Transcripts

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: 

Transcripts of genes producing secreted proteins

Organism: 
Heterodera glycines v2 (Soybean Cyst Nematode (v2))
Program, Pipeline Name or Method Name: 
Braker genes, SignalP and Tmhmm
Program, Pipeline or Method version: 
braker 1.9, SignalP 4.1, Tmhmm 2.0
Source Name: 
Baum/Severin Labs
Time Executed: 
07/18/2019
Materials & Methods (Description and/or Program Settings): 
Genes with N terminal secretion signals, and lacking transmembrane domains.
Category: 

Trinity Transcripts form Gardner et al 2017

Organism: 
Heterodera glycines v2 (Soybean Cyst Nematode (v2))
Program, Pipeline Name or Method Name: 
Gmap alignment
Program, Pipeline or Method version: 
gmap alignment
Source Name: 
NCBI Bioproject PRJNA415980
Time Executed: 
12/20/2018
Materials & Methods (Description and/or Program Settings): 
A PA3 trinity transcriptome downloaded from NCBI Bioproject PRJNA415980. Gardner M et al., "Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines.", Sci Rep, 2018 Feb 6;8(1):2505
Category: 

Consensus Isoseq Transcriptome from PA3 and TN19

Organism: 
Heterodera glycines v2 (Soybean Cyst Nematode (v2))
Program, Pipeline Name or Method Name: 
SmartPortal, Gmap
Program, Pipeline or Method version: 
Gmap 2016-04-04
Source Name: 
H.glycines Isoseq Consensus isoforms
Time Executed: 
04/05/2018
Materials & Methods (Description and/or Program Settings): 
Samples: idx1 = W82_PA3_Eggs idx2 = W82_PA3_J2/J3 idx3 = W82_PA3_J4/Adult idx4 = W82_TN19_Eggs idx5 = W82_TN19_J4/Adult idx6 = W82_TN19_J2/J3 First reads of inserts were generated using the pacbio smrtanalysis RS_ReadsOfInsert protocol. This was done on the pool as a whole, then reads were segregated based on exact matched to the index sequences. The indexed results then each went into the isoseq protocol, which identified full length transcripts by identifying the 5' and 3' adapters as well as the polyA tail. Next the Full length nonchimeric reads are clustered for correction using the ICE algorithm that is part of the isoseq protocol. #reads were aligned with GMAP gmap -D /data013/GIF/remkv6/Baum/CamTechGenomeComparison/34_IsoSeq/ -d 738.genome -B 5 -t 16 --input-buffer-size=1000000 --output-buffer-size=1000000 -f 2 all_isoseq_reads.fasta >isoseq_738.gff
Category: 

PA3 Transcriptome on susceptible and resistant soybean

Organism: 
Heterodera glycines v2 (Soybean Cyst Nematode (v2))
Program, Pipeline Name or Method Name: 
Trinity transcriptome with Gmap alignment
Program, Pipeline or Method version: 
Trinity 2.3.2, Gmap 2016-04-04
Source Name: 
PA3 H. glycines transcriptome. Grown on susceptible and resistant soybean cultivars
Source Version: 
Grown on susceptible and resistant soybean cultivars Williams 82 or EXF63
Time Executed: 
04/05/2018
Materials & Methods (Description and/or Program Settings): 
Trinity transcriptome was genome guided under default parameters. gmap -D /data013/GIF/remkv6/Baum/CamTechGenomeComparison/30_transcriptMappingUpdated/ -d genome738sl.polished.mitoFixed -B 5 -t 16 --input-buffer-size=1000000 --output-buffer-size=1000000 -f 2 nematode_transcripts_full_Trinity_genome_guided.fasta
Category: 

NCBI_ESTs_All

Organism: 
Heterodera glycines (Soybean Cyst Nematode (v1))
Program, Pipeline Name or Method Name: 
GMAP,Tabix
Program, Pipeline or Method version: 
gmap-gsnap/20160404, tabix/0.2.6
Source Name: 
ISU Genome Informatics Facility and Thomas Baum Lab
Time Executed: 
02/17/2017
Materials & Methods (Description and/or Program Settings): 
Raw downloaded ESTs to H.glycines
Category: 

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