Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology

PLoS One

Todd M. Lowe¹  Dylan B. Udy²  Mark Voorhies³  Patricia P. Chan⁴  Sophie Dumont⁴ 

[1] Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America;Department of Cell & Tissue Biology, University of California San Francisco, San Francisco, CA, United States of America;Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, United States of America;Maverix Biomics, Inc., San Mateo, CA, United States of America

关键词: Transcriptome analysis;    Small interfering RNAs;    Sequence alignment;    Sequence assembly tools;    Cytokinesis;    Sequence similarity searching;    Nucleotide sequencing;    Protein domains;   

DOI  :  10.1371/journal.pone.0134738

学科分类：医学（综合）

来源: Public Library of Science

【 摘 要 】

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.

【 授权许可】

CC BY