Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

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Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_223C09C9C506
Type
Article: article from journal or magazin.
Publication sub-type
Minutes: analyse of a published work.
Collection
Publications
Institution
Title
Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
Journal
BMC Biology
Author(s)
Waterhouse Robert M., Aganezov Sergey, Anselmetti Yoann, Lee Jiyoung, Ruzzante Livio, Reijnders Maarten J. M. F., Feron Romain, Bérard Sèverine, George Phillip, Hahn Matthew W., Howell Paul I., Kamali Maryam, Koren Sergey, Lawson Daniel, Maslen Gareth, Peery Ashley, Phillippy Adam M., Sharakhova Maria V., Tannier Eric, Unger Maria F., Zhang Simo V., Alekseyev Max A., Besansky Nora J., Chauve Cedric, Emrich Scott J., Sharakhov Igor V.
ISSN
1741-7007
Publication state
Published
Issued date
12/2020
Peer-reviewed
Oui
Volume
18
Number
1
Language
english
Abstract
Background
New 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.
Results
We 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.
Conclusions
Experimental 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.
Keywords
Biotechnology, Plant Science, General Biochemistry, Genetics and Molecular Biology, Developmental Biology, Cell Biology, Physiology, Ecology, Evolution, Behavior and Systematics, Structural Biology, General Agricultural and Biological Sciences
Pubmed
Open Access
Yes
Funding(s)
Swiss National Science Foundation / Careers / PP00P3_170664
Create date
03/01/2020 18:04
Last modification date
11/01/2020 7:16
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