Difference between revisions of "Species list"

From "A B C"
Jump to navigation Jump to search
 
(6 intermediate revisions by the same user not shown)
Line 1: Line 1:
 +
=== Lists ===
 +
 +
For the current table and assignment to student IDs, see [[BIO_Assignment_Week_2#Choosing_YFO_.28Your_Favourite_Organism.29]].
 +
 +
<source lang="text">
 +
Ajellomyces dermatitidis [ORGN]
 +
OR Arthroderma gypseum [ORGN]
 +
OR Ashbya gossypii [ORGN]
 +
OR Aspergillus clavatus [ORGN]
 +
OR Aspergillus flavus [ORGN]
 +
OR Aspergillus nidulans [ORGN]
 +
OR Botryotinia fuckeliana [ORGN]
 +
OR Candida albicans [ORGN]
 +
OR Candida glabrata [ORGN]
 +
OR Chaetomium globosum [ORGN]
 +
OR Clavispora lusitaniae [ORGN]
 +
OR Coccidioides immitis [ORGN]
 +
OR Coprinopsis cinerea [ORGN]
 +
OR Debaryomyces hansenii [ORGN]
 +
OR Gibberella zeae [ORGN]
 +
OR Kluyveromyces lactis [ORGN]
 +
OR Komagataella pastoris [ORGN]
 +
OR Laccaria bicolor [ORGN]
 +
OR Lachancea thermotolerans [ORGN]
 +
OR Lodderomyces elongisporus [ORGN]
 +
OR Magnaporthe oryzae [ORGN]
 +
OR Malassezia globosa [ORGN]
 +
OR Meyerozyma guilliermondii [ORGN]
 +
OR Nectria haematococca [ORGN]
 +
OR Neosartorya fischeri [ORGN]
 +
OR Neurospora crassa [ORGN]
 +
OR Paracoccidioides brasiliensis [ORGN]
 +
OR Penicillium chrysogenum [ORGN]
 +
OR Phaeospheria nodorum [ORGN]
 +
OR Puccinia graminis [ORGN]
 +
OR Pyrenophora teres [ORGN]
 +
OR Saccharomyces cerevisiae [ORGN]
 +
OR Scheffersomyces stipitis [ORGN]
 +
OR Schizophyllum commune [ORGN]
 +
OR Schizosaccharomyces japonicus [ORGN]
 +
OR Schizosaccharomyces pombe [ORGN]
 +
OR Sclerotinia sclerotiorum [ORGN]
 +
OR Talaromyces stipitatus [ORGN]
 +
OR Trichophyton rubrum [ORGN]
 +
OR Uncinocarpus reesii [ORGN]
 +
OR Ustilago maydis [ORGN]
 +
OR Vanderwaltozyma polyspora [ORGN]
 +
OR Verticillium albo-atrum [ORGN]
 +
OR Yarrowia lipolytica [ORGN]
 +
OR Zygosaccharomyces rouxii [ORGN]
 +
</source>
 +
 +
 +
 +
The TaxIDs can be used e.g. on the iTOL site, however these are '''strain-level''' ID's harvested from a PSI-BLAST search, not species level.
 +
 +
<source lang="text">
 +
559298
 +
535722
 +
284811
 +
344612
 +
332952
 +
227321
 +
332648
 +
237561
 +
284593
 +
306901
 +
306902
 +
246410
 +
240176
 +
284592
 +
229533
 +
284590
 +
644223
 +
486041
 +
559295
 +
379508
 +
242507
 +
425265
 +
294746
 +
660122
 +
331117
 +
367110
 +
121759
 +
500485
 +
13684
 +
418459
 +
861557
 +
559292
 +
322104
 +
578458
 +
402676
 +
284812
 +
665079
 +
441959
 +
559305
 +
336963
 +
237631
 +
436907
 +
526221
 +
284591
 +
559307
 +
</source>
 +
 +
'''Species-level''' IDs for reference organisms:
 +
<source lang="text">
 +
 +
4932
 +
5476
 +
162425
 +
5141
 +
4896
 +
5270
 +
 +
</source>
 +
 
===The BCH441 Students &amp; Species List (Fall 2011)===
 
===The BCH441 Students &amp; Species List (Fall 2011)===
  
Line 57: Line 173:
 
