Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms

December 2019


Kelsi A. Lindblad, Jananan S. Pathmanathan, Sandrine Moreira, John R. Bracht, Robert P. Sebra, Elizabeth R. Hutton & Laura F. Landweber

Researchers sequenced the whole genome of Oxytricha trifallax, a model protozoan ciliate, using long read sequencing. Since Oxytricha trifallax has 16,000 chromosomes that only average 3.2 kpb in length, its much of the genome was sequenced with chromosomal-length single reads without assembly. By comparing the results to the reference sequence assemblies the researchers demonstrated that short read sequencing can mask considerable structural variation.
BluePippin was used to size-select PacBio SMRT libraries.

Author Affiliations:
Columbia University, New York, NY
Princeton University, Princeton, NJ
American University, Washington DC
Icahn School o f Medicine at Mt Sinai, New York, NY
Cold Spring Harbor Laboratories, Cold Spring Harbor, NY

BMC Genomics
DOI: 10.1186/s12864-019-6189-9

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