A 2-approximation algorithm for the contig-based genomic scaffold filling problem

The genomic scaffold filling problem has attracted a lot of attention recently. The problem is on filling an incomplete sequence (scaffold) [Formula: see text] into [Formula: see text], with respect to a complete reference genome [Formula: see text], such that the number of common/shared adjacencies between [Formula: see text] and [Formula: see text] is maximized. The problem is NP-complete, and admits a constant-factor approximation. However, the sequence input [Formula: see text] is not quite practical and does not fit most of the real datasets (where a scaffold is more often given as a list of contigs). In this paper, we revisit the genomic scaffold filling problem by considering this important case when a scaffold [Formula: see text] is given, the missing genes can only be inserted in between the contigs, and the objective is to maximize the number of common adjacencies between [Formula: see text] and the filled genome [Formula: see text]. For this problem, we present a simple NP-completeness proof, we then present a factor-2 approximation algorithm.

Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population

Brassica rapa is a model species for agronomic, ecological, evolutionary, and translational studies. Here, we describe high-density SNP discovery and genetic map construction for a B. rapa recombinant inbred line (RIL) population derived from field collected RNA sequencing (RNA-Seq) data. This high-density genotype data enables the detection and correction of putative genome misassemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1–8.0% of the annotated B. rapa genome. We demonstrate how using this new resource leads to a significant improvement for QTL analysis over the current low-density genetic map. Improvements are achieved by the increased mapping resolution and by having known genomic coordinates to anchor the markers for candidate gene discovery. These new molecular resources and improvements in the genome annotation will benefit the Brassicaceae genomics community and may help guide other communities in fine-tuning genome annotations.

Using RNA-seq for genomic scaffold placement, correcting assemblies, and genetic map creation in a common Brassica rapa mapping population

Brassica rapa is a model species for agronomic, ecological, evolutionary and translational studies. Here we describe high-density SNP discovery and genetic map construction for a Brassica rapa recombinant inbred line (RIL) population derived from field collected RNA-seq data. This high-density genotype data enables the detection and correction of putative genome mis-assemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1-8.0% of the annotated Brassica rapa genome. We demonstrate how using this new resource leads to a significant improvement for QTL analysis over the current low-density genetic map. Improvements are achieved by the increased mapping resolution and by having known genomic coordinates to anchor the markers for candidate gene discovery. These new molecular resources and improvements in the genome annotation will benefit the Brassicaceae genomics community and may help guide other communities in finetuning genome annotations.

Efficient Recovery of Centric Heterochromatin P-Element Insertions in Drosophila melanogaster

Approximately one-third of the human and Drosophila melanogaster genomes are heterochromatic, yet we know very little about the structure and function of this enigmatic component of eukaryotic genomes. To facilitate molecular and cytological analysis of heterochromatin we introduced a yellow+ (y+)-marked P element into centric heterochromatin by screening for variegated phenotypes, that is, mosaic gene inactivation. We recovered >110 P insertions with variegated yellow expression from ∼3500 total mobilization events. FISH analysis of 71 of these insertions showed that 69 (97%) were in the centric heterochromatin, rather than telomeres or euchromatin. High-resolution banding analysis showed a wide but nonuniform distribution of insertions within centric heterochromatin; variegated insertions were predominantly recovered near regions of satellite DNA. We successfully used inverse PCR to clone and sequence the flanking DNA for ∼63% of the insertions. BLAST analysis of the flanks demonstrated that either most of the variegated insertions could not be placed on the genomic scaffold, and thus may be inserted within novel DNA sequence, or that the flanking DNA hit multiple sites on the scaffold, due to insertions within different transposons. Taken together these data suggest that screening for yellow variegation is a very efficient method for recovering centric insertions and that a large-scale screen for variegated yellow P insertions will provide important tools for detailed analysis of centric heterochromatin structure and function.