Journal Article

Effect of sequence depth and length in long-read assembly of the maize inbred NC358

Liu, Jianing, Snodgrass, Samantha J., Koren, Sergey, Ou, Shujun, Seetharam, Arun S., Fengler, Kevin, Manchanda, Nancy, Chin, Chen-Shan, Hufnagel, David E., Phillippy, Adam M., Ware, Doreen, Fungtammasan, Arkarachai, Hannigan, Brett T., Pedersen, Sarah, Dawe, R. Kelly, Gilbert, Amanda M., Chougule, Kapeel M., Woodhouse, Margaret, Hufford, Matthew B., Walenz, Brian P., Hirsch, Candice N., Stein, Joshua C., Llaca, Victor, Wei, Sharon

2020

Overview

Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11–21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature. Sequence depth and read length determine the quality of genome assembly. Here, the authors leverage a set of PacBio reads to develop guidelines for sequencing and assembly of complex plant genomes in order to allocate finite resources using maize as an example.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 38 / 38/90 / 38/91 / 45 / 45/23 / 631/208/212/2302 / 631/208/8 / 631/449/447/8 / Assemblies / Assembly / Base Sequence / Centromeres / Corn / DNA Transposable Elements - genetics / Gene mapping / genome / Genome, Plant / Genomes / genomics / High-Throughput Nucleotide Sequencing - methods / Humanities and Social Sciences / inbred lines / Inbreeding / Knobs / microarray technology / multidisciplinary / Nucleotide sequence / open reading frames / Repetitive Sequences, Nucleic Acid - genetics / Resource allocation / Scaffolding / Science / Science (multidisciplinary) / tandem repeat sequences / Telomeres / transposons / Zea mays / Zea mays - genetics