Novel Splice Junctions in H. glycines genome V1

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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). 

Heterodera glycines
Dinucleotide Donor Donor % Acceptor Acceptor %
AG 2 0.0% 202,556 99.9%
AC 11 0.0% 3 0.0%
AT 16 0.0% 6 0.0%
AA 23 0.0% 16 0.0%
CA 6 0.0% 11 0.0%
CT 7 0.0% 10 0.0%
CC 4 0.0% 6 0.0%
CG 6 0.0% 6 0.0%
GC 8,679 4.3% 5 0.0%
GA 3 0.0% 8 0.0%
GT 193,858 95.6% 5 0.0%
GG 15 0.0% 6 0.0%
TT 17 0.0% 23 0.0%
TA 6 0.0% 7 0.0%
TC 14 0.0% 7 0.0%
TG 12 0.0% 4 0.0%

The most predominant donor splice site was GT (yellow), however 4.3% of exon splice sites were GC (yellow). The salmon pink color denotes a single splice acceptor sequence at 99%.

 

1) Eves-van den Akker, Sebastian, et al. "The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence." Genome biology 17.1 (2016): 124.

2) Hoff, Katharina J., et al. "BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS." Bioinformatics 32.5 (2015): 767-769.

3) 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.

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