Fungal Genome Collection
University of Nebraska Lincoln
School of Biological Sciences and Center for Plant Science Innovation
Home About FGC Use Cases Species List

[Case 1] Searching cystathionine beta-lyase (STR3) orthologues
Wilson, RA, Fernandez, J, Quispe, CF, Gradnigo, J, Seng, A, Moriyama, EN, Wright, JD (2012) Towards defining nutrient conditions encountered by the rice blast fungus during host infection. PLoS ONE 7: e47392.

STR3 (YGL184C) in Saccharomyces cerevisiae is known to encode cystathione beta-lyase.

Fig. 1 shows the distribution of YGL184C orthologues among fungal species. Following are the steps to reproduce this image:

  • From the home page, choose Saccharomyces group.
  • Next choose Saccharomyces cerevisiae S288C.
  • Use "Search sequence annotation" to find the record whose Sequence ID is YGL184C.
  • Click on the green "Ortho" button next to YGL184C.
  • Change "% identity" threshold to 30, and click on "Change limits".

Dots in the matrix are color-coded for sequence identity: >90%, >80%, >70%, >60%, >50%, >40%, and >30%

How FGC finds orthologue candidates is described on this page.

str3 orthologs
Fig. 1. (click the image to enlarge)
YGL184C orthologue distribution using 30% identity as the threshold.

From Fig. 1, we can find MGG_07074 as the Magnaporthe oryzae orthologue.

Clicking on the MGG_07074 link in the orthologue matrix produces the MGG_07074 orthologue matrix (Fig. 2), which is very similar to Fig. 1

From these ortholog matrices, we can confirm that YGL184C in S. cerevisiae S288C and MGG_07074 in M. oryzae are orthologues.

Orthologues in Aspergillus nidulans (ANID_07051, metG) and in Neurospora crassa (NCU07987, met-2), for example, can also be identified.

Note that many orthologues are highly similar to MGG_07074 (60% or higher).

In contrast, the S. cerevisiae orthologue (YGL184C) has much weaker similarity compared to others. Yellow, orange, and red dots indicate that YGL184C has % identity lower than 60% against any other orthologues (Fig. 1 and Fig. 2)

MGG_07074 orthologs
Fig. 2. (click the image to enlarge)
MGG_07074 orthologue distribution using 30% identity as the threshold.

Some of the STR3 orthologues have longer sequences.

In Fig. 3, MGG_07074 orthologues are now shown using thresholds of 30% sequence identity but 0.5 alignment-to-hit length ratio.

The alignment-to-hit length ratio is the proportion of the length of the aligned region to the hit length. If an orthologue (hit) is longer than the query (MGG_07074), this ratio becomes smaller.

By changing the length ratio threshold from unlimited (blank) to 0.5, orthologues much longer than MGG_07074 are filtered out (Fig. 3).

Comparing Fig. 2 and Fig. 3, clearly orthologues found in the Basidiomycota are twice or more longer than MGG_07074.

MGG_07074 orthologs short
Fig. 3. (click the image to enlarge)
MGG_07074 orthologue distribution using 30% identity and 0.5 length ratio thresholds.

Length variation among MGG_07074 orthologues is clearly seen in the visual alignment shown in Fig. 4.

To see this image, use the "Coverage Graphic" button at the top of the orthologue matrix page.

These long extra C-terminal regions found in Basidiomycota orthologues contain sequences similar to mevalonate kinase (e.g., XP_567850).

See Wilson et al. (2012) for more details.

MGG_07074 ortholog alignment
Fig. 4. (click the image to enlarge)
Visual alignment of MGG_07074 orthologues.