Secreted Genes in the H. glycines V1 genome


Because secreted proteins play a vital role in H. glycines parasitism, iwe surveyed the H. glycines annotation for genes with a signal peptide for secretion that also lack a transmembrane domain (1).  A total of 2,222 genes were classified as secreted using Phobius (2) and SignalP (3) annotations obtained using interproscan(4).  However, due to a coding error, these annotations were incomplete.  With SignalP 4.0 (3) we have identified a larger set of secreted genes, 4,656.


Functional annotations of secreted genes in the H. glycines genome V1 publication (1):   secretedgenesannotatedaugustusgff3.rtf

The revised set of functional annotations of secreted genes in the H. glycines genome:  reworkedfunctionalaugustussecreted_sorted.rtf


1) Masonbrink, Rick E., et al. "The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes." bioRxiv (2018): 391276.

2) Käll, Lukas, Anders Krogh, and Erik LL Sonnhammer. "A combined transmembrane topology and signal peptide prediction method." Journal of molecular biology 338.5 (2004): 1027-1036.

3) Melhem, Hind, Xiang Jia Min, and Greg Butler. "The impact of SignalP 4.0 on the prediction of secreted proteins." CIBCB. 2013.

 4) Jones, Philip, et al. "InterProScan 5: genome-scale protein function classification." Bioinformatics 30.9 (2014): 1236-1240.