家蚕后部丝腺差异蛋白组学及microRNA表达谱研究
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摘要
作为鳞翅目昆虫的典型代表,家蚕拥有其他昆虫无法替代的经济性状；而更重要的是,作为仅次于果蝇的第二大模式昆虫,它又几乎囊括了其他昆虫的所有生物性状。众多的特点不仅造就了一个可持续发展的经济产业,而且也吸引了一大批蚕桑科研领域之外的多学科人员的共同参与,使得近几年来蚕桑科研领域的蓬勃发展,取得了令人瞩目的学术成果。家蚕基因组计划的顺利完成,为进一步在后基因组时代中的研究提供了关键的理论基础和技术平台。后基因组时代的研究内容有很多,对基因组序列进行准确的注释是至关重要的任务之一,而且事实证明,生物体以一个复杂的系统,其基因的表达受到很多因子的调控,使得其表达水平与蛋白的表达水平存在一定的开差。要解决这一问题,我们不仅要依赖于对蛋白质的研究,而且也要深入探索其他调控因子的作用,比如1microRNA (miRNA)。本文就有关家蚕后部丝腺的蛋白质组和miRNA表达谱方面的工作进行了初步研究,取得的主要的研究结果如下：
1、高温胁迫下家蚕后部丝腺差异蛋白质组分析
我们用比较蛋白质组学和磷酸化蛋白质组学技术研究了高温胁迫下家蚕原种和杂交种后部丝腺蛋白质表达差异。结果发现,在获得的所有蛋白点中,有82.07%的蛋白点显示假性效应,6.17%显示超显性,11.76%的蛋白点为显性不足。我们用质谱鉴定了15个差异表达的蛋白点,其中,4个点包括热激蛋白和抑制素蛋白直接与热激应答有关,其余11个蛋白点在蚕丝的合成中发挥着重要作用。我们还鉴定了9个蛋白与蛋白质磷酸化有关。根据基因注释和代谢途径分析,这九个蛋白在高温胁迫后的信号转导过程中发挥着重要功能。在三个品种中大部分与丝腺合成有关的蛋白随着时间变化其表达被抑制,而与应激类相关蛋白则呈现上调趋势。而月.,与原种比较,杂交种中鉴定的大部分蛋白呈现超显性或显性不足的状态。结果表明高温刺激会影响后部丝腺中与热激和蚕丝合成相关蛋白的表达,更重要的是,在原种和杂交种中差异表达的蛋白在一定程度上揭示了杂种优势的存在
2. miRNA识别软件的筛选
虽然借助高通量测序可以发现大量的候选1niRNAs,但也会产生大量的真假难辨的数据从而给新miRNAs的鉴定带来很大的挑战。基于前人的研究,三种基于支持向量机的软件可以有效地去除一些假阳性的miRNAs。由于这些软件的设计大都建立在人类已矢miRNA前体的结构特征,所以有必要对人类和昆虫miRNAs前体特征进行对比,并比较它们对昆虫miRNAs的预测性能,进而挑选出最适合昆虫的软件。我们利用现有的数据库和生物信息学工具,系统地分析了人类miRNA前体和昆虫前体的特征差异以及昆虫24个不同种类之间的结构特征。结果表明,人类和昆虫miRNA前体的核苷酸组成,序列长度,核苷酸偏好和二级结构的特点是不同的。随后,借助三个现有的支持向量机的miRNA识别程序对这些已知的miRNA进行评分,以此来判断miRNA识别软件的性能高低。结果表明,2,633条昆虫前体中有2,229条被mirident分类器成功识别,比例高达84.66%,高于triplet-svm(72.50%)和(72.65%)pmirpo我们分别用软件检测每一个现有的昆虫物种,结果发现有四个物种,包括家蚕,果蝇,蜂和赤拟谷盗,获得了较低的成绩。特别是,与其他物种相比,家蚕的识别率最低,平均MFE指数也最小(0.73)。总的来说,这些结果为我们了解昆虫miRNA前体的特异性和多样性提供了线索,也为进一步开发出针对昆虫前体特征的rniRNA识别软件奠定了基础。
3、家蚕后部丝腺1miRNAs表达谱分析
我们用solexa技术对六个小RNA文库进行了深度测序,并用DASP方法检测到293个已知家蚕miRNAs,它们分成66个家族。从物种保守性来看,有40个家族保守在昆虫和其他物种间,剩下的26个家族只在家蚕上发现。另外，根据系统发育分析,这些miRNAs分布在14个从无脊椎动物到脊椎动物的物种上,为进一步研究动物的进化提供了系统发育标记和进化信号。同时,我们分析了不同产丝量品种之间miRNAs的表达差异,结果发现多丝量品种J1中下调表达的miRNAs远远多于裸蛹品种R1。而对两个不同发育时期的家蚕进行分析表明,丝腺细胞快速发育期比前期也同样拥有较多的下调miRNAS。两个独立实验分别印证了丝蛋白基因的表达可能受到了miRNAs的调控,从而造成丝心蛋白表达量的变化。我们随后采用mireap对未注释序列进行新miRNA的预测得到1，373条候选miRNAS。同时利用本实验筛选出的miRNA前体检测软件mirident程序,成功地从六个文库的候选miRNA中检验出414条非冗余新miRNA口432条前体序列,其中有50对miRNA/miRNA*复合体,结果大大丰富了家蚕miRNA数据库。借助生物信息学软件,我们对差异表达的miRNA进行靶标预测、GO分类和KEGG分析。我们发现，多丝量品种下调miRNAs对应的KEGG的靶基因数量明显高于上调表达的miRNAS。这些通路涉及范围较广,包括细胞凋亡,精氨酸脯氨酸代谢,氨基酸-tRNA生物合成,丙氨酸、天冬氨酸和谷氨酸代谢,氨基酸和核酸糖代谢等。通过对以丙氨酸、天冬氨酸和谷氨酸代谢通路的分析,结果表明下调miRNA对应靶基因更多地参与丙氨酸代谢途径,结茧蚕比裸蛹可能要合成更多的丙氨酸来促进丝腺细胞的发育。我们推测多丝量家蚕后部丝腺miRNAs的下调表达有利于家蚕囤积与丝蛋白合成相关的物质,储存能量,来促进蚕茧高产。
4、家蚕后部丝腺]miRNA表达谱芯片分析
为了更全面的验证五龄第三天家蚕后部丝腺miRNA表达谱,我们定制了一个囊括家蚕数据库,果蝇数据库,最近发表文章以及本实验预测的miRNAs的全方位探针,并最终鉴定出333条niRNAs,包含家蚕已矢miRNA213条和120条新miRNA,其中,在新miRNAs中发现有13条保守在果蝇中。我们对芯片的结果进行重复性检测以及与solexa测序相关性分析,发现芯片重复性高,与solexa相比更适合1niRNAs的定量分析。随后,我们分析了秋丰和白玉雌雄以及品种之间的差异性,结果表明无论性别还是品种,它们的miRNAs表达差异在总体水平上不显著,这可能与秋丰、白玉二者产丝性状相差很小有关。
