Species list

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 dermatitidis	AJEDE
Rose Marie Badarre	Arthroderma gypseum	ARTGY
Albi Celaj	Ashbya gossypii	ASHGO
Amanda Chan	Aspergillus clavatus	ASPCL
Carly Ching	Aspergillus flavus	ASPFL
Claire Choe	Botryotinia fuckeliana	BOTFU
Inna Dimenshtein	Candida glabrata	CANGL
Yue Dong	Chaetomium globosum	CHAGL
Conner Emdin	Clavispora lusitaniae	CLALU
William Grecia	Coccidioides immitis	COCIM
Martin He	Coprinopsis cinerea	COPCI
Jason Hendry	Debaryomyces hansenii	DEBHA
Duncan Holbrook-Smith	Gibberella zeae	GIBZE
Yuan Ji	Kluyveromyces lactis	KLULA
Uzma Khan	Komagataella pastoris	KOMPA
Ana Konvalinka	Laccaria bicolor	LACBI
Priya Krithivasan	Lachancea thermotolerans	LACTH
Hojun Lee	Lodderomyces elongisporus	LODEL
Hao Li	Magnaporthe oryzae	MAGOR
Kumararaaj Manoharan	Malassezia globosa	MALGL
Nick Moss	Meyerozyma guilliermondii	MEYGU
Ahmed Muneer	Nectria haematococca	NECHA
Alexander Munteanu	Neosartorya fischeri	NEOFI
Rihan Nathoo	Paracoccidioides brasiliensis	PARBR
Nirvana Nursimulu	Penicillium chrysogenum	PENCH
Shabaz Patel	Puccinia graminis	PUCGR
Diana Resetca	Pyrenophora teres	PYRTE
Alex Sadowski	Scheffersomyces stipitis	SCHST
Gavneet Sandhu	Schizophyllum commune	SCHCO
Ravneet Sandhu	Phaeospheria nodorum	PHANO
Alexander Sharov	Schizosaccharomyces japonicus	SCHJA
Joseph Sinopoli	Sclerotinia sclerotiorum	SCLSC
Pietro Sollazzo	Talaromyces stipitatus	TALST
Amit Srivastava	Trichophyton rubrum	TRIRU
Amandeep Virk	Uncinocarpus reesii	UNCRE
Eniana Vrenozaj	Vanderwaltozyma polyspora	VANPO
Dechen Wangmo	Verticillium albo-atrum	VERAL
Linna Wei	Yarrowia lipolytica	YARLI
Yanyan Wu	Zygosaccharomyces rouxii	ZYGRO
(Reference)	Aspergillus nidulans	ASPNI
(Reference)	Candida albicans	CANAL
(Reference)	Neurospora crassa	NEUCR
(Reference)	Saccharomyces cerevisiae	SACCE
(Reference)	Schizosaccharomyces pombe	SCHPO
(Reference)	Ustilago maydis	USTMA