title: Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the "Finished" C. elegans Genome.
abstract: Most next-generation sequencing platforms permit acquisition of high-throughput DNA sequences, but the relatively short read length limits their use in genome assembly or finishing. Illumina has recently released a technology called Synthetic Long-Read Sequencing that can produce reads of unusual length, i.e., predominately around 10 Kb. However, a systematic assessment of their use in genome finishing and assembly is still lacking. We evaluate the promise and deficiency of the long reads in these aspects using isogenic C. elegans genome with no gap. First, the reads are highly accurate and capable of recovering most types of repetitive sequences. However, the presence of tandem repetitive sequences prevents pre-assembly of long reads in the relevant genomic region. Second, the reads are able to reliably detect missing but not extra sequences in the C. elegans genome. Third, the reads of smaller size are more capable of recovering repetitive sequences than those of bigger size. Fourth, at least 40 Kbp missing genomic sequences are recovered in the C. elegans genome using the long reads. Finally, an N50 contig size of at least 86 Kbp can be achieved with 24 × reads but with substantial mis-assembly errors, highlighting a need for novel assembly algorithm for the long reads.
authors.affiliation: Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong, China.
authors.forename: Runsheng
authors.initials: R
authors.lastname: Li
authors.affiliation: Illumina Inc., 5200 Illumina Way, San Diego, 92122, USA.
authors.forename: Chia-Ling
authors.initials: CL
authors.lastname: Hsieh
authors.affiliation: Illumina Inc., 5200 Illumina Way, San Diego, 92122, USA.
authors.forename: Amanda
authors.initials: A
authors.lastname: Young
authors.affiliation: Illumina Inc., 5200 Illumina Way, San Diego, 92122, USA.
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong, China.
authors.forename: Xiaoliang
authors.initials: X
authors.lastname: Ren
authors.affiliation: 1] Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong, China [2] State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.
authors.forename: Zhongying
authors.initials: Z
authors.lastname: Zhao
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D014644:Genetic Variation; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D008969:Molecular Sequence Data; D012091:Repetitive Sequences, Nucleic Acid; D015203:Reproducibility of Results