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测序数据量对褐斑鲬和条纹斑竹鲨线粒体基因组组装效率的影响

Effect of sequencing data quantity on mitochondrial genome assembling efficiency of Platycephalus yoshinoi and Chiloscyllium plagiosum mitochondria
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摘要 高通量测序技术及生物信息学分析方法的快速发展为大规模开展非模式生物基因组测序工作提供了可能,然而如何在低成本的基础上获得基因组信息成为高通量测序技术推广的重要限制因素。鉴于海洋鱼类多样性及其基因组大小的异质性,本研究以硬骨鱼褐斑鲬和软骨鱼条纹斑竹鲨为研究对象,对两者进行线粒体基因组组装与分析,探讨测序数据量及测序深度对海洋鱼类线粒体基因组组装效率的影响。根据对褐斑鲬和条纹斑竹鲨样品开展高深度Illumina测序,利用生物信息学软件分别构建10个测序数据量梯度,并使用NOVOPlasty软件进行线粒体基因组组装,从组装效果、时间两方面统计分析线粒体组装结果。结果显示,随着测序数据量及测序深度的下降,线粒体组装时间呈显著下降趋势(Wilcoxon signed rank test,P<0.01)。褐斑鲬数据量0.3 Gb(测序深度~0.4 x)后无法成功组装线粒体基因组、条纹斑竹鲨数据量0.15 Gb(~0.03 x)后线粒体组装时间逐步增加。对组装效果和组装时间进行综合分析,确定褐斑鲬和条纹斑竹鲨线粒体基因组组装的最优数据量分别为0.3 Gb和0.5 Gb,提示0.5 Gb的测序数据量可能是海洋鱼类线粒体基因组组装的最优方案。本研究初步给出了海洋鱼类线粒体基因组组装的最优测序数据量(~0.5 Gb),可为后续相关研究工作提供参考,同时有助于在低成本基础上进行海洋鱼类线粒体基因组组装。 The rapid development of high-throughput sequencing technologies and bioinformatic methods has made it possible to conduct large-scale genomic sequencing of non-model organisms.However,how to obtain genomic information cost-effectively has become an important limitation for the promotion of high-throughput sequencing technologies.Given the diversity and genome size heterogeneity of marine fishes,herein the Osteichthyes Platycephalus yoshinoi and Chondrichthyes Chiloscyllium plagiosum were chosen to conduct mitochondrial genome assembling,and investigate the effect of sequencing data quantity and depth on mitochondrial genome assembling efficiency of marine fish species.High depth Illumina sequencing data of P.yoshinoi and C.plagiosum were generated and 10 sequencing data gradients each species were constructed using in silico bioinformatic approaches.Mitochondrial genome assembly was performed using NOVOPlasty software and the effectiveness and times of assembly were statistically analyzed.The results showed that the assembly time reduced significantly with the decrease of sequencing data and depth(Wilcoxon signed rank test,P<0.01).The mitochondrial genome of P.yoshinoi was failed to assemble when sequencing data were less than 0.3 Gb(sequencing depth~0.4x)while the assembly time of C.plagiosum increased gradually when sequencing data were less than 0.15 Gb(~0.03x).Integrating the assembly effectiveness and times,the optimal sequencing data for mitochondrial genome assembly of P.yoshinoi and C.plagiosum were determined to be 0.3 Gb and 0.5 Gb,respectively,suggesting that 0.5 Gb sequencing data is optimal for mitochondrial genome assembly of marine fish.Our results not only provided references for subsequent related studies,but also facilitated mitochondrial assembly of marine fishes in a cost-effective manner,which will widen population genetic and phylogeny studies at the genomics level.Considering the limited numbers of investigated species,further studies with increased species are warranted to verify the reliability of the optimal sequencing data in this study.
作者 赵蕊蕊 陆定方 李鹏飞 韩志强 徐胜勇 ZHAO Ruirui;LU Dingfang;LI Pengfei;HAN Zhiqiang;XU Shengyong(Fishery College,Zhejiang Ocean University,Zhoushan 316022,China;Zhejiang Marine Fisheries Research Institute,Zhoushan 316021,China)
出处 《海洋湖沼通报(中英文)》 北大核心 2025年第2期93-99,共7页 Transactions of Oceanology and Limnology
基金 浙江省属高校基本科研业务费(2019JZ00001)。
关键词 高通量测序 褐斑鲬 条纹斑竹鲨 线粒体基因组组装 比较分析 high-throughput sequencing Platycephalus yoshinoi Chiloscyllium plagiosum mitochondrial genome assembly comparative analysis
作者简介 第一作者:赵蕊蕊(1997-),女,安徽濉溪人,硕士研究生,研究方向为渔业资源养护与利用。E-mail:3245828525@qq.com;通信作者:徐胜勇(1989-),男,山东青岛人,博士,副研究员,研究方向为渔业资源生物学。E-mail:kevin890223@163.com。
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