Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Robert M Waterhouse,Sèverine Bérard,Maria V Sharakhova,Jiyoung Lee,Daniel Lawson,Adam M Phillippy,Sergey Koren,Maryam Kamali,Matthew W Hahn,Ashley Peery,Yoann Anselmetti,Simo V Zhang,Igor V Sharakhov,Max A Alekseyev,Nora J Besansky,Phillip George,Maarten J.m.f Reijnders ,Éric Tannier ,Paul Howell ,G Maslen ,Romain Féron ,Scott M Emrich ,Maria Unger ,Cédric Chauve ,Livio Ruzzante,Sergey Aganezov

doi:10.1186/s12915-019-0728-3

Abstract

BackgroundNew sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies.ResultsWe evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi.ConclusionsExperimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.

Highlights

New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’
Extensive contiguity and chromosome-level anchoring are clearly important when addressing questions concerning karyotype evolution or smaller-scale inversions and translocations, re-sequencing analyses of population-level samples, reconstructing rearrangement-based phylogenies, identifying and characterising genes that localise within quantitative trait loci (QTL), examining genomic sexual conflicts, or tracing drivers of speciation
Integrating results from 3 gene synteny-based computational approaches to build superscaffolds from all scaffold neighbours and reconciling these with the experimental datasets resulted in 20 new assemblies with variable levels of improved contiguities (Table 1), as well as chromosome mapping spanning 88% of the Anopheles arabiensis assembly, and updated chromosome maps for 6 other anophelines (Table 2)

Summary

Introduction

New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Extensive contiguity and chromosome-level anchoring are clearly important when addressing questions concerning karyotype evolution or smaller-scale inversions and translocations, re-sequencing analyses of population-level samples, reconstructing rearrangement-based phylogenies, identifying and characterising genes that localise within quantitative trait loci (QTL), examining genomic sexual conflicts, or tracing drivers of speciation In many such studies, assembly improvements were critical to enable more robust analyses, e.g. QTL analysis with rape mustard floweringtime phenotypes [11], contrasting genomic patterns of diversity between barley cultivars [12], defining rearrangements of the typical avian karyotype [13], detecting chromosome fusion events during butterfly evolution [14], characterising the ancestral lepidopteran karyotype [15], identifying the chromosomal position and structure of the male determining locus in Ae. aegypti [10], and characterising a melon fly genetic sexing strain as well as localising the sexing trait [16]

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Conclusion