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Efficient COI barcoding using high throughput single-end 400 bp sequencing by Yang, Chentao; Zheng, Yuxuan; Tan, Shangjin; Meng, Guanliang; Rao, Wei; Yang, Caiqing; Bourne, David G.; OâBrien, Paul A.; Xu, Junqiang; Liao, Sha; Chen, Ao; Chen, Xiaowei; Jia, Xinrui; Zhang, Ai-bing; Liu, Shanlin is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.
What is Efficient COI barcoding using high throughput single-end 400 bp sequencing about?
## Abstract ## Background Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current high-throughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (e.g. a maximum read length of 300 bp for the Illumina’s MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio’s SEQUEL II system). ## Results Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the MGISEQ-2000 platform using the single-end 400 bp (SE400) module. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5′ and 3′ ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter, assign, assembly and taxonomy. We applied the HIFI-SE to a set of 845 samples (30 marine invertebrates, 815 insects) and delivered a total of 747 fully assembled COI barcodes as well as 70 Wolbachia and f
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It is typically read by researchers, students, and practitioners in Biochemistry, Genetics and Molecular Biology.
- Author
- Yang, Chentao; Zheng, Yuxuan; Tan, Shangjin; Meng, Guanliang; Rao, Wei; Yang, Caiqing; Bourne, David G.; OâBrien, Paul A.; Xu, Junqiang; Liao, Sha; Chen, Ao; Chen, Xiaowei; Jia, Xinrui; Zhang, Ai-bing; Liu, Shanlin
- Publisher
- BioMed Central; Springer (Biomed Central Ltd.); London: BioMed Central, 2000-; Springer Science and Business Media LLC; Society for Mining, Metallurgy and Exploration Inc. (ISSN 1471-2164)
- Published
- 2020
- Language
- EN
- Field
- Biochemistry, Genetics and Molecular Biology (Life Sciences)