Transcripts

Genes that lack expression -- protein fasta sequences

Organism: 
Heterodera glycines tn10 (Soybean Cyst Nematode (tn10))
Program, Pipeline Name or Method Name: 
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks
Program, Pipeline or Method version: 
Mikado 1.24
Source Name: 
Masonbrink
Time Executed: 
04/16/2021
Materials & Methods (Description and/or Program Settings): 
These are protein sequences of genes that lacked more than a single unique RNAseq read mapping from Gardner et al's RNA-seq dataset SRX3339090- SRX3339098.
Category: 
Default Track?: 

Genes that lack expression -- transcript fasta sequences

Organism: 
Heterodera glycines tn10 (Soybean Cyst Nematode (tn10))
Program, Pipeline Name or Method Name: 
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks
Program, Pipeline or Method version: 
Mikado 1.24
Source Name: 
Masonbrink
Time Executed: 
04/16/2021
Materials & Methods (Description and/or Program Settings): 
Transcript fasta sequences of transcripts that did not have more than 1 unique read mapping from Gardner et al -- SRX3339090- SRX3339098
Category: 
Default Track?: 

Repetitive Genes that overlap repeatmasker protein fasta

Organism: 
Heterodera glycines tn10 (Soybean Cyst Nematode (tn10))
Program, Pipeline Name or Method Name: 
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks
Program, Pipeline or Method version: 
Mikado 1.24
Source Name: 
Masonbrink
Time Executed: 
04/16/2021
Materials & Methods (Description and/or Program Settings): 
Protein sequences of genes with a repeatmasker repeat overlapping at least two CDS sequences by at least 30%.
Category: 
Default Track?: 

Repetitive Genes that overlap repeatmasker transcript fasta

Organism: 
Heterodera glycines tn10 (Soybean Cyst Nematode (tn10))
Program, Pipeline Name or Method Name: 
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks
Program, Pipeline or Method version: 
Mikado 1.24
Source Name: 
Masonbrink
Time Executed: 
04/16/2021
Materials & Methods (Description and/or Program Settings): 
Fasta sequences of those transcripts that overlapped a repeatmasker repeat by at least 30% in two CDS sequences
Category: 
Default Track?: 

Fasta sequences of the 80 published effector genes

Organism: 
Heterodera glycines v2 (Soybean Cyst Nematode (v2))
Program, Pipeline Name or Method Name: 
Collected from literature
Program, Pipeline or Method version: 
Collected in 2017
Source Name: 
Baum/Severin Labs
Time Executed: 
07/18/2019
Materials & Methods (Description and/or Program Settings): 
Gene sequences were obtained from the Thomas Baum lab and aligned to the genome using Gmap under default parameters. Effectors uses are referenced in these publications: Gao B, Allen R, Maier T, Davis EL, Baum TJ, Hussey RS (2001) Identification of putative parasitism genes expressed in the esophageal gland cells of the soybean cyst nematode Heterodera glycines. Molecular Plant-Microbe Interactions 14:1247-1254 Gao B, Allen R, Maier T, Davis EL, Baum TJ, Hussey RS (2001) Identification of putative parasitism genes expressed in the esophageal gland cells of the soybean cyst nematode Heterodera glycines. Molecular Plant-Microbe Interactions 14:1247-1254 Gao B, Allen R, Maier T, Davis EL, Baum TJ, Hussey RS (2003) The parasitome of the phytonematode Heterodera glycines. Molecular Plant-Microbe Interactions 16:720-726 Noon JB, Hewezi T, Maier TR, Simmons C, Wei J-Z, Wu G, Llaca V, Deschamps S, Davis EL, Mitchum MG (2015) Eighteen new candidate effectors of the phytonematode Heterodera glycines produced specifically in the secretory esophageal gland cells during parasitism. Phytopathology 105:1362-1372
Category: 

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