<tr style="background: #FFFFFF;"><td>Alex Sadowski </td><td>''Scheffersomyces stipitis''</td><td><tt>'''SCHST'''</tt></td></tr>
 
<tr style="background: #FFFFFF;"><td>Alex Sadowski </td><td>''Scheffersomyces stipitis''</td><td><tt>'''SCHST'''</tt></td></tr>
 
<tr style="background: #E9EBF3;"><td>Gavneet Sandhu </td><td>''Schizophyllum commune''</td><td><tt>'''SCHCO'''</tt></td></tr>
 
<tr style="background: #E9EBF3;"><td>Gavneet Sandhu </td><td>''Schizophyllum commune''</td><td><tt>'''SCHCO'''</tt></td></tr>
−
<tr style="background: #FFFFFF;"><td>Alexander Sharov </td><td>''Schizosaccharomyces japonicus''</td><td><tt>'''SCHJA'''</tt></td></tr>
+
<tr style="background: #FFFFFF;"><td>Ravneet Sandhu </td><td>''Phaeospheria nodorum''</td><td><tt>'''PHANO'''</tt></td></tr>
−
<tr style="background: #E9EBF3;"><td>Joseph Sinopoli </td><td>''Sclerotinia sclerotiorum''</td><td><tt>'''SCLSC'''</tt></td></tr>
+
<tr style="background: #E9EBF3;"><td>Alexander Sharov </td><td>''Schizosaccharomyces japonicus''</td><td><tt>'''SCHJA'''</tt></td></tr>
−
<tr style="background: #FFFFFF;"><td>Pietro Sollazzo </td><td>''Talaromyces stipitatus''</td><td><tt>'''TALST'''</tt></td></tr>
+
<tr style="background: #FFFFFF;"><td>Joseph Sinopoli </td><td>''Sclerotinia sclerotiorum''</td><td><tt>'''SCLSC'''</tt></td></tr>
−
<tr style="background: #E9EBF3;"><td>Amit Srivastava </td><td>''Trichophyton rubrum''</td><td><tt>'''TRIRU'''</tt></td></tr>
+
<tr style="background: #E9EBF3;"><td>Pietro Sollazzo </td><td>''Talaromyces stipitatus''</td><td><tt>'''TALST'''</tt></td></tr>
−
<tr style="background: #FFFFFF;"><td>Amandeep Virk </td><td>''Uncinocarpus reesii''</td><td><tt>'''UNCRE'''</tt></td></tr>
+
<tr style="background: #FFFFFF;"><td>Amit Srivastava </td><td>''Trichophyton rubrum''</td><td><tt>'''TRIRU'''</tt></td></tr>
−
<tr style="background: #E9EBF3;"><td>Eniana Vrenozaj </td><td>''Vanderwaltozyma polyspora''</td><td><tt>'''VANPO'''</tt></td></tr>
+
<tr style="background: #E9EBF3;"><td>Amandeep Virk </td><td>''Uncinocarpus reesii''</td><td><tt>'''UNCRE'''</tt></td></tr>
−
<tr style="background: #FFFFFF;"><td>Dechen Wangmo </td><td>''Verticillium albo-atrum''</td><td><tt>'''VERAL'''</tt></td></tr>
+
<tr style="background: #FFFFFF;"><td>Eniana Vrenozaj </td><td>''Vanderwaltozyma polyspora''</td><td><tt>'''VANPO'''</tt></td></tr>
−
<tr style="background: #E9EBF3;"><td>Linna Wei </td><td>''Yarrowia lipolytica''</td><td><tt>'''YARLI'''</tt></td></tr>
+
<tr style="background: #E9EBF3;"><td>Dechen Wangmo </td><td>''Verticillium albo-atrum''</td><td><tt>'''VERAL'''</tt></td></tr>
−
<tr style="background: #FFFFFF;"><td>Yanyan Wu </td><td>''Zygosaccharomyces rouxii''</td><td><tt>'''ZYGRO'''</tt></td></tr>
+
<tr style="background: #FFFFFF;"><td>Linna Wei </td><td>''Yarrowia lipolytica''</td><td><tt>'''YARLI'''</tt></td></tr>
 +
<tr style="background: #E9EBF3;"><td>Yanyan Wu </td><td>''Zygosaccharomyces rouxii''</td><td><tt>'''ZYGRO'''</tt></td></tr>
 +
 