本论文所取得的成果为研究生物在高温胁迫条件下的抗逆性以及杂种优势及抗性机理提供理论依据,为丰富家蚕miRNAs数据库提供了资源储备,同时也为研究后部丝腺1niRNAs在五龄期间蚕丝合成过程发挥的作用提供了参考。
As a typical representative Lepidoptera insect, silkworm Bombyx mori not only has irreplaceable economic traits, but more importantly, as a second model insect only next to Drosophila, it possesses almost all the biological characteristic of other insects. Such outstanding features collectively support a sustainable economy industry, and moreover, a large number of multidisciplinary participation is also attracted. All of these have contributed lots of valuable findings to the researches on silkworm in recent years. Especially, the successful accomplishment of silkworm genome project provides us critical theoretical basis and technological platform to further study in the post-genomic era. There are many research contents in post genomic era. For instance, the accurate annotation to the genome is one of the important tasks. It has been proved that organisms are complex systems, and its gene expression is regulated by many factors. To some extent, the expression levels of mRNA do not represent the protein levels. To solve this problem and further reveal the complex mechanisms in organisms which are under physiological or pathological conditions, we should not only rely on the study of proteins, but also to explore other regulatory factors, such as microRNA (miRNA). This study focused on comparative proteomics and expression profile of miRNAs in the posterior silk glands of Bombyx mori and obtained several preliminary findings as follows:
1. Comparative proteomic and phosphoproteomic analysis of the silkworm posterior silk gland under high temperature treatment
The proteins from the posterior silk gland of silkworm hybrids and their parents reared under high temperatures were studied by using comparative proteomic and phosphoproteomic analysis. A total of82.07%.6.17%and11.76%protein spots showed additivity. overdominance and underdominance patterns, respectively. Fifteen differentially expressed protein spots were identified by peptide mass fingerprinting. Among these, four spots, including sHSPs and prohibitin protein that were directly relevant to heat response, were identified. Eleven protein spots were found to play an important role in silk synthesis, and nine protein spots expressed phosphorylation states. According to Gene ontology (GO) and KEGG pathway analysis, these nine spots played