title: Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology.
abstract: The rat kangaroo (long-nosed potoroo, Potorous tridactylus) is a marsupial native to Australia. Cultured rat kangaroo kidney epithelial cells (PtK) are commonly used to study cell biological processes. These mammalian cells are large, adherent, and flat, and contain large and few chromosomes-and are thus ideal for imaging intra-cellular dynamics such as those of mitosis. Despite this, neither the rat kangaroo genome nor transcriptome have been sequenced, creating a challenge for probing the molecular basis of these cellular dynamics. Here, we present the sequencing, assembly and annotation of the draft rat kangaroo de novo transcriptome. We sequenced 679 million reads that mapped to 347,323 Trinity transcripts and 20,079 Unigenes. We present statistics emerging from transcriptome-wide analyses, and analyses suggesting that the transcriptome covers full-length sequences of most genes, many with multiple isoforms. We also validate our findings with a proof-of-concept gene knockdown experiment. We expect that this high quality transcriptome will make rat kangaroo cells a more tractable system for linking molecular-scale function and cellular-scale dynamics.
authors.affiliation: Department of Cell & Tissue Biology, University of California San Francisco, San Francisco, CA, United States of America.
authors.forename: Dylan B
authors.initials: DB
authors.lastname: Udy
authors.affiliation: Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, United States of America.
authors.forename: Mark
authors.initials: M
authors.lastname: Voorhies
authors.affiliation: Maverix Biomics, Inc., San Mateo, CA, United States of America; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America.
authors.forename: Patricia P
authors.initials: PP
authors.lastname: Chan
authors.affiliation: Maverix Biomics, Inc., San Mateo, CA, United States of America; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America.
authors.forename: Todd M
authors.initials: TM
authors.lastname: Lowe
authors.affiliation: Department of Cell & Tissue Biology, University of California San Francisco, San Francisco, CA, United States of America; Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA, United States of America.
authors.forename: Sophie
authors.initials: S
authors.lastname: Dumont
mesh_terms: D000818:Animals; D003585:Cell Biology; D002455:Cell Division / Q000235:genetics; D002460:Cell Line; D033181:Information Dissemination; D058977:Molecular Sequence Annotation; D048328:Potoroidae / Q000235:genetics*; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics*
chemical_list: D020033:Protein Isoforms; D012333:RNA, Messenger