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

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  • Additional Information
    • Source:
      Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
    • Publication Information:
      Original Publication: London : BioMed Central, [2000-
    • Subject Terms:
    • Abstract:
      Background: Whole-genome shotgun sequencing, which stitches together millions of short sequencing reads into a single genome, ushered in the era of modern genomics and led to a rapid expansion of the number of genome sequences available. Nevertheless, assembly of short reads remains difficult, resulting in fragmented genome sequences. Ultimately, only a sequencing technology capable of capturing complete chromosomes in a single run could resolve all ambiguities. Even "third generation" sequencing technologies produce reads far shorter than most eukaryotic chromosomes. However, the ciliate Oxytricha trifallax has a somatic genome with thousands of chromosomes averaging only 3.2 kbp, making it an ideal candidate for exploring the benefits of sequencing whole chromosomes without assembly.
      Results: We used single-molecule real-time sequencing to capture thousands of complete chromosomes in single reads and to update the published Oxytricha trifallax JRB310 genome assembly. In this version, over 50% of the completed chromosomes with two telomeres derive from single reads. The improved assembly includes over 12,000 new chromosome isoforms, and demonstrates that somatic chromosomes derive from variable rearrangements between somatic segments encoded up to 191,000 base pairs away. However, while long reads reduce the need for assembly, a hybrid approach that supplements long-read sequencing with short reads for error correction produced the most complete and accurate assembly, overall.
      Conclusions: This assembly provides the first example of complete eukaryotic chromosomes captured by single sequencing reads and demonstrates that traditional approaches to genome assembly can mask considerable structural variation.
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    • Grant Information:
      R35 GM122555 United States GM NIGMS NIH HHS; 122555 United States GM NIGMS NIH HHS; R01 GM059708 United States GM NIGMS NIH HHS; R01 GM109459 United States GM NIGMS NIH HHS; 109459 United States GM NIGMS NIH HHS; 1F32GM099462 United States NH NIH HHS; 59708 United States GM NIGMS NIH HHS; T32 HG003284 United States HG NHGRI NIH HHS
    • Contributed Indexing:
      Keywords: Alternative fragmentation; Ciliate; Genome assembly; Oxytricha; PacBio; SMRT sequencing
    • Publication Date:
      Date Created: 20200101 Date Completed: 20200507 Latest Revision: 20200514
    • Publication Date:
      20211214
    • Accession Number:
      PMC6937825
    • Accession Number:
      10.1186/s12864-019-6189-9
    • Accession Number:
      31888453