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Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-1-4939-8775-7_13openalex-snapshot

Physical Genome Mapping Using Fluorescence In Situ Hybridization with Mosquito Chromosomes

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Long Range Sequencing and Validation of Insect Genome Assemblies

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A new method for fluorescence microscopical localization of specific DNA sequences by in situ hybridization of fluorochrome-labelled RNA

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Scaffold assembly based on genome rearrangement analysis

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Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy

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RGAAT: A Reference-Based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes

inferredcites →https://doi.org/10.1016/j.ibmb.2016.07.005openalex-snapshot

Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta

inferredcites →https://doi.org/10.1016/j.pt.2018.10.003openalex-snapshot

Of Genes and Genomes: Mosquito Evolution and Diversity

inferredcites →https://doi.org/10.1038/hdy.2015.39openalex-snapshot

Genome-wide QTL mapping of saltwater tolerance in sibling species of Anopheles (malaria vector) mosquitoes

inferredcites →https://doi.org/10.1038/nature22043openalex-snapshot

A chromosome conformation capture ordered sequence of the barley genome

inferredcites →https://doi.org/10.1038/nbt.2727openalex-snapshot

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

inferredcites →https://doi.org/10.1038/nbt.2768openalex-snapshot

High-throughput genome scaffolding from in vivo DNA interaction frequency

inferredcites →https://doi.org/10.1038/ncomms5105openalex-snapshot

Mesoporous silicon sponge as an anti-pulverization structure for high-performance lithium-ion battery anodes

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Improved reference genome of Aedes aegypti informs arbovirus vector control

inferredcites →https://doi.org/10.1073/pnas.1220349110openalex-snapshot

Reference-assisted chromosome assembly

inferredcites →https://doi.org/10.1093/gbe/evv115openalex-snapshot

Complete Dosage Compensation inAnopheles stephensiand the Evolution of Sex-Biased Genes in Mosquitoes

inferredcites →https://doi.org/10.1093/gbe/evy108openalex-snapshot

The Effect of Hybridization on Dosage Compensation in Member Species of the Anopheles gambiae Species Complex

inferredcites →https://doi.org/10.1093/jhered/esh011openalex-snapshot

A Microsatellite Map of the African Human Malaria Vector Anopheles funestus

inferredcites →https://doi.org/10.1093/jhered/esx058openalex-snapshot

Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly

inferredcites →https://doi.org/10.1093/molbev/mss010openalex-snapshot

Sex Chromosomes Evolved from Independent Ancestral Linkage Groups in Winged Insects

inferredcites →https://doi.org/10.1093/nar/gkt484openalex-snapshot

The Genome of Anopheles darlingi , the main neotropical malaria vector

inferredcites →https://doi.org/10.1093/nar/gku1117openalex-snapshot

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

inferredcites →https://doi.org/10.1093/nar/gkw1119openalex-snapshot

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

inferredcites →https://doi.org/10.1101/267393openalex-snapshot

GENOME REPORT: High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing

inferredcites →https://doi.org/10.1101/gr.193474.115openalex-snapshot

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

inferredcites →https://doi.org/10.1101/gr.213652.116openalex-snapshot

Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data

inferredcites →https://doi.org/10.1101/gr.213660.116openalex-snapshot

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

inferredcites →https://doi.org/10.1101/gr.217216.116openalex-snapshot

Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes

inferredcites →https://doi.org/10.1101/gr.236273.118openalex-snapshot

Chromosome assembly of large and complex genomes using multiple references

inferredcites →https://doi.org/10.1111/j.1365-2583.2008.00772.xopenalex-snapshot

The Aedes aegypti genome: a comparative perspective

inferredcites →https://doi.org/10.1111/mec.14335openalex-snapshot

Chromosome arm‐specific patterns of polymorphism associated with chromosomal inversions in the major African malaria vector, Anopheles funestus

inferredcites →https://doi.org/10.1111/mve.12113openalex-snapshot

A standard photomap of ovarian nurse cell chromosomes in the E uropean malaria vector A nopheles atroparvus

