Oxytricha trifallax JRB310

Tetmemena sp. SeJ-2015

Euplotes woodruffi Iz01

Citing the <mds_ies_db>

Burns J, Kukushkin D, Lindblad K, Chen X, Jonoska N, Landweber LF (2016) <mds_ies_db>: a database of ciliate genome rearrangements. Nucleic Acids Res. 44 (Database issue) doi: gkv1190

Genome Assemblies

Species (nucleus) Citation
Euplotes woodruffi (MAC 2022/MIC 2022),
Tetmemena sp. (MIC 2022)
Yi Feng, Rafik Neme, Leslie Y Beh, Xiao Chen, Jasper Braun, Michael W Lu, Laura F Landweber (2022). Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes. eLife 11:e82979.
Tetmemena sp. (MAC 2015) Chen X, Jung S, Beh LY, Eddy SR, Landweber LF (2015). Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates. Genome Biol Evol. 7(10):2859–70.
Oxytricha trifallax (MAC 2013) Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, Khurana JS, Goldman AD, Nowacki M, Schotanus K, Jung S, Fulton RS, Ly A, McGrath S, Haub K, Wiggins JL, Storton D, Matese JC, Parsons L, Chang W, Bowen MS, Stover NA, Jones TA, Eddy SR, Herrick GA, Doak TG, Wilson RK, Mardis ER, Landweber LF (2013). The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biology 11 (1): e1001473.
Oxytricha trifallax (MIC 2014) Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, Perlman DH, Doak TG, Stuart A, Amemiya CT, Sebra RP, Landweber LF (2014). The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development. Cell 158 (5): 1187–98.
Oxytricha trifallax (MAC 2019) Kelsi A. Lindblad, Jananan S. Pathmanathan, Sandrine Moreira, John R. Bracht, Robert P. Sebra, Elizabeth R. Hutton & Laura F. Landweber (2019). Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms. BMC Genomics 20, 1037.

Software

Name Citation
SDRAP Jasper Braun, Rafik Neme, Yi Feng, Laura F. Landweber, NataĊĦa Jonoska (2021). SDRAP for Annotating Scrambled or Rearranged Genomes. In review.