摘要
目的了解冈田绕眼果蝇(Amiota okadai, A. o)基因组序列特征。方法采用Genscan、Augustus、Glimmer、HMM、GeneID和SNAP等软件对冈田绕眼果蝇基因组测序数据进行从头预测;用GeMoMa软件进行同源预测,利用EVM软件对预测结果进行整合,并结合已获得的冈田绕眼果蝇RNA-seq数据对冈田绕眼果蝇基因进行结构优化、以预测其基因组全部基因并在公共数据库及专有数据库中进行注释。结果对冈田绕眼果蝇基因组进行注释及优化分析,共得到11 510个具有较高可信度的基因;在公共数据库中进行BLAST比对,98.53%的基因得到注释,其中NR数据库中注释的基因数目(占98.20%)较多,可富集到KEGG的基因数目(占43.15%)较少;通过KOG数据库分析功能基因,共得到4 967个功能基因。在3个专有数据库中(TCDB、CAZyme和PHI)中进行比对,分别注释获得了291、359和2 574个基因,其中PHI数据库中可注释的基因(2 574个)较多。结论初步揭示了冈田绕眼果蝇基因组序列特征和注释信息,共得到11 510个基因,为其基因组序列特征研究奠定了基础。
Objective To ascertain the characteristics of the genomic sequence of Amiota okadai.Methods Data on the gene sequence of the A.okadai genome were annotated using a combination of ab initio gene prediction methods with the software Genscan,Augustus,Glimmer,HMM,GeneID,and SNAP,and the homology of the experimentally confirmed genes was predicted using the software GeMoMa.The results were integrated in the software EVM to predict all genes of the genome.Based on previously obtained A.okadai RNA-seq data,the composition of known genes was optimized to determine all of the genes in the genome.The obtained genes were annotated in public databases and dedicated databases.Results Annotating and optimizing the A.okadai genome yielded a total of 11 510 genes with a high level of confidence.The sequence search was conducted in public databases using BLASTx,and 98.53%of the genes were annotated.Most genes were annotated in the NR database(98.20%),while KEGG pathway analysis suggested that few genes(43.15%)were engaged in pathways.Gene function was analyzed using the KOG database,and a total of 4,967 genes were found.Three proprietary databases(TCDB,CAZyme,and PHI)were used to annotate predicted genes;291,359,and 2,574 genes were respectively annotated in the three databases,most of which were annotated in the PHI database(2,574).Conclusion This work preliminarily revealed the characteristics of the A.okadai genomic sequence and annotation information,and a total of 11,510 genes were obtained.These findings have laid the foundation for a study of the characteristics of this genomic sequence.
作者
王莉君
马培玉
蔡娟
黄琳
王灵军
刘晖
曹建平
郑明辉
WANG Li-jun;MA Pei-yu;CAI Juan;HUANG Lin;WANG Ling-jun;LIU Hui;CAO Jian-ping;ZHENG Ming-hui(Department of Parasitology,Zunyi Medical University,China;Institute of Criminal Science and Technology,Jiaozuo Municipal Public Security Bureau,Henan Province,China;Chinese Center For Disease Control And Prevention)
出处
《中国病原生物学杂志》
CSCD
北大核心
2019年第8期925-929,934,共6页
Journal of Pathogen Biology
基金
国家自然科学基金项目(No.81560336,81760373)
贵州省科技厅科技基金(黔科合基础[2016]1168)
遵义医学院博士启动基金项目(No.F-795)
卫生部寄生虫病原与媒介生物学重点实验室开放课题(No.WSBKFKT-201609)
