旁系同源基因24对,直系同源基因50对; 番木瓜没有旁系同源基因。6个物种中,木本植物比草本植物直系同源基因更多,双子叶植物比单子叶植物直系同源基因更多; 所有旁系同源和直系同源基因的Ka/Ks值均小于1。系统发育树的分析结果与基因同源性分析基本吻合,证明了这两种分析方法具有较高的可靠性。此次研究选取了簸箕柳同一植株上开花和不开花的枝条进行了转录组测序分析,差异表达分析发现了1个SPL基因(willow_GLEAN_10025160)在两种枝条的转录组中表达差异显著(P≤0.01),其在开花枝条中的表达量显著高于未开花枝条,该基因被选为SPL基因家族中参与簸箕柳开花调控的候选基因。【结论】通过对6个物种SPL基因家族的分析,发现6个物种中所有直系同源和旁系同源基因都经历了纯化选择(Ka/Ks<1),基因功能保守。这6个物种除了经历过全基因组复制事件,还发生过大规模的基因丢失或者通过其他方式产生的基因扩张,阐明了它们在进化历史上的复制事件及SPL基因在不同物种中的选择性保留与丢失情况,为进一步研究其在调控簸箕柳开花中的作用提供了有力证据。
【Objective】This study focused mainly on the differential retention and expansion of the SPL gene family in different species and provided a basis for future study of floral development in angiosperms. 【Method】The SPL gene families of Arabidopsis thaliana, Populus trichocarpa, Salix suchowensis, Vitis vinifera, Carica papaya and Oryza sativa were identified using homology comparison against the SPL domain. BLASTN was used to identify different types of homologous gene pairs. We used in-house Perl scripts combined with KaKs_Calculator to calculate the non-synonymous mutation(Ka)and synonymous mutation(Ks)values of each SPL gene pair. Differential retention and expansion of the SPL gene families of these six angiosperms were determined by synteny analysis. 【Result】 We detected 120 SPL genes in the examined plants. By analyzing the paralogous and orthologous SPL genes among the six species, we found that the species of Salicaceae have a total of 24 paralogous SPLs and 50 orthologous SPLs, which are the most abundant among the six species; papaya had no paralogous SPL. Among these six species, woody plants had the most abundant orthologous SPLs compared with herbaceous plants, and dicotyledons were found to have more orthologous SPLs than monocotyledons. It is noteworthy that all the Ka/Ks values for the paralogous and orthologous SPL gene pairs were less than 1.0. In transcriptome analysis, we detected an SPL gene(willow_GLEAN_10025160)that showed significant different expression in flowering tillers compared to vegetative tillers(P≤ 0.01). 【Conclusion】On the basis of bioinformatic analysis, we found that all the Ka/Ks values for the paralogous and orthologous SPL gene pairs were less than 1.0, indicating that the SPL genes in the six examined species have been undergoing purifying selection during the course of evolution, and that their functions should be relatively conserved. We also found that despite whole-genome duplication events, these angiosperms have undergone large-scale gene loss and gene expansion. Based on the results of sequence collinearity, we explored the intraspecific collinearity of SPL genes and tracked their genome duplication events during the evolutionary history of the six plants. This study provides useful information and clues for further studies of the function of SPL genes in the regulation of plant flowering.


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收稿日期:2016-07-19 修回日期:2016-12-20
基金项目:国家林业公益性行业科研重大项目(201304102); 国家自然科学基金项目(31500533); 江苏高校优势学科建设工程资助项目(PAPD)
第一作者:冯凯(kaifeng@njfu.edu.cn)。*通信作者:李淑娴(shuxianli@njfu.edu.cn), 教授。
引文格式:冯凯, 侯静, 戴晓港,等. 簸箕柳SPL基因家族分析[J]. 南京林业大学学报(自然科学版),2017,41(2):55-62.
更新日期/Last Update: 2017-03-23