The yellow potato cyst nematode, Globodera rostoschiensis had novel GC donor splice sites at a frequency of 3.46% of the exons in the genome(1). To determine the extent of novel exon splicing we used custom bash scripts and exon predictions identified with Braker.pl V1(2) in the V1 genome publication (3). Read more about Novel Splice Junctions in H. glycines genome V1
An alien index (AI) analysis (1) identified horizontally transferred genes in the H. glycines genome V1 . The alien index is a ratio of BLAST similarity between metazoan and non-metazoan sequences. While 1,678 genes had alien indices greater than zero, only 151 had strong support (>30)(2).
AI analysis of all 1,678 genes : geneswithaiover0.xlsx Read more about Horizontal Gene Transfer in H. glycines genome V1
RedTandem (1) was implemented to identify tandem duplications in the H. glycines V1 genome (2). A total of 6,730/29,769 of the genes in the genome colocalize to the same regions as tandem duplications.
Functional annotations of genes in tandem duplications in a GFF3 form: tandemduplicatedgenesannotatedaugustusgff3.rtf Read more about Tandem Duplications in the H. glycines V1 Genome
Eighty effectors have been previously identified in H. glycines (1-2). The mRNA sequences of these effectors were aligned to the H. glycines genome V1 to identify their genomic sources. Many of the functions of these effectors have been characterized, some of include: defense suppression, alterations of plant hormone signaling, epigenetic modification, metabolic manipulation, and cytoskeletal modifications (reviewed by 3-6). Read more about Eighty Known Effectors Aligned to H. glycines Genome V1
DOG-box DNA motifs were enriched in the promoters of dorsal gland expressed genes in Globodera rostochiensis (1). As a modulus to identify putative effectors, we searched for a similar motif in H. glycines. A set of DOG-box containing genes from G. rostochiensis and glutathione synthetase genes from both H. glycines and G. rostochiensis were used to refine a H. glycines DOG box using MEME. The promoters of the genes in H. Read more about H. glycines Genes with Promoters Enriched for DOG-box Motifs
80 effector proteins were known at the time of the H. glycines genome publication (1). Protein motifs were identified from the predicted proteins of these 80 effectors. The motifs were implemented in a FIMO search of the the predicted proteins from the H. glycines gene annotations.
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.