簸箕柳SPL基因家族分析
发布时间：2018-10-11 07:43
【摘要】：【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K_aK_s_Calculator计算SPL同源基因的非同义突变(K_a)以及同义突变(K_s)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K_a/K_s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(K_a/K_s1),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。
[Abstract]:[objective] to determine the selective retention and loss of SPL gene family among different species, [methods] the SPL domain was found in the genome of six angiosperms (Oryza sativa) from six angiosperms of Arabidopsis thaliana (Arabidopsis thaliana), poplar (Populus trichocarpa), dustpan willow (Salix suchowensis), grape (Vitis vinifera), papaya (Carica papaya), rice. SPL homologous sequences of 6 species were found. The SPL sequence was identified by BLASTN alignment. Using self-made Perl script and K_aK_s_Calculator to calculate the values of SPL homologous gene's non-synonymous mutation (K _ A) and synonymous mutation (K _ s), and using collinear analysis to determine the way of replication and expansion of the gene family. [results] in six angiosperms genomes, 120 SPL genes were found. According to the homology of intraspecific and interspecific lineal homologous genes and the selection pressure of these homologous genes, the results showed that the homologous genes of SPL in willow family were the most, with 24 pairs of homologous genes and 50 pairs of homologous genes of lineal line. Among the six species, there were more homologous genes in woody plants than in herbaceous plants, and more homologous genes in dicotyledonous plants than in monocotyledonous plants, and the K_a/K_s values of all homologous and lineal homologous genes were less than 1. The results of phylogenetic tree analysis are basically consistent with that of gene homology analysis, which proves that the two methods are reliable. In this study, the flowering and non-flowering branches on the same plant were selected for transcriptome sequencing analysis. Differential expression analysis showed that a SPL gene (willow_GLEAN_10025160) was significantly different in the transcriptional group of two branches (P 鈮，
本文编号：2263397
[Abstract]:[objective] to determine the selective retention and loss of SPL gene family among different species, [methods] the SPL domain was found in the genome of six angiosperms (Oryza sativa) from six angiosperms of Arabidopsis thaliana (Arabidopsis thaliana), poplar (Populus trichocarpa), dustpan willow (Salix suchowensis), grape (Vitis vinifera), papaya (Carica papaya), rice. SPL homologous sequences of 6 species were found. The SPL sequence was identified by BLASTN alignment. Using self-made Perl script and K_aK_s_Calculator to calculate the values of SPL homologous gene's non-synonymous mutation (K _ A) and synonymous mutation (K _ s), and using collinear analysis to determine the way of replication and expansion of the gene family. [results] in six angiosperms genomes, 120 SPL genes were found. According to the homology of intraspecific and interspecific lineal homologous genes and the selection pressure of these homologous genes, the results showed that the homologous genes of SPL in willow family were the most, with 24 pairs of homologous genes and 50 pairs of homologous genes of lineal line. Among the six species, there were more homologous genes in woody plants than in herbaceous plants, and more homologous genes in dicotyledonous plants than in monocotyledonous plants, and the K_a/K_s values of all homologous and lineal homologous genes were less than 1. The results of phylogenetic tree analysis are basically consistent with that of gene homology analysis, which proves that the two methods are reliable. In this study, the flowering and non-flowering branches on the same plant were selected for transcriptome sequencing analysis. Differential expression analysis showed that a SPL gene (willow_GLEAN_10025160) was significantly different in the transcriptional group of two branches (P 鈮，
本文编号：2263397
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