 +
<tr style="background: #FFFFFF;"><td colspan="3" style="border-bottom: solid 1px #000000;">&nbsp;</td></tr>
 +
<tr style="background: #FFFFFF;"><td colspan="3">&nbsp;</td></tr>
 +
 
 
<tr style="background: #E9EBF3;"><td>(Reference) </td><td>''Aspergillus nidulans''</td><td><tt>'''ASPNI'''</tt></td></tr>
 
<tr style="background: #E9EBF3;"><td>(Reference) </td><td>''Aspergillus nidulans''</td><td><tt>'''ASPNI'''</tt></td></tr>
 
<tr style="background: #FFFFFF;"><td>(Reference) </td><td>''Candida albicans''</td><td><tt>'''CANAL'''</tt></td></tr>
 
<tr style="background: #FFFFFF;"><td>(Reference) </td><td>''Candida albicans''</td><td><tt>'''CANAL'''</tt></td></tr>

Latest revision as of 18:19, 26 November 2012

Lists

For the current table and assignment to student IDs, see BIO_Assignment_Week_2#Choosing_YFO_.28Your_Favourite_Organism.29. 

Ajellomyces dermatitidis [ORGN]
OR Arthroderma gypseum [ORGN]
OR Ashbya gossypii [ORGN]
OR Aspergillus clavatus [ORGN]
OR Aspergillus flavus [ORGN]
OR Aspergillus nidulans [ORGN]
OR Botryotinia fuckeliana [ORGN]
OR Candida albicans [ORGN]
OR Candida glabrata [ORGN]
OR Chaetomium globosum [ORGN]
OR Clavispora lusitaniae [ORGN]
OR Coccidioides immitis [ORGN]
OR Coprinopsis cinerea [ORGN]
OR Debaryomyces hansenii [ORGN]
OR Gibberella zeae [ORGN]
OR Kluyveromyces lactis [ORGN]
OR Komagataella pastoris [ORGN]
OR Laccaria bicolor [ORGN]
OR Lachancea thermotolerans [ORGN]
OR Lodderomyces elongisporus [ORGN]
OR Magnaporthe oryzae [ORGN]
OR Malassezia globosa [ORGN]
OR Meyerozyma guilliermondii [ORGN]
OR Nectria haematococca [ORGN]
OR Neosartorya fischeri [ORGN]
OR Neurospora crassa [ORGN]
OR Paracoccidioides brasiliensis [ORGN]
OR Penicillium chrysogenum [ORGN]
OR Phaeospheria nodorum [ORGN]
OR Puccinia graminis [ORGN]
OR Pyrenophora teres [ORGN]
OR Saccharomyces cerevisiae [ORGN]
OR Scheffersomyces stipitis [ORGN]
OR Schizophyllum commune [ORGN]
OR Schizosaccharomyces japonicus [ORGN]
OR Schizosaccharomyces pombe [ORGN]
OR Sclerotinia sclerotiorum [ORGN]
OR Talaromyces stipitatus [ORGN]
OR Trichophyton rubrum [ORGN]
OR Uncinocarpus reesii [ORGN]
OR Ustilago maydis [ORGN]
OR Vanderwaltozyma polyspora [ORGN]
OR Verticillium albo-atrum [ORGN]
OR Yarrowia lipolytica [ORGN]
OR Zygosaccharomyces rouxii [ORGN]


The TaxIDs can be used e.g. on the iTOL site, however these are strain-level ID's harvested from a PSI-BLAST search, not species level. 

559298
535722
284811
344612
332952
227321
332648
237561
284593
306901
306902
246410
240176
284592
229533
284590
644223
486041
559295
379508
242507
425265
294746
660122
331117
367110
121759
500485
13684
418459
861557
559292
322104
578458
402676
284812
665079
441959
559305
336963
237631
436907
526221
284591
559307

Species-level IDs for reference organisms: 

4932
5476
162425
5141
4896
5270

The BCH441 Students & Species List (Fall 2011)

Every student in the course is being assigned a species for study.