an important role in stress-induced signal transduction. Expression of most silk synthesis-related proteins was reduced, whereas stress-responsive proteins increased with heat exposure time in three breeds. Furthermore, most proteins showed under-or overdominance in the hybrids compared to the parents. The results suggested that high temperature could alter the expression of proteins related to silk synthesis and heat response in silkworm. Moreover, differentially expressed proteins occurring in the hybrid and its parents may be the main explanation of the observed heterosis.
2. Bioinformatics analysis and screening of miRNA prediction programs
Although thousands of candidate novel miRNAs can be found by deep-sequencing technology, many pseudo-miRNAs might be produced and bring challenge to further miRNAs identification. Based on the previous research, three SVM-based predictions were selected due to their good performance on distinguishing real-or pseudo-miRNAs. Because all of them were developed based on the known human pre-miRNA characteristics, it sounds reasonable to compare the feature differences between humans and insects, and then select a more suitable program according to their predicting performances on insects. In the present work, we have systematically analyzed, utilizing bioinformatics tools, the featural differences between human and insect pre-miRNAs, as well as differences across24insect species. Results showed that the nucleotide composition, sequence length, nucleotides preference and secondary structure features between human and insects were different. Subsequently, with the aid of three available SVM-based prediction programs, pre-miRNA sequences were evaluated and given corresponding scores. Thus it was found that of2633sequences from the24chosen insect species.2229(84.7%) were successfully recognized by the Mirident classifier, higher than Triplet-SVM (72.5%) and PMirP (72.6%). In contrast, four species, including the domestic silkworm moth, the fruit fly. Drosophila melanogaster Meigen, the honeybee. Apis mellifera L. and the Red Flour beetle, Tribolium castaneum (Herbst). were found to be largely responsible for the poor performance of some sequence matching. Compared with other species. B. mori especially showed the worst performance with the lowest average MFE index (0.73). Collectively these results pave the way for understanding specificity and diversity of miRNA precursors in insects, and lay the foundation for the further development of more suitable algorisms for insects.
