Exploring the potential of nuclear and mitochondrial sequencing data generated through genome‐skimming for plant phylogenetics: A case study from a clade of neotropical lianas

2019 ◽  
Vol 58 (1) ◽  
pp. 18-32 ◽  
Author(s):  
Luiz Henrique M. Fonseca ◽  
Lúcia G. Lohmann
Keyword(s):  
Sequencing Data ◽  
Genome Skimming ◽  
Plant Phylogenetics

scholarly journals Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

2009 ◽  
Vol 75 (23) ◽  
pp. 7537-7541 ◽  
Author(s):  
Patrick D. Schloss ◽  
Sarah L. Westcott ◽  
Thomas Ryabin ◽  
Justine R. Hall ◽  
Martin Hartmann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Software Package ◽  
Sequence Data ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Laptop Computer ◽  
Operational Taxonomic Units ◽  
Β Diversity ◽  
Single Piece

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

scholarly journals Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data

2020 ◽  
Author(s):  
Junpeng Zhang ◽  
Lin Liu ◽  
Taosheng Xu ◽  
Wu Zhang ◽  
Chunwen Zhao ◽  
...  
Keyword(s):  
Single Cell ◽  
Regulatory Networks ◽  
Single Cells ◽  
Small Scale ◽  
Mirna Regulation ◽  
Sequencing Data ◽  
Resolution Level ◽  
Novel Strategy ◽  
Cell Cell

AbstractBackgroundExisting computational methods for studying miRNA regulation are mostly based on bulk miRNA and mRNA expression data. However, bulk data only allows the analysis of miRNA regulation regarding a group of cells, rather than the miRNA regulation unique to individual cells. Recent advance in single-cell miRNA-mRNA co-sequencing technology has opened a way for investigating miRNA regulation at single-cell level. However, as currently single-cell miRNA-mRNA co-sequencing data is just emerging and only available at small-scale, there is a strong need of novel methods to exploit existing single-cell data for the study of cell-specific miRNA regulation.ResultsIn this work, we propose a new method, CSmiR (Cell-Specific miRNA regulation) to use single-cell miRNA-mRNA co-sequencing data to identify miRNA regulatory networks at the resolution of individual cells. We apply CSmiR to the miRNA-mRNA co-sequencing data in 19 K562 single-cells to identify cell-specific miRNA-mRNA regulatory networks to understand miRNA regulation in each K562 single-cell. By analyzing the obtained cell-specific miRNA-mRNA regulatory networks, we observe that the miRNA regulation in each K562 single-cell is unique. Moreover, we conduct detailed analysis on the cell-specific miRNA regulation associated with the miR-17/92 family as a case study. Finally, through exploring cell-cell similarity matrix characterized by cell-specific miRNA regulation, CSmiR provides a novel strategy for clustering single-cells to help understand cell-cell crosstalk.ConclusionsTo the best of our knowledge, CSmiR is the first method to explore miRNA regulation at a single-cell resolution level, and we believe that it can be a useful method to enhance the understanding of cell-specific miRNA regulation.

HPLC-UV, Metabarcoding and Genome Skims of Botanical Dietary Supplements: A Case Study in Echinacea

Planta Medica ◽  
2021 ◽  
Author(s):  
Sara M. Handy ◽  
Rahul S. Pawar ◽  
Andrea R. Ottesen ◽  
Padmini Ramachandran ◽  
Satyanarayanaraju Sagi ◽  
...  
Keyword(s):  
Dietary Supplements ◽  
Chemical Methods ◽  
Botanical Dietary Supplements ◽  
Closely Related Species ◽  
Trade Offs ◽  
The Family ◽  
Genome Skimming ◽  
Discriminatory Capacity ◽  
Generation Sequencing

AbstractThe use of DNA-based methods to authenticate botanical dietary supplements has been vigorously debated for a variety of reasons. More comparisons of DNA-based and chemical methods are needed, and concordant evaluation of orthogonal approaches on the same products will provide data to better understand the strengths and weaknesses of both approaches. The overall application of DNA-based methods is already firmly integrated into a wide array of continually modernizing stand alone and complementary authentication protocols. Recently, the use of full-length chloroplast genome sequences provided enhanced discriminatory capacity for closely related species of Echinacea compared to traditional DNA barcoding approaches (matK and rbcL). Here, two next-generation sequencing approaches were used: (1) genome skimming and (2) PCR amplicon (metabarcoding). The two genetic approaches were then combined with HPLC-UV to evaluate 20 commercially available dietary supplements of Echinacea representing “finished” products. The trade-offs involved in different DNA approaches were discussed, with a focus on how DNA methods support existing, accepted chemical methods. In most of the products (19/20), HPLC-UV suggested the presence of Echinacea spp. While metabarcoding was not useful with this genus and instead only resolved 7 products to the family level, genome skimming was able to resolve to species (9) or genus (1) with the 10/20 products where it was successful. Additional ingredients that HPLC-UV was unable to identify were also found in four products along with the relative sequence proportion of the constituents. Additionally, genome skimming was able to identify one product that was a different Echinacea species entirely.

scholarly journals Changes in Microsatellite Motifs in Response to Abiotic Stresses: a Case Study Using Wheat and Rice RNA-sequencing Data

2017 ◽  
Vol 11 (1) ◽  
pp. 12-21
Author(s):  
Arghavan Alisoltani ◽  
Behrouz Shiran ◽  
Narjes Rahpeyma Sarvestani ◽  
Hossein Fallahi ◽  
Naser Aliye Feto ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Abiotic Stresses ◽  
Sequencing Data

scholarly journals Normalizing single-cell RNA sequencing data with internal spike-in-like genes

2020 ◽  
Author(s):  
Li Lin ◽  
Minfang Song ◽  
Yong Jiang ◽  
Xiaojing Zhao ◽  
Haopeng Wang ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Single Cells ◽  
Sequencing Depth ◽  
Sequencing Data ◽  
Crucial Step ◽  
Single Cell Rna Sequencing ◽  
Whole Transcriptome

ABSTRACTNormalization with respect to sequencing depth is a crucial step in single-cell RNA sequencing preprocessing. Most methods normalize data using the whole transcriptome based on the assumption that the majority of transcriptome remains constant and are unable to detect drastic changes of the transcriptome. Here, we develop an algorithm based on a small fraction of constantly expressed genes as internal spike-ins to normalize single cell RNA sequencing data. We demonstrate that the transcriptome of single cells may undergo drastic changes in several case study datasets and accounting for such heterogeneity by ISnorm improves the performance of downstream analyzes.

scholarly journals LSTrAP-Cloud: A User-friendly Cloud Computing Pipeline to Infer Co-functional and Regulatory Networks

2020 ◽  
Author(s):  
Qiao Wen Tan ◽  
William Goh ◽  
Marek Mutwil
Keyword(s):  
Rna Sequencing ◽  
Gene Function ◽  
Regulatory Networks ◽  
Large Scale ◽  
Function Prediction ◽  
Sequencing Data ◽  
Gene Function Prediction ◽  
Analysis Pipeline ◽  
User Friendly

AbstractAs genomes become more and more available, gene function prediction presents itself as one of the major hurdles in our quest to extract meaningful information on the biological processes genes participate in. In order to facilitate gene function prediction, we show how our user-friendly pipeline, Large-Scale Transcriptomic Analysis Pipeline in Cloud (LSTrAP-Cloud), can be useful in helping biologists make a shortlist of genes that they might be interested in. LSTrAP-Cloud is based on Google Colaboratory and provides user-friendly tools that process and quality-control RNA sequencing data streamed from the European Sequencing Archive. LSTRAP-Cloud outputs a gene co-expression network that can be used to identify functionally related genes for any organism with a sequenced genome and publicly available RNA sequencing data. Here, we used the biosynthesis pathway of Nicotiana tabacum as a case study to demonstrate how enzymes, transporters and transcription factors involved in the synthesis, transport and regulation of nicotine can be identified using our pipeline.

scholarly journals The Unexpected Depths of Genome-Skimming Data: A Case Study Examining Goodeniaceae Floral Symmetry Genes

2017 ◽  
Vol 5 (10) ◽  
pp. 1700042 ◽  
Author(s):  
Brent A. Berger ◽  
Jiahong Han ◽  
Emily B. Sessa ◽  
Andrew G. Gardner ◽  
Kelly A. Shepherd ◽  
...  
Keyword(s):  
Floral Symmetry ◽  
Genome Skimming

scholarly journals A comprehensive toolkit to enable MinION sequencing in any laboratory

2018 ◽  
Author(s):  
Miriam Schalamun ◽  
David Kainer ◽  
Eleanor Beavan ◽  
Ramawatar Nagar ◽  
David Eccles ◽  
...  
Keyword(s):  
Read Length ◽  
Full Potential ◽  
Sequencing Data ◽  
Special Equipment ◽  
High Quality ◽  
Sequencing Technologies ◽  
Entry Cost ◽  
Long Read ◽  
Hmw Dna

AbstractLong-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realising their full potential relies crucially on extracting high quality, high molecular weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which potentiates all laboratories to undertake their own genome sequencing projects, due to its low entry cost and minimal spatial footprint. One challenge of the MinION is that each group has to independently establish effective protocols for using the instrument, which can be time consuming and costly. Here we present a workflow and protocols that enabled us to establish MinION sequencing in our own laboratories, based on optimising DNA extractions from a challenging plant tissue as a case study. Following the workflow illustrated we were able to reliably and repeatedly obtain > 8.5 Gb of long read sequencing data with a mean read length of 13 kb and an N50 of 26 kb. Our protocols are open-source and can be performed in any laboratory without special equipment. We also illustrate some more elaborate workflows which can increase mean and average read lengths if this is desired. We envision that our workflow for establishing MinION sequencing, including the illustration of potential pitfalls, will be useful to others who plan to establish long-read sequencing in their own laboratories.

scholarly journals Geneious! Simplified Genome Skimming Methods for Phylogenetic Systematic Studies: A Case Study inOreocarya(Boraginaceae)

2014 ◽  
Vol 2 (12) ◽  
pp. 1400062 ◽  
Author(s):  
Lee A. Ripma ◽  
Michael G. Simpson ◽  
Kristen Hasenstab-Lehman
Keyword(s):  
Genome Skimming
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