(in English) Botanical Garden in Smíchov formed one of the foundations for the study of medicine, chemistry, and other natural sciences in our territoryfrom the second half of the 18thcentury to the late 20thcentury. The aim of the study is to demonstrate the possibilities of using archival sources not only for the study of the history of botany, but also for finding and locating objects of the garden on historic maps and plans.The work also combines multiple disciplines and also offers new knowledge about the history of botany, postal and architecture

Jonathan Jones (411666)

Kamil Witek (110919)

Matthew Clark (133816)

Michael Giolai (4279378)

Pirita Paajanen (4279381)

Walter Verweij (394220)

BMC Genomics

Paulus, Filip

National Repository of Grey Literature

The History of the Botanic Garden in Smíchov in Light of Archival Sources

Background: The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are a key source of new genetic resistance to pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified. Results: Sequence yields per MinION run are lower than Illumina, making targeted resequencing an efficient approach. While MinION generates long reads similar to PacBio it doesn’t generate the highly accurate multipass consensus reads, which presents downstream bioinformatics challenges. Here we demonstrate how MinION data can be used for RenSeq achieving similar results to the PacBio and how novel NLR gene fusions can be identified via a Nanopore RenSeq pipeline. Conclusion: The described library preparation and bioinformatics methods should be applicable to other gene families or any targeted long DNA fragment nanopore sequencing project

Giolai, Michael

Paajanen, Pirita

Verweij, Walter

Witek, Kamil

Jones, Jonathan D. G.

Clark, Matthew D.

University of East Anglia digital repository

Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire

Michael Giolai

Pirita Paajanen

Walter Verweij

Kamil Witek

Jonathan D. G. Jones

Matthew D. Clark

Crossref

The amplification trace of the capture library and R7.3 Nanopore RenSeq flow cell yields. All commands used for data analysis (PDF 652 kb

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Additional file 1 of Comparative analysis of targeted long read sequencing approaches for characterization of a plantâs immune receptor repertoire

Abstract Background The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are a key source of new genetic resistance to pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified. Results Sequence yields per MinION run are lower than Illumina, making targeted resequencing an efficient approach. While MinION generates long reads similar to PacBio it doesn’t generate the highly accurate multipass consensus reads, which presents downstream bioinformatics challenges. Here we demonstrate how MinION data can be used for RenSeq achieving similar results to the PacBio and how novel NLR gene fusions can be identified via a Nanopore RenSeq pipeline. Conclusion The described library preparation and bioinformatics methods should be applicable to other gene families or any targeted long DNA fragment nanopore sequencing project

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https://figshare.com/articles/Additional_file_1_of_Comparative_analysis_of_targeted_long_read_sequencing_approaches_for_characterization_of_a_plant_s_immune_receptor_repertoire/5248525

The History of the Botanic Garden in Smíchov in Light of Archival Sources

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National Repository of Grey Literature

University of East Anglia digital repository

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