3. miRNAs profiling in posterior silk gland of silkworm identified by solexa deep-sequencing
In order to study the miRNAs expression profiling of silkworm posterior silk gland, we sequenced six small RNA libraries and obtained293known miRNAs. We found that all the known miRNAs were divided into65miRNA families with the exception of undefined miRNAs, in which,40families were conserved in insects, the left families were only discovered in silkworm. From phylogenetic analysis, those conserved miRNAs were widely distributed in over14species from invertebrates to vertebrates. Result showed that these conserved miRNAs might serve as potential phylogenetic markers and rapid evolutionary signaling molecules. At meantime, we analyzed different expression profiling of two strains with different silk-synthesis traits. One named J1is a strain of silkworm which can normally produce silk, the other termed R1which is the mutant of J1, lack of the ability of spinning cocoon. We found more down-regulated miRNAs in J1compared with it counterpart. We also analyzed the different expression profiles of two developmental stages, specifically,4th-instar molting to5th-instar day-2and5th-instar day-3to5th-instar day-8before spinning. Result showed that the miRNAs expression of stage2obviously declined compared to stage1. Two individual experiments confirmed that silk synthesis related genes might be regulated by miRNAs, which influenced the expression profile of silk proteins. Meanwhile, we employed mireap to predict the novel miRNAs in six libraries with the result of1.373new findings. Utilizing mirident program,432pre-miRNA sequences and414non-redundant miRNAs were successfully recognized to be novel miRNAs. Among these novel miRNAs, we found50pairs of miRNA/miRNA*duplex, which largely enriched the miRNA database. Furthermore, Utilizing RNAhybrid to predict the target genes of differentially expressed miRNAs, we found that many down-regulated miRNAs in J1or stage2were in connection with metabolism and synthesis, which further illustrated the likely function which miRNAs played in silk synthesis.
4. Identification of miRNAs in5th-3day of PSG by microarray
With the aid of microarray.333mature miRNAs were confirmed, and in which,213miRNAs were known miRNAs, and the left, including13conserved in Drosophila, were novel. We also analyzed their different expression profiling between genders and breeds. Results showed that there were no significant differences in genders and in breeds. There were28differentially expressed miRNAs in male and female of Q. Twenty of them were up-regulated in female silkworms, while only8of them were up-regulated in male. On the other hand, sixteen differentially expressed miRNAs were identified in two genders of B, in which, seven were up-regualted in female, while the left in male. Meantime, we also compared the differences between two breeds and observed that4miRNAs up-regulated in Q, contrary to8up-regulated in B. Nevertheless, the newly identified miRNAs largely enrich the repertoire of silkworm miRNAs. Moreover, comparative analysis of known and novel miRNAs indicated that the expression level of miRNAs might be the key reason to interpret different yields of cocoon.
