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

Species	Nucleus	Citation
Oxytricha trifallax	Macronucleus	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	Micronucleus	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.
Tetrahymena thermophila	Macronucleus	Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK Jr, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. (2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biology Sep;4(9):e286
Tetrahymena thermophila	Micronucleus	Tetrahymena Comparative Sequencing Project, Broad Institute of Harvard and MIT (http://www.broadinstitute.org/)
Oxytricha trifallax	Macronucleus	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.

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