Remember which species is listed here, you will be using your species for the rest of the assignments.


Construction of the Species List

For the purposes of the course assignments, we need species

  • that contain APSES transcription factors;
  • whose genome has been sequenced;
  • for which records exist in RefSeq.

Therefore the following steps have been executed:

  1. Performed a PSI BLAST search with the APSES domain sequence copied from Saccharomyces cerevisiae Mbp1. Restricted the search to the refseq_protein database and an Entrez query limit of fungi (taxid: 4751).
  2. Iterated the search two or three times, taking care to manually exclude uncertain sequences (i.e. an E value > 10e-04). The objective here is not be as inclusive as possible but to prevent inclusion of false positives. The resulting list contains examples from all fungal species.
  3. Followed the link to [Taxonomy reports] in the header of the BLAST results page. This contains a list of all hits, sorted by species. We can see the number of hits, but not whether the hits came from a genome sequence or have been contributed ad hoc as individual sequences. In the latter case, not all of the species' APSES domain proteins might be included in the RefSeq database.
  4. To confirm the sequencing status, navigated to the table of organims available for genomic BLAST. Clicked on the link to the eukaryotic genomes tree. For each species name in the taxonomy report, confirm that the species' genome sequence is available, has been annotated, and the protein sequences have been included in RefSeq (in that table, species for which this is true are marked with a red P).
  5. For didactic reasons, I have included only species with at least three hits in the BLAST results.


Name Species Code
Christine Achampong Ajellomyces dermatitidisAJEDE
Rose Marie Badarre Arthroderma gypseumARTGY
Albi Celaj Ashbya gossypiiASHGO
Amanda Chan Aspergillus clavatusASPCL
Carly Ching Aspergillus flavusASPFL
Claire Choe Botryotinia fuckelianaBOTFU
Inna Dimenshtein Candida glabrataCANGL
Yue Dong Chaetomium globosumCHAGL
Conner Emdin Clavispora lusitaniaeCLALU
William Grecia Coccidioides immitisCOCIM
Martin He Coprinopsis cinereaCOPCI
Jason Hendry Debaryomyces hanseniiDEBHA
Duncan Holbrook-Smith Gibberella zeaeGIBZE
Yuan Ji Kluyveromyces lactisKLULA
Uzma Khan Komagataella pastorisKOMPA
Ana Konvalinka Laccaria bicolorLACBI
Priya Krithivasan Lachancea thermotoleransLACTH
Hojun Lee Lodderomyces elongisporusLODEL
Hao Li Magnaporthe oryzaeMAGOR
Kumararaaj Manoharan Malassezia globosaMALGL
Nick Moss Meyerozyma guilliermondiiMEYGU
Ahmed Muneer Nectria haematococcaNECHA
Alexander Munteanu Neosartorya fischeriNEOFI
Rihan Nathoo Paracoccidioides brasiliensisPARBR
Nirvana Nursimulu Penicillium chrysogenumPENCH
Shabaz Patel Puccinia graminisPUCGR
Diana Resetca Pyrenophora teresPYRTE
Alex Sadowski Scheffersomyces stipitisSCHST
Gavneet Sandhu Schizophyllum communeSCHCO
Ravneet Sandhu Phaeospheria nodorumPHANO
Alexander Sharov Schizosaccharomyces japonicusSCHJA
Joseph Sinopoli Sclerotinia sclerotiorumSCLSC
Pietro Sollazzo Talaromyces stipitatusTALST
Amit Srivastava Trichophyton rubrumTRIRU
Amandeep Virk Uncinocarpus reesiiUNCRE
Eniana Vrenozaj Vanderwaltozyma polysporaVANPO
Dechen Wangmo Verticillium albo-atrumVERAL
Linna Wei Yarrowia lipolyticaYARLI
Yanyan Wu Zygosaccharomyces rouxiiZYGRO
 
 
(Reference) Aspergillus nidulansASPNI
(Reference) Candida albicansCANAL
(Reference)Neurospora crassaNEUCR
(Reference)Saccharomyces cerevisiaeSACCE
(Reference)Schizosaccharomyces pombeSCHPO
(Reference)Ustilago maydisUSTMA
Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=Species_list&oldid=6188"