Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

摘要

Genomic spans of scaffolds and superscaffolds with and without chromosome anchoring or arm assignments for 20 improved assemblies. Consensus gene synteny-based methods were employed across the 21-assembly input dataset (also including ) to delineate scaffold adjacencies and build new superscaffolded assemblies with improved contiguities. These were integrated with results from additional complementary approaches for subsets of the anophelines including transcriptome (RNAseq) and genome sequencing data, whole genome alignments, and chromosome anchoring data from physical mapping of probes. Chromosome mapping data for 7 assemblies enabled anchoring of superscaffolds and scaffolds to their chromosomal locations (purple colours). Enumerating shared orthologues further enabled the assignment of non-anchored superscaffolds and scaffolds to chromosome arms (blue colours). Unplaced superscaffolds and scaffolds (orange colours) still comprise the majority of the least contiguous input assemblies, but they make up only a small proportion of the assemblies for which the available data allowed for substantial improvements to assembly contiguity and/or anchoring and/or arm assignments. Results for two strains are shown for , SINENSIS and Chinese (C), and , SDA-500 and Indian (I)