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
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
RepeatExplorer is an online tool that can give a bioinformatician a grasp on what repeats are in a genome, as well as their relative abundance. Here, I took TN20 reads from NCBI (SRR1800548), trimmed with trimmomatic, converted to fasta with the fastx-toolkit, and sorted and interlaced with seqtk. 200,000 reads were retained that maintained the maximum length (150bp) and had a full length mate. Classified repeats were also obtained from running RepeatModeler on the H. glycines genome [1]. Read more about Repeat Explorer of TN20
The H. glycines mitochondria was initially mis-assembled into a 269kb scaffold. Previous publication has the mitochondrial genome at a size of ~20kb (Figure 1)(1). A single best copy was selected from assembled preads using gene predictions(Table 1), phylogenetics (Figure 2), and alignments (Figure 3) to the previously published mitochondrial genome (1)
Read more about H. glycines Mitochondrial Assembly and Annotation
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.