All of the results shed light to further illustration of stress response and heteosis occurring in organisms under high tempreture stress. The newly identified miRNAs provided first hand data for extending the miRNA database, and more important, these findings might pave the way for elucidating likely function of miRNAs in the silk production of posterior silk gland at final moth of silkworm.
1、高温胁迫下家蚕后部丝腺差异蛋白质组分析
我们用比较蛋白质组学和磷酸化蛋白质组学技术研究了高温胁迫下家蚕原种和杂交种后部丝腺蛋白质表达差异。结果发现,在获得的所有蛋白点中,有82.07%的蛋白点显示假性效应,6.17%显示超显性,11.76%的蛋白点为显性不足。我们用质谱鉴定了15个差异表达的蛋白点,其中,4个点包括热激蛋白和抑制素蛋白直接与热激应答有关,其余11个蛋白点在蚕丝的合成中发挥着重要作用。我们还鉴定了9个蛋白与蛋白质磷酸化有关。根据基因注释和代谢途径分析,这九个蛋白在高温胁迫后的信号转导过程中发挥着重要功能。在三个品种中大部分与丝腺合成有关的蛋白随着时间变化其表达被抑制,而与应激类相关蛋白则呈现上调趋势。而月.,与原种比较,杂交种中鉴定的大部分蛋白呈现超显性或显性不足的状态。结果表明高温刺激会影响后部丝腺中与热激和蚕丝合成相关蛋白的表达,更重要的是,在原种和杂交种中差异表达的蛋白在一定程度上揭示了杂种优势的存在
2. miRNA识别软件的筛选
虽然借助高通量测序可以发现大量的候选1niRNAs,但也会产生大量的真假难辨的数据从而给新miRNAs的鉴定带来很大的挑战。基于前人的研究,三种基于支持向量机的软件可以有效地去除一些假阳性的miRNAs。由于这些软件的设计大都建立在人类已矢miRNA前体的结构特征,所以有必要对人类和昆虫miRNAs前体特征进行对比,并比较它们对昆虫miRNAs的预测性能,进而挑选出最适合昆虫的软件。我们利用现有的数据库和生物信息学工具,系统地分析了人类miRNA前体和昆虫前体的特征差异以及昆虫24个不同种类之间的结构特征。结果表明,人类和昆虫miRNA前体的核苷酸组成,序列长度,核苷酸偏好和二级结构的特点是不同的。随后,借助三个现有的支持向量机的miRNA识别程序对这些已知的miRNA进行评分,以此来判断miRNA识别软件的性能高低。结果表明,2,633条昆虫前体中有2,229条被mirident分类器成功识别,比例高达84.66%,高于triplet-svm(72.50%)和(72.65%)pmirpo我们分别用软件检测每一个现有的昆虫物种,结果发现有四个物种,包括家蚕,果蝇,蜂和赤拟谷盗,获得了较低的成绩。特别是,与其他物种相比,家蚕的识别率最低,平均MFE指数也最小(0.73)。总的来说,这些结果为我们了解昆虫miRNA前体的特异性和多样性提供了线索,也为进一步开发出针对昆虫前体特征的rniRNA识别软件奠定了基础。
3、家蚕后部丝腺1miRNAs表达谱分析
我们用solexa技术对六个小RNA文库进行了深度测序,并用DASP方法检测到293个已知家蚕miRNAs,它们分成66个家族。从物种保守性来看,有40个家族保守在昆虫和其他物种间,剩下的26个家族只在家蚕上发现。另外，根据系统发育分析,这些miRNAs分布在14个从无脊椎动物到脊椎动物的物种上,为进一步研究动物的进化提供了系统发育标记和进化信号。同时,我们分析了不同产丝量品种之间miRNAs的表达差异,结果发现多丝量品种J1中下调表达的miRNAs远远多于裸蛹品种R1。而对两个不同发育时期的家蚕进行分析表明,丝腺细胞快速发育期比前期也同样拥有较多的下调miRNAS。两个独立实验分别印证了丝蛋白基因的表达可能受到了miRNAs的调控,从而造成丝心蛋白表达量的变化。我们随后采用mireap对未注释序列进行新miRNA的预测得到1，373条候选miRNAS。同时利用本实验筛选出的miRNA前体检测软件mirident程序,成功地从六个文库的候选miRNA中检验出414条非冗余新miRNA口432条前体序列,其中有50对miRNA/miRNA*复合体,结果大大丰富了家蚕miRNA数据库。借助生物信息学软件,我们对差异表达的miRNA进行靶标预测、GO分类和KEGG分析。我们发现，多丝量品种下调miRNAs对应的KEGG的靶基因数量明显高于上调表达的miRNAS。这些通路涉及范围较广,包括细胞凋亡,精氨酸脯氨酸代谢,氨基酸-tRNA生物合成,丙氨酸、天冬氨酸和谷氨酸代谢,氨基酸和核酸糖代谢等。通过对以丙氨酸、天冬氨酸和谷氨酸代谢通路的分析,结果表明下调miRNA对应靶基因更多地参与丙氨酸代谢途径,结茧蚕比裸蛹可能要合成更多的丙氨酸来促进丝腺细胞的发育。我们推测多丝量家蚕后部丝腺miRNAs的下调表达有利于家蚕囤积与丝蛋白合成相关的物质,储存能量,来促进蚕茧高产。
4、家蚕后部丝腺]miRNA表达谱芯片分析
为了更全面的验证五龄第三天家蚕后部丝腺miRNA表达谱,我们定制了一个囊括家蚕数据库,果蝇数据库,最近发表文章以及本实验预测的miRNAs的全方位探针,并最终鉴定出333条niRNAs,包含家蚕已矢miRNA213条和120条新miRNA,其中,在新miRNAs中发现有13条保守在果蝇中。我们对芯片的结果进行重复性检测以及与solexa测序相关性分析,发现芯片重复性高,与solexa相比更适合1niRNAs的定量分析。随后,我们分析了秋丰和白玉雌雄以及品种之间的差异性,结果表明无论性别还是品种,它们的miRNAs表达差异在总体水平上不显著,这可能与秋丰、白玉二者产丝性状相差很小有关。
本论文所取得的成果为研究生物在高温胁迫条件下的抗逆性以及杂种优势及抗性机理提供理论依据,为丰富家蚕miRNAs数据库提供了资源储备,同时也为研究后部丝腺1niRNAs在五龄期间蚕丝合成过程发挥的作用提供了参考。
