东方蜜蜂微孢子虫的基因结构优化及新基因鉴定
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摘要
东方蜜蜂微孢子虫Nosema ceranae是一种寄生于蜜蜂中肠上皮细胞的单细胞真菌,对蜜蜂的健康危害严重,给世界各国的养蜂业造成较大损失。本研究基于前期获得的N.ceranae孢子的转录组数据对其已注释基因进行结构优化,并对未注释基因进行预测和分析。通过将测序得到的clean reads比对参考基因组和转录本重构,共对10个N.ceranae的已注释基因的5'端或3'端进行了延长。利用Cuffcompare软件将重构转录本与参考基因组进行比对,共鉴定出27个新基因,随机挑选9个新基因进行RT-PCR验证,均能扩增出符合预期的目的片段,表明预测出的新基因真实存在。有6个新基因能够注释到GO数据库和6个基因注释到KEGG数据库。进一步分析结果显示上述新基因注释到细胞等10个GO条目上,它们可能在N.ceranae的生命活动中具有重要功能。研究结果为N.ceranae的基因结构和功能注释信息的完善提供了有益补充,也为新基因的功能研究打下了基础。
Nosema ceranae is a kind of single-cell fungi that specially parasite honeybee midgut's epithelial cell, it severely damage honeybees' health and leads to great damage for apiculture in various countries. Based on the previously obtained transcriptome data of N. ceranae spores, structural optimization of annotated genes and prediction and analysis of novel genes in N. ceranae were performed in this study. In total, 5′ or 3′ end of ten annotated genes were prolonged through mapping of clean reads to the reference genome and reconstruction of transcripts. In addition, the reconstructed transcripts were mapped to the reference genome and 27 novel genes were predictd, nine were randomly selected for RT-PCR validation, and expected fragments could be amplified from all of them, demonstrating the ture existence of the predicted genes in N. ceranae. Six novel genes could be annotated to GO, and six novel genes could be annotated to KEGG databases, respectively. Further investigation showed that these novel genes can be annotated to ten GO terms such as cell, implying their key role during the vital activities of N. ceranae. Our results not only provide beneficial supplement for the improvement of structural and functional annotation of N. ceranae genes, but also offer some foundation for the functional study of these novel genes.
Nosema ceranae is a kind of single-cell fungi that specially parasite honeybee midgut's epithelial cell, it severely damage honeybees' health and leads to great damage for apiculture in various countries. Based on the previously obtained transcriptome data of N. ceranae spores, structural optimization of annotated genes and prediction and analysis of novel genes in N. ceranae were performed in this study. In total, 5′ or 3′ end of ten annotated genes were prolonged through mapping of clean reads to the reference genome and reconstruction of transcripts. In addition, the reconstructed transcripts were mapped to the reference genome and 27 novel genes were predictd, nine were randomly selected for RT-PCR validation, and expected fragments could be amplified from all of them, demonstrating the ture existence of the predicted genes in N. ceranae. Six novel genes could be annotated to GO, and six novel genes could be annotated to KEGG databases, respectively. Further investigation showed that these novel genes can be annotated to ten GO terms such as cell, implying their key role during the vital activities of N. ceranae. Our results not only provide beneficial supplement for the improvement of structural and functional annotation of N. ceranae genes, but also offer some foundation for the functional study of these novel genes.
引文
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Nie SJ, Liu YQ, Wang CC, et al. Assembly of an early-matured japonica (Geng) rice genome, Suijing18, based on PacBio and Illumina sequencing [J]. Sci.Data, 2017, 19: 4.
Traver BE, Fell RD.Nosema ceranae in drone honey bees (Apis mellifera) [J]. Journal of Invertebrate Pathology, 2011, 107 (3): 234-6.
Traver BE, Fell RD. Low natural levels of Nosema ceranae in Apis mellifera queens [J]. Journal of Invertebrate Pathology, 2012, 110 (3): 408.
Chaimanee V, Chantawannakul P, Chen Y,et al. Differential expression of immune genes of adult honey bee (Apis mellifera) after inoculated by Nosema ceranae [J]. Journal of Insect Physiology, 2012, 58 (8): 1090.
Cornman RS, Chen YP, Schatz MC,et al. Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees [J]. PLoS Pathogens, 2009, 5 (6): e1000466.
Cox-Foster DL, Conlan S, Holmes EC,et al. A metagenomic survey of microbes in honey bee colony collapse disorder [J]. Science, 2007, 318 (5848): 283-7.
Elsik CG, Worley KC, Bennett AK,et al. Finding the missing honey bee genes: Lessons learned from a genome upgrade [J]. BMC Genomics, 2014, 15 (1): 86.
Guo R,Chen DF,Xiong CL,et al.First identification of long non-coding RNAS in fungal parasite Nosema ceranae[J].Apidologie,2018,49(5):660-670.
Guo R,Chen DF,Chen HZ,et al.Genome-wide identification of circular RNAS in fungal parasite Nosema caranae[J].Current Microbiology,2018,75(12):1665-1660.
Huang WF, Solter LF. Comparative development and tissue tropism of Nosema apis and Nosema ceranae [J]. Journal of Invertebrate Pathology, 2013, 113 (1): 35.
Heil JR, Lynch MDJ, Cheng J,et al. The completed PacBio single-molecule real-time sequence of Methylosinus trichosporium strain OB3b reveals the presence of a third large plasmid [J]. Genome Announcements, 2017, 5 (49).
Korlach J, Gedman G, Kingan SB,et al. De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads [J]. Gigascience, 2017, 6 (10): 1.
Martín-Hernández R, Botías C, Barrios L, et al. Comparison of the energetic stress associated with experimental Nosema ceranae and Nosema apis infection of honeybees (Apis mellifera) [J]. Parasitology Research, 2011, 109 (3): 605-12.
Nie SJ, Liu YQ, Wang CC, et al. Assembly of an early-matured japonica (Geng) rice genome, Suijing18, based on PacBio and Illumina sequencing [J]. Sci.Data, 2017, 19: 4.
Traver BE, Fell RD.Nosema ceranae in drone honey bees (Apis mellifera) [J]. Journal of Invertebrate Pathology, 2011, 107 (3): 234-6.
Traver BE, Fell RD. Low natural levels of Nosema ceranae in Apis mellifera queens [J]. Journal of Invertebrate Pathology, 2012, 110 (3): 408.