H. glycines Mitochondrial Assembly and Annotation

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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)

 

Figure 1. Comparison of the final annotated mitochondrial genome (23kb, blue), and ~12.2 mitochondrial genomes misassembled into a 269kb contig. Each color represents a different mitochondrial genome, and black dots represent gene annotations.

 

Name    Start   Stop    Strand  Length  Structure
trnT(tgt)   5203    5260    +   58  svg ps
trnG(tcc)   6277    6334    -   58  svg ps
cob-1_b     7382    8050    -   669     
trnP(tgg)   8562    8609    -   48  svg ps
trnD(gtc)   8619    8672    -   54  svg ps
nad6-3_c    8993    9106    -   114     
nad6-1  9108    9470    -   363     
nad6-3_a    9498    9524    -   27  
nad6-3_b    9528    9530    -   3   
nad5-1  9580    9594    -   15  
trnF(gaa)   9585    9640    -   56  svg ps
trnV(tac)   9649    9704    -   56  svg ps
cob-0_b     9738    10172   -   435     
cob-0_a     10087   10764   -   678     
nad4    10934   11857   -   924     
nad6-2  11942   12142   -   201     
cox3    12109   12825   -   717     
trnI(gat)   12862   12919   -   58  svg ps
nad2    12982   13782   -   801     
cox1    13894   15303   -   1410    
nad3    15318   15608   -   291     
rrnL    15647   16091   -   445     svg ps
cox2    16464   17081   -   618     
trnC(gca)   17125   17180   -   56  svg ps
trnS2(aga)  17196   17252   +   57  svg ps
nad5-0  17991   18977   -   987     
nad4l   19109   19366   -   258     
atp6    19333   19572   -   240     
nad6-0  19684   20067   -   384     
nad1    20022   20777   -   756     
trnY(gta)   20802   20859   -   58  svg ps
atp8    21541   21690   -   150  

Table 1. Mitos webserver was used to annotate the ~269kb ~23kb genome.  Two genes were added to the 23kb consensus genome, which were misannotated, due to variation in two mononucleotide repeat tracts.
 

 

Figure 2. Cap3-assembled mitochondrial p-reads were subjected to a Maximum Likelihood analysis with 1000 bootstraps using Bioedit.  Total alignment length was 3,984bp for 17 preads.  One p-read "000114|qui" had a large inversion in the center of a large mitochondrial repeat p-read.

 

#########################################################################################################################

 (((222818:0.00004,(252874:0.00004,(((((053248:0.00004,
 173260:0.00004):0.00004,322144:0.00004):0.00004,
 ((042966:0.00024,264906:0.00004):0.00004,((280396:0.00020,
 322148:0.00004):0.00004,(112708:0.00004,280820:0.00013):0.00013):0.00004):0.00004):0.00004,
 024091:0.00049):0.00004,(261038:0.00127,160407:0.00004):0.00050):0.00004):0.00004):0.00045,
 224883:0.00075):0.00004,219030:0.00004,296912:0.00004);

#########################################################################################################################

 

 

Figure 3.  Meme on the 19 Cap3-assembled mitochondrial p-reads.  Sequence 12 represents p-read 000114|qui in the Figure 2. The numerous black motifs in the center of each sequence represent a tandemly repeated sequence of ~5kb in length. 

 

 

 

1) Gibson, Tracey, et al. "The mitochondrial genome of the soybean cyst nematode, Heterodera glycines." Genome 54.7 (2011): 565-574.

 

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