inferredcites →https://doi.org/10.1126/science.1076181openalex-snapshot

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

inferredcites →https://doi.org/10.1126/science.1076803openalex-snapshot

Inversions and Gene Order Shuffling in Anopheles gambiae and A. funestus

inferredcites →https://doi.org/10.1126/science.1195755openalex-snapshot

Widespread Divergence Between Incipient Anopheles gambiae Species Revealed by Whole Genome Sequences

inferredcites →https://doi.org/10.1126/science.1258522openalex-snapshot

Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

inferredcites →https://doi.org/10.1126/science.1258524openalex-snapshot

Extensive introgression in a malaria vector species complex revealed by phylogenomics

inferredcites →https://doi.org/10.1126/science.aal3327openalex-snapshot

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

inferredcites →https://doi.org/10.1186/1471-2148-11-337openalex-snapshot

A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits

inferredcites →https://doi.org/10.1186/1471-2164-15-349openalex-snapshot

A network-based approach to identify substrate classes of bacterial glycosyltransferases

inferredcites →https://doi.org/10.1186/1471-2164-15-42openalex-snapshot

Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites

inferredcites →https://doi.org/10.1186/gb-2007-8-1-r5openalex-snapshot

Update of the Anopheles gambiaePEST genome assembly

inferredcites →https://doi.org/10.1186/gb-2009-10-8-r88openalex-snapshot

Assisted assembly: how to improve a de novo genome assembly by using related species

inferredcites →https://doi.org/10.1186/s12859-017-1919-yopenalex-snapshot

CAMSA: a tool for comparative analysis and merging of scaffold assemblies

inferredcites →https://doi.org/10.1186/s12859-018-2026-4openalex-snapshot

Inferring synteny between genome assemblies: a systematic evaluation

inferredcites →https://doi.org/10.1186/s12864-018-4466-7openalex-snapshot

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes

inferredcites →https://doi.org/10.1186/s12864-018-4663-4openalex-snapshot

Partial-arm translocations in evolution of malaria mosquitoes revealed by high-coverage physical mapping of the Anopheles atroparvus genome

inferredcites →https://doi.org/10.1186/s12936-017-1888-7openalex-snapshot

Comparative physical genome mapping of malaria vectors Anopheles sinensis and Anopheles gambiae

inferredcites →https://doi.org/10.1186/s13059-014-0459-2openalex-snapshot

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi

inferredcites →https://doi.org/10.1186/s13742-016-0136-3openalex-snapshot

AGOUTI: improving genome assembly and annotation using transcriptome data

inferredcites →https://doi.org/10.1186/s13742-016-0141-6openalex-snapshot

Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences

inferredcites →https://doi.org/10.1242/dev.001065openalex-snapshot

The rise and fall of Hox gene clusters

inferredcites →https://doi.org/10.1371/journal.pbio.1002078openalex-snapshot

Numerous Transitions of Sex Chromosomes in Diptera

inferredcites →https://doi.org/10.1371/journal.pgen.1006303openalex-snapshot

The Genetic Basis of Host Preference and Resting Behavior in the Major African Malaria Vector, Anopheles arabiensis

inferredcites →https://doi.org/10.1371/journal.pone.0010592openalex-snapshot

Genome Landscape and Evolutionary Plasticity of Chromosomes in Malaria Mosquitoes

inferredcites →https://doi.org/10.1534/g3.111.001412openalex-snapshot

Evolution of a Large, Conserved, and Syntenic Gene Family in Insects

inferredcites →https://doi.org/10.1534/g3.113.006247openalex-snapshot

The Evolution of the Anopheles 16 Genomes Project

inferredcites →https://doi.org/10.1534/g3.114.010264openalex-snapshot

Sequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations

inferredcites →https://doi.org/10.1534/g3.115.023655openalex-snapshot

Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution

inferredcites →https://doi.org/10.1534/g3.116.034959openalex-snapshot

The Physical