As a typical representative Lepidoptera insect, silkworm Bombyx mori not only has irreplaceable economic traits, but more importantly, as a second model insect only next to Drosophila, it possesses almost all the biological characteristic of other insects. Such outstanding features collectively support a sustainable economy industry, and moreover, a large number of multidisciplinary participation is also attracted. All of these have contributed lots of valuable findings to the researches on silkworm in recent years. Especially, the successful accomplishment of silkworm genome project provides us critical theoretical basis and technological platform to further study in the post-genomic era. There are many research contents in post genomic era. For instance, the accurate annotation to the genome is one of the important tasks. It has been proved that organisms are complex systems, and its gene expression is regulated by many factors. To some extent, the expression levels of mRNA do not represent the protein levels. To solve this problem and further reveal the complex mechanisms in organisms which are under physiological or pathological conditions, we should not only rely on the study of proteins, but also to explore other regulatory factors, such as microRNA (miRNA). This study focused on comparative proteomics and expression profile of miRNAs in the posterior silk glands of Bombyx mori and obtained several preliminary findings as follows:
1. Comparative proteomic and phosphoproteomic analysis of the silkworm posterior silk gland under high temperature treatment
The proteins from the posterior silk gland of silkworm hybrids and their parents reared under high temperatures were studied by using comparative proteomic and phosphoproteomic analysis. A total of82.07%.6.17%and11.76%protein spots showed additivity. overdominance and underdominance patterns, respectively. Fifteen differentially expressed protein spots were identified by peptide mass fingerprinting. Among these, four spots, including sHSPs and prohibitin protein that were directly relevant to heat response, were identified. Eleven protein spots were found to play an important role in silk synthesis, and nine protein spots expressed phosphorylation states. According to Gene ontology (GO) and KEGG pathway analysis, these nine spots played an important role in stress-induced signal transduction. Expression of most silk synthesis-related proteins was reduced, whereas stress-responsive proteins increased with heat exposure time in three breeds. Furthermore, most proteins showed under-or overdominance in the hybrids compared to the parents. The results suggested that high temperature could alter the expression of proteins related to silk synthesis and heat response in silkworm. Moreover, differentially expressed proteins occurring in the hybrid and its parents may be the main explanation of the observed heterosis.
