Long-read, whole-genome shotgun sequence data for five model organisms

Abstract

Single molecule, real-time (SMRT) sequencing from Pacific Biosciences is increasingly used in many areas of biological research including de novo genome assembly, structural-variant identification, haplotype phasing, mRNA isoform discovery, and base-modification analyses. High-quality, public datasets of SMRT sequences can spur development of analytic tools that can accommodate unique characteristics of SMRT data (long read lengths, lack of GC or amplification bias, and a random error profile leading to high consensus accuracy). In this paper, we describe eight high-coverage SMRT sequence datasets from five organisms (Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, Arabidopsis thaliana, and Drosophila melanogaster) that have been publicly released to the general scientific community (NCBI Sequence Read Archive ID SRP040522). Data were generated using two sequencing chemistries (P4C2 and P5C3) on the PacBio RS II instrument. The datasets reported here can be used without restriction by the research community to generate whole-genome assemblies, test new algorithms, investigate genome structure and evolution, and identify base modifications in some of the most widely-studied model systems in biological research.

Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation

“…However, repetitive regions such as centromeres, constitutive heterochromatin and associated repetitive elements remain challenging to sequence, assemble and characterize (Kim et al . ), hindering our understanding of their role in population divergence and speciation. Cytogenetic techniques specifically targeting these regions are complementary to next‐generation sequencing approaches.…”

“…Thanks to the advent of massive parallel sequencing technologies, considerable progress has been made in the past decade to decipher the genetic basis of adaptation and speciation (Seehausen et al 2014). However, repetitive regions such as centromeres, constitutive heterochromatin and associated repetitive elements remain challenging to sequence, assemble and characterize (Kim et al 2014), hindering our understanding of their role in population divergence and speciation. Cytogenetic techniques specifically targeting these regions are complementary to next-generation sequencing approaches.…”

A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System

“…Arthropod genome assembly projects face unique challenges stemming from their small body size and high heterozygosity. Due to the limited quantities of genomic DNA that can be extracted from a small-bodied animal, researchers may pool multiple individuals, such as by generating NGS libraries of different insert sizes, each from a different individual [10,13], or by pooling multiple individuals for a single long-read sequencing library from an iso-female laboratory strain [14][15][16][17][18] or colony [5,19]. Pooling introduces multiple haplotypes into the sample and complicates the assembly and curation process [19], and while this issue may be ameliorated by inbreeding it is not always an option for organisms that cannot be cultured in the laboratory.…”

Chromosome-level hybrid de novo genome assemblies as an attainable option for non-model organisms

“…DNA purity was verified using a NanoDrop One Microvolume UV Spectrophotometer 122 with ratios 260/280 and 260/230 over 1.8. Quantity (150 ng/µL in 180 µL = 27 µg) was determined 123 the D. melanogaster assembly (hereafter, Dmel), PacBio data was retrieved from the 136 NCBI Short-read Archive SRX499318(Kim et al, 2014). This data set contained 42 PacBio RS 137 II SMRT cells from male D. melanogaster ISO1 flies.…”