Open Access. Powered by Scholars. Published by Universities.®
Articles 1 - 3 of 3
Full-Text Articles in Life Sciences
Efficient Coi Barcoding Using High Throughput Single-End 400 Bp Sequencing, Chentao Yang, Yuxuan Zheng, Shangjin Tan, Guanliang Meng, Wei Rao, Caiqing Yang, David G. Bourne, Paul A. O'Brien, Junqiang Xu, Sha Liao, Ao Chen, Xiaowei Chen, Xinrui Jia, Ai-Bing Zhang, Shanlin Liu
Efficient Coi Barcoding Using High Throughput Single-End 400 Bp Sequencing, Chentao Yang, Yuxuan Zheng, Shangjin Tan, Guanliang Meng, Wei Rao, Caiqing Yang, David G. Bourne, Paul A. O'Brien, Junqiang Xu, Sha Liao, Ao Chen, Xiaowei Chen, Xinrui Jia, Ai-Bing Zhang, Shanlin Liu
Harold W. Manter Laboratory: Library Materials
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 highthroughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (for example, 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 …
Repositories For Taxonomic Data: Where We Are And What Is Missing, Aurélian Miralles, Teddy Bruy, Katherine Wolcott, Mark D. Scherz, Dominik Begerow, Bank Beszteri, Michael Bonkowski, Janine Felden, Birgit Gemeinholzer, Frank Glaw, Frank Oliver Glöckner, Oliver Hawlitschek, Ivaylo Kostadinov, Tim W. Nattkemper, Christian Printzen, Jasmin Renz, Nataliya Rybalka, Marc Stadler, Tanja Weibulat, Thomas Wilke, Susanne S. Renner, Miguel Vences
Repositories For Taxonomic Data: Where We Are And What Is Missing, Aurélian Miralles, Teddy Bruy, Katherine Wolcott, Mark D. Scherz, Dominik Begerow, Bank Beszteri, Michael Bonkowski, Janine Felden, Birgit Gemeinholzer, Frank Glaw, Frank Oliver Glöckner, Oliver Hawlitschek, Ivaylo Kostadinov, Tim W. Nattkemper, Christian Printzen, Jasmin Renz, Nataliya Rybalka, Marc Stadler, Tanja Weibulat, Thomas Wilke, Susanne S. Renner, Miguel Vences
Harold W. Manter Laboratory: Library Materials
Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000–20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4,113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use …
Genbank, Dennis A. Benson, Ilene Karasch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers
Genbank, Dennis A. Benson, Ilene Karasch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers
Harold W. Manter Laboratory: Library Materials
GenBank(R) is a comprehensive database that contains publicly available nucleotide sequences for more than 380,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data …