2. Bioinformatics analysis and screening of miRNA prediction programs
Although thousands of candidate novel miRNAs can be found by deep-sequencing technology, many pseudo-miRNAs might be produced and bring challenge to further miRNAs identification. Based on the previous research, three SVM-based predictions were selected due to their good performance on distinguishing real-or pseudo-miRNAs. Because all of them were developed based on the known human pre-miRNA characteristics, it sounds reasonable to compare the feature differences between humans and insects, and then select a more suitable program according to their predicting performances on insects. In the present work, we have systematically analyzed, utilizing bioinformatics tools, the featural differences between human and insect pre-miRNAs, as well as differences across24insect species. Results showed that the nucleotide composition, sequence length, nucleotides preference and secondary structure features between human and insects were different. Subsequently, with the aid of three available SVM-based prediction programs, pre-miRNA sequences were evaluated and given corresponding scores. Thus it was found that of2633sequences from the24chosen insect species.2229(84.7%) were successfully recognized by the Mirident classifier, higher than Triplet-SVM (72.5%) and PMirP (72.6%). In contrast, four species, including the domestic silkworm moth, the fruit fly. Drosophila melanogaster Meigen, the honeybee. Apis mellifera L. and the Red Flour beetle, Tribolium castaneum (Herbst). were found to be largely responsible for the poor performance of some sequence matching. Compared with other species. B. mori especially showed the worst performance with the lowest average MFE index (0.73). Collectively these results pave the way for understanding specificity and diversity of miRNA precursors in insects, and lay the foundation for the further development of more suitable algorisms for insects.
3. miRNAs profiling in posterior silk gland of silkworm identified by solexa deep-sequencing
In order to study the miRNAs expression profiling of silkworm posterior silk gland, we sequenced six small RNA libraries and obtained293known miRNAs. We found that all the known miRNAs were divided into65miRNA families with the exception of undefined miRNAs, in which,40families were conserved in insects, the left families were only discovered in silkworm. From phylogenetic analysis, those conserved miRNAs were widely distributed in over14species from invertebrates to vertebrates. Result showed that these conserved miRNAs might serve as potential phylogenetic markers and rapid evolutionary signaling molecules. At meantime, we analyzed different expression profiling of two strains with different silk-synthesis traits. One named J1is a strain of silkworm which can normally produce silk, the other termed R1which is the mutant of J1, lack of the ability of spinning cocoon. We found more down-regulated miRNAs in J1compared with it counterpart. We also analyzed the different expression profiles of two developmental stages, specifically,4th-instar molting to5th-instar day-2and5th-instar day-3to5th-instar day-8before spinning. Result showed that the miRNAs expression of stage2obviously declined compared to stage1. Two individual experiments confirmed that silk synthesis related genes might be regulated by miRNAs, which influenced the expression profile of silk proteins. Meanwhile, we employed mireap to predict the novel miRNAs in six libraries with the result of1.373new findings. Utilizing mirident program,432pre-miRNA sequences and414non-redundant miRNAs were successfully recognized to be novel miRNAs. Among these novel miRNAs, we found50pairs of miRNA/miRNA*duplex, which largely enriched the miRNA database. Furthermore, Utilizing RNAhybrid to predict the target genes of differentially expressed miRNAs, we found that many down-regulated miRNAs in J1or stage2were in connection with metabolism and synthesis, which further illustrated the likely function which miRNAs played in silk synthesis.
4. Identification of miRNAs in5th-3day of PSG by microarray
With the aid of microarray.333mature miRNAs were confirmed, and in which,213miRNAs were known miRNAs, and the left, including13conserved in Drosophila, were novel. We also analyzed their different expression profiling between genders and breeds. Results showed that there were no significant differences in genders and in breeds. There were28differentially expressed miRNAs in male and female of Q. Twenty of them were up-regulated in female silkworms, while only8of them were up-regulated in male. On the other hand, sixteen differentially expressed miRNAs were identified in two genders of B, in which, seven were up-regualted in female, while the left in male. Meantime, we also compared the differences between two breeds and observed that4miRNAs up-regulated in Q, contrary to8up-regulated in B. Nevertheless, the newly identified miRNAs largely enrich the repertoire of silkworm miRNAs. Moreover, comparative analysis of known and novel miRNAs indicated that the expression level of miRNAs might be the key reason to interpret different yields of cocoon.
All of the results shed light to further illustration of stress response and heteosis occurring in organisms under high tempreture stress. The newly identified miRNAs provided first hand data for extending the miRNA database, and more important, these findings might pave the way for elucidating likely function of miRNAs in the silk production of posterior silk gland at final moth of silkworm.
引文
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