T
Thomas J. Poorten
Researcher at University of California, Berkeley
Publications - 25
Citations - 1517
Thomas J. Poorten is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Chytridiomycosis & Genome. The author has an hindex of 16, co-authored 23 publications receiving 1167 citations. Previous affiliations of Thomas J. Poorten include University of Idaho & Wake Forest University.
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Journal ArticleDOI
Origin and evolution of the octoploid strawberry genome.
Patrick P. Edger,Thomas J. Poorten,Robert VanBuren,Michael A. Hardigan,Marivi Colle,Michael R. McKain,Ronald D. Smith,Scott J. Teresi,Andrew D. L. Nelson,Ching Man Wai,Elizabeth I. Alger,Kevin A. Bird,Alan E. Yocca,Nathan Pumplin,Shujun Ou,Gil Ben-Zvi,Avital Brodt,Kobi Baruch,Thomas Swale,Lily Shiue,Charlotte B. Acharya,Glenn S. Cole,Jeffrey P. Mower,Kevin L. Childs,Ning Jiang,Eric Lyons,Michael Freeling,Joshua R. Puzey,Steven J. Knapp +28 more
TL;DR: A near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) is reported and the origin and evolutionary processes that shaped this complex allopolyploid are uncovered, providing a useful resource for genome-wide analyses and molecular breeding.
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Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data
Erica Bree Rosenblum,Timothy Y. James,Kelly R. Zamudio,Thomas J. Poorten,Daniel C. Ilut,David Rodriguez,Jonathan M. Eastman,Katy Richards-Hrdlicka,Suzanne Joneson,Thomas S. Jenkinson,Joyce E. Longcore,Gabriela Parra Olea,LuÃs Felipe Toledo,Maria Luz Arellano,Edgar M. Medina,Silvia Restrepo,Sandra V. Flechas,Lee Berger,Cheryl J. Briggs,Jason E. Stajich +19 more
TL;DR: Evidence for selection acting on the Bd genome is reported, supporting the hypothesis that protease genes are important in evolutionary transitions in this group, and it is found that even the most recently evolved Bd clade contained more genetic variation than previously reported.
Journal ArticleDOI
Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity.
Patrick P. Edger,Robert VanBuren,Marivi Colle,Thomas J. Poorten,Ching Man Wai,Chad E. Niederhuth,Elizabeth I. Alger,Shujun Ou,Charlotte B. Acharya,Jie Wang,Pete Callow,Michael R. McKain,Jinghua Shi,Chad Collier,Zhiyong Xiong,Jeffrey P. Mower,Janet P. Slovin,Timo Hytönen,Ning Jiang,Kevin L. Childs,Steven J. Knapp +20 more
TL;DR: A near-complete genome of diploid woodland strawberry (Fragaria vesca) is reported using single-molecule real-time sequencing from Pacific Biosciences and how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions is demonstrated.
Journal ArticleDOI
Genome-Wide Transcriptional Response of Silurana (Xenopus) tropicalis to Infection with the Deadly Chytrid Fungus
Erica Bree Rosenblum,Erica Bree Rosenblum,Thomas J. Poorten,Matthew L. Settles,Gordon K. Murdoch,Jacques Robert,Nicole Maddox,Michael B. Eisen +7 more
TL;DR: This study uses whole-genome microarrays to monitor the transcriptional responses to Bd infection in the model frog species, Silurana (Xenopus) tropicalis, which is susceptible to chytridiomycosis, and detects a strong transcriptional response for genes involved in physiological processes that can help explain some clinical symptoms of chy TRD at the organismal level.
Journal ArticleDOI
Only skin deep: shared genetic response to the deadly chytrid fungus in susceptible frog species.
TL;DR: It is demonstrated that Bd-infected frogs show massive disruption of skin function and show no evidence of a robust immune response, suggesting a common effect of Bd on susceptible frogs.