Mitochondrial Genome Assembly from Peronospora

Contigs from a de novo genomic assembly in CLC Genomics Workbench (v9; Qiagen, Redwood City, CA) were identified as mitochondrial due to sequence similarity with P. tabacina mitochondrial sequences (KT893455) by BLAST analysis (Derevnina et al. 2015 (link)). These were used as templates for further assembly with SeqMan NGen (v16.0.0, DNASTAR, Madison, WI, USA). The resulting assemblies were evaluated for uniformity and depth of coverage. Contigs were broken when gaps/low coverage or inconsistencies were observed and the set of smaller contigs reassembled using the reference-guided assembly—special workflows assembly option of SeqMan NGen to extend the ends of the contigs and close the gaps. Open reading frames (ORFs) were predicted and annotated with Geneious v9.1.8 (Biomatters, New Zealand) using the universal genetic code. Encoded products of genes were identified using BLAST (Altschul et al. 1990 (link)) analysis against mitochondrial genome sequences published for Peronospora tabacina (Derevnina et al. 2015 (link)). Genes encoding tRNAs were identified using tRNAscan-SE v1.3.1 (Lowe and Eddy 1997 (link)).

Free full text: Click here

Fletcher K., Martin F., Isakeit T., Cavanaugh K., Magill C, & Michelmore R. (2023). The genome of the oomycete Peronosclerospora sorghi, a cosmopolitan pathogen of maize and sorghum, is inflated with dispersed pseudogenes. G3: Genes|Genomes|Genetics, 13(3), jkac340.

Publication 2023

CLC Genomics Workbench SeqMan NGen

Genes Genes products Genetic code Genomic Mitochondrial Mitochondrial genome Open reading frames Peronospora Redwood Sequences analysis Trnas

Corresponding Organization : University of California, Davis

Other organizations : United States Department of Agriculture, Texas A&M University

Top 5 similar protocols

Variable analysis

independent variables

De novo genomic assembly in CLC Genomics Workbench (v9; Qiagen, Redwood City, CA)

dependent variables

Identification of mitochondrial contigs based on sequence similarity with Peronospora tabacina mitochondrial sequences
Further assembly of mitochondrial contigs using SeqMan NGen (v16.0.0, DNASTAR, Madison, WI, USA)
Evaluation of uniformity and depth of coverage of the resulting assemblies
Prediction and annotation of open reading frames (ORFs) using Geneious v9.1.8 (Biomatters, New Zealand)
Identification of encoded products of genes using BLAST analysis against mitochondrial genome sequences published for Peronospora tabacina
Identification of genes encoding tRNAs using tRNAscan-SE v1.3.1

control variables

Peronospora tabacina mitochondrial sequences (KT893455) used as references for BLAST analysis

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!