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.

Species-level IDs for reference organisms:

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:

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).
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.
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.
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).
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`

Species list

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The BCH441 Students & Species List (Fall 2011)

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