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Reconstruction of mitochondrial genomes from raw sequencing data provides insights on the phylogeny of Ixodes ticks and cautions for species misidentification

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Title: Reconstruction of mitochondrial genomes from raw sequencing data provides insights on the phylogeny of Ixodes ticks and cautions for species misidentification
Authors: Mohamed, Wessam Mohamed Ahmed Browse this author
Moustafa, Mohamed Abdallah Mohamed Browse this author
Kelava, Samuel Browse this author
Barker, Dayana Browse this author
Matsuno, Keita Browse this author →KAKEN DB
Nonaka, Nariaki Browse this author →KAKEN DB
Shao, Renfu Browse this author
Mans, Ben J. Browse this author
Barker, Stephen C. Browse this author
Nakao, Ryo Browse this author →KAKEN DB
Keywords: High-throughput sequencing
Ixodes persulcatus
Phylogenetic analysis
Issue Date: 1-Jan-2022
Publisher: Elsevier
Journal Title: Ticks and Tick-Borne Diseases
Volume: 13
Issue: 1
Start Page: 101832
Publisher DOI: 10.1016/j.ttbdis.2021.101832
Abstract: High-throughput sequencing (HTS) technology has profoundly been involved in sequencing whole genomes of several organisms in a fast and cost-effective manner. Although HTS provides an alternative biomonitoring method to the time-consuming and taxonomy-expertise dependent morphological approach, still we cannot rule out the possibility of the impediment and misidentification biases. In this article we aim to retrieve whole mitochondrial genome (mitogenome) sequences from publicly available raw sequencing data for phylogenetic comparison of Ixodes persulcatus. For this comparison, we sequenced whole mitogenomes of four I. persulcatus ticks from Japan and constructed mitogenomes from raw sequencing data of 74 I. persulcatus ticks from China. Bayesian phylogenetic trees were inferred by the concatenated fifteen mitochondrial genes. We further tested our results by the phylogenetic analysis of cytochrome c oxidase subunit 1 (cox1) gene and internal transcribed spacer 2 (ITS2) sequences. Our findings showed that 70 constructed mitogenomes from China were clustered with the sequenced four mitogenomes of I. persulcatus from Japan. We also revealed that mitogenome sequences retrieved from two data sets CRR142297 and CRR142298 were clustered with Ixodes nipponensis. Moreover, other two mitogenome sequences from CRR142310 and CRR142311 formed a clade with Ixodes pavlovskyi. The phylogenetic analysis of cox1 gene and ITS2 sequences confirmed the identification errors of these four samples. The overall phylogenetics in our study concluded that accurate morphological identification is necessary before implementing HTS to avoid any misidentification biases.
Rights: © 2022. This manuscript version is made available under the CC-BY-NC-ND 4.0 license
Type: article (author version)
Appears in Collections:獣医学院・獣医学研究院 (Graduate School of Veterinary Medicine / Faculty of Veterinary Medicine) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 中尾 亮

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