An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues : A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches

• Kinjo Yukihiro

  Tropical Biosphere Research Center, University of the Ryukyus Graduate School of Engineering and Science, University of the Ryukyus Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology

• Saitoh Seikoh

  Tropical Biosphere Research Center, University of the Ryukyus

• Tokuda Gaku

  Tropical Biosphere Research Center, University of the Ryukyus Graduate School of Engineering and Science, University of the Ryukyus

書誌事項

タイトル別名

• An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of <i>Blattabacterium cuenoti</i> Inhabiting the Fat Bodies of Cockroaches

抄録

Whole-genome sequencing has emerged as one of the most effective means to elucidate the biological roles and molecular features of obligate intracellular symbionts (endosymbionts). However, the de novo assembly of an endosymbiont genome remains a challenge when host and/or mitochondrial DNA sequences are present in a dataset and hinder the assembly of the genome. By focusing on the traits of genome evolution in endosymbionts, we herein developed and investigated a genome-assembly strategy that consisted of two consecutive procedures: the selection of endosymbiont contigs from an output obtained from a de novo assembly performed using a TBLASTX search against a reference genome, named TBLASTX Contig Selection and Filtering (TCSF), and the iterative reassembling of the genome from reads mapped on the selected contigs, named Iterative Mapping and ReAssembling (IMRA), to merge the contigs. In order to validate this approach, we sequenced two strains of the cockroach endosymbiont Blattabacterium cuenoti and applied this strategy to the datasets. TCSF was determined to be highly accurate and sensitive in contig selection even when the genome of a distantly related free-living bacterium was used as a reference genome. Furthermore, the use of IMRA markedly improved sequence assemblies: the genomic sequence of an endosymbiont was almost completed from a dataset containing only 3% of the sequences of the endosymbiont’s genome. The efficiency of our strategy may facilitate further studies on endosymbionts.

収録刊行物

• Ｍｉｃｒｏｂｅｓ　ａｎｄ　ｅｎｖｉｒｏｎｍｅｎｔｓ

  Ｍｉｃｒｏｂｅｓ　ａｎｄ　ｅｎｖｉｒｏｎｍｅｎｔｓ 30 (3), 208-220, 2015

  日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会 / 極限環境微生物学会

キーワード

• Endosymbiont
• genome assembly
• gap closing
• targeted genome reconstruction
• bacterial gene identification

詳細情報

• CRID: 1390282679321979136
• NII論文ID: 130005099210
• NII書誌ID: AA11551577
• DOI: 10.1264/jsme2.me14153
• ISSN: 13474405
• ISSN: 13426311
• NDL書誌ID: 026766248
• PubMed: 26156552
• Web Site: https://ndlsearch.ndl.go.jp/books/R000000004-I026766248
• Web Site: https://www.jstage.jst.go.jp/article/jsme2/30/3/30_ME14153/_pdf
• 本文言語コード: en
• データソース種別:
  • JaLC
  • NDL
  • Crossref
  • PubMed
  • CiNii Articles
  • KAKEN
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