对双棘蝽(鞘翅目:蝶蛾科:棘蝽科)有丝分裂基因组的多样本长读纳米孔测序为下游分析提供了有效可靠的数据。

IF 2.1 3区 农林科学 Q1 ENTOMOLOGY
Olena Bielikova, Ondrej Vargovčík, Zuzana Čiamporová-Zaťovičová, Fedor Čiampor
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引用次数: 0

摘要

线粒体基因组是各种下游分析的丰富数据来源,如群体遗传学,系统发育和系统学。今天,主要采用下一代测序和第三代测序技术,可以快速组装大量有丝分裂基因组。然而,通常缺乏对生成序列正确性的验证,特别是对于非编码、长度可变的部分。在这里,我们利用长读纳米孔序列数据,组装了四种Agabus bipustulatus (L.)标本的线粒体基因组(mitogenome)。最新纳米孔化学技术(V14)的使用与全面的错误纠正工作流程相结合,使有丝分裂基因组的生成具有高精度和可重复性,在四个样品上进行了测试。得到的有丝分裂基因组全长17876 bp,包括13个蛋白质编码基因、22个转移RNA基因、2个核糖体RNA基因和一个控制区。样本间控制区长度的差异很小。蛋白质编码基因、转移rna和核糖体rna的排列与祖先昆虫的有丝分裂基因组相似。最后,我们使用组装好的、支持良好的有丝分裂基因组对与所研究物种相关的部分Dytiscidae进行了系统发育分析,并将结果与先前的假设进行了比较。对它们的系统发育的相互矛盾的估计表明,要对它们的进化史作出一个合理的描述,还需要相当多的可靠数据。我们的研究已经证实,现成的第三代测序技术,如牛津纳米孔技术,结合长读测序,提供了一种高效、可靠、经济的方法来生成完整的有丝分裂基因组和潜在的其他更长的基因组区域。使用可靠的数据将最终有助于更深入地了解和改进对潜水甲虫和其他生物的保护策略。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Multi-sample long-read nanopore sequencing of Agabus bipustulatus (Coleoptera: Dytiscidae: Agabinae) mitogenome produces effectively reliable data for downstream analyses.

Mitochondrial genomes are a rich source of data for various downstream analyses such as population genetics, phylogeny, and systematics. Today it is possible to assemble rapidly large numbers of mitogenomes, mainly employing next-generation sequencing and third-generation sequencing. However, verification of the correctness of the generated sequences is often lacking, especially for noncoding, length-variable parts. Here we have assembled the mitochondrial genome (mitogenome) from four specimens of Agabus bipustulatus (L.) using long-read nanopore sequence data. The use of the latest nanopore chemistry (V14) combined with a comprehensive error correction workflow enabled the generation of mitogenomes with high accuracy and reproducibility, as tested on four samples. The resulting mitogenome is 17,876 bp long, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. Differences in the control region length between samples were minimal. The arrangement of protein-coding genes, transfer RNAs, and ribosomal RNAs is similar to that of the ancestral insect mitogenome. Finally, we used the assembled, well-supported mitogenomes in the phylogenetic analysis of a part of the Dytiscidae related to the studied species and confronted the results with previous hypotheses. Conflicting estimates of their phylogeny suggest that considerably more robust data are required for a plausible sketch of their evolutionary history. Our research has confirmed that readily available third-generation sequencing technologies, such as Oxford Nanopore Technologies, combined with long-read sequencing, offer a highly efficient, reliable, and cost-effective approach to generate complete mitogenomes and potentially other longer regions of the genome. The use of reliable data will ultimately contribute to a deeper understanding and improved conservation strategies for diving beetles and other organisms.

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来源期刊
Journal of Insect Science
Journal of Insect Science 生物-昆虫学
CiteScore
3.70
自引率
0.00%
发文量
80
审稿时长
7.5 months
期刊介绍: The Journal of Insect Science was founded with support from the University of Arizona library in 2001 by Dr. Henry Hagedorn, who served as editor-in-chief until his death in January 2014. The Entomological Society of America was very pleased to add the Journal of Insect Science to its publishing portfolio in 2014. The fully open access journal publishes papers in all aspects of the biology of insects and other arthropods from the molecular to the ecological, and their agricultural and medical impact.
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