Gene Feature Symbols Defined
| ID | This is the literal gene name |
| Symbols | This is the name of the gene locus, which was used in the gene prediction, but is otherwise uninformative. |
| Cdd | This represents a BLAST hit to the Conserved Domains Database |
| Coils/Sfld/Mobidblite | Programs ran as part of Interproscan. Coils database, Structure Function Linkage Database, and MobiDB-lite database |
| Effector DNA Alignment (Gmapeffectorsallmrna) | This is an alignment of DNA sequences of transcripts from 80 previously published effector sequences. All of these can be found in the NCBI Nucleotide database. https://db.scnbase.org/downloads/59 |
| Effector Protein To Protein Alignment (Diamondeffectorsallmrna) | This is an alignment of the predicted protein sequences from the 80 previously published effector sequences to the TN10 genome's predicted proteins. https://db.scnbase.org/downloads/59 |
| Geneallvsalldowngland | If not N/A, then this represents the log fold change of a significantly differentially expressed gene that is "upregulated" in whole worm RNAseq (Gardner et al 2018 ) versus Gland RNAseq (Maier et al 2021). A negative value represents the opposite, i.e. upregulated in gland. |
| Geneallvsallupgland | If not N/A, then this represents the log fold change of a significantly differentially expressed gene that is "downregulated" in whole worm RNAseq (Gardner et al 2018 ) versus Gland RNAseq (Maier et al 2021). A negative value represents the opposite, i.e. downregulated in gland. |
| GenecvsIc_Upc | If not N/A, then this represents the log fold change of a significantly differentially expressed gene that is "upregulated" in a compatible interaction versus an incompatible interaction. A negative value represents the opposite, i.e. upregulated in the incompatible interaction. RNAseq derived from Gardner et al 2018. |
| GenecvsIc_Upic | If not N/A, then this represents the log fold change of a significantly differentially expressed gene that is "downregulated" in a compatible interaction versus an incompatible interaction. A negative value represents the opposite, i.e. downregulated in the incompatible interaction. RNAseq derived from Gardner et al 2018. |
| Genecvspp_Upc | If not N/A, then this represents the log fold change of a significantly differentially expressed gene that is "upregulated" in a compatible interaction versus an pre-parasitic J2 nematodes. A negative value represents the opposite, i.e. upregulated in gland. RNAseq derived from Gardner et al 2018. |
| Genecvspp_Uppp | If not N/A, then this represents the log fold change of a significantly differentially expressed gene that is "downregulated" in a compatible interaction versus an pre-parasitic J2 nematodes. A negative value represents the opposite, i.e. downregulated in preparasitic J2 nematodes. RNAseq derived from Gardner et al 2018. |
| Genemm10vspa3glandmm10up | If not N/A, then this represents the log fold change of a significantly differentially expressed gene that is "upregulated" in the MM10 Gland RNAseq versus PA3 Gland RNAseq (Maier et al 2021). A negative value represents the opposite, i.e. upregulated in PA3 gland. |
| Genemm10vspa3glandpa3up | If not N/A, then this represents the log fold change of a significantly differentially expressed gene that is "downregulated" in the MM10 Gland RNAseq versus PA3 Gland RNAseq (Maier et al 2021). A negative value represents the opposite, i.e. downregulated in PA3 gland. |
| Genepa3glandvspa3wormdowngland | If not N/A, then this represents the log fold change of a significantly differentially expressed gene that is "downregulated" in PA3 Gland RNAseq versus the PA3 compatible interaction RNAseq from whole worms. A negative value represents the opposite, i.e. downregulated in PA3 compatible interaction from whole worms. Gland RNAseq was from Maier et al 2021 and whole worm RNAseq was from Gardner et al 2018. |
| Genepa3glandvspa3wormupgland | If not N/A, then this represents the log fold change of a significantly differentially expressed gene that is "upregulated" in PA3 Gland RNAseq versus the PA3 compatible interaction RNAseq from whole worms. A negative value represents the opposite, i.e. upregulated in PA3 compatible interaction from whole worms. Gland RNAseq was from Maier et al 2021 and whole worm RNAseq was from Gardner et al 2018. |
| Geneppvsic_Upic | If not N/A, then this represents the log fold change of a significantly differentially expressed gene that is "upregulated" in an incompatible interaction versus compatible interaction. A negative value represents the opposite, i.e. upregulated in the compatible interaction. RNAseq derived from Gardner et al 2018. |
| Geneppvsic_Uppp | If not N/A, then this represents the log fold change of a significantly differentially expressed gene that is "upregulated" in pre-parasitic stages versus an incompatible interaction. A negative value represents the opposite, i.e. upregulated in the incompatible interaction. RNAseq derived from Gardner et al 2018. |
| Mrnalocationssorted | This is the location of the gene in the genome. Use these coordinates to copy and paste in JBrowse to easily find the gene. |
| Nls Nlstradamus (A Score Is Indicative Of Positive) | Nuclear localization signal predicted using NLStradamus. |
| Note | This is all the functional information formatted into one line. |
| Nr_Blastp | This is a blast of the predicted protein to the NCBI NR database (Non-Redundant). |
| Nt_Blastn | This is a blast of the transcript sequence to the NCBI NT database (Nucleotide) |
| Panther_Smart_Superfamily | Programs ran as part of Interproscan. Panther, SMART, and SUPERFAMILY databases. |
| Pfam | Program ran as part of Interproscan on the predicted proteins. |
| Prints_Prositepatterns_Prositeprofiles_Prodom_Tigrfam_Hamap | Programs that were ran as part of Interproscan: PRINTS, PROSITE patterns, PROSITE profiles, ProDom, TIGRFAM, and HAMAP |
| Repetitive-High Liklihood of Te (Edtaallmrna) | If not N/A, this indicates that the transcript had at least some overlap with an EDTA repeat (Extensive De-novo TE Annotator) |
| Repetitive (Repeatmodeler) | If not N/A, this indicates that the transcript had at least some overlap with a RepeatModeler repeat. |
| SignalP5 | Signal peptide prediction by SignalP 5. If the score is above 0.5, then this transcript likely produces a secreted protein. |
| Tm Domains | This is the number of transmembrane domains in the predicted protein, predicted via TMHMM. |
| Up_Blastp | This is a BLASTp of the predicted protein to the UniProt database. |
| Up_Blastx | This is a BLASTx of the transcripts to the UniProt database. |
All of these features here were developed as part of the soybean cyst nematode genome publication
Masonbrink, Rick E., et al. "A chromosomal assembly of the soybean cyst nematode genome." Molecular ecology resources 21.7 (2021): 2407-2422.
RNAseq information for differentially expressed genes
1. Gardner, Michael, et al. "Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines." Scientific reports 8.1 (2018): 1-15.
2. Maier, Tom R., et al. "Esophageal Gland RNA-Seq Resource of a Virulent and Avirulent Population of the Soybean Cyst Nematode Heterodera glycines." Molecular Plant-Microbe Interactions 34.9 (2021): 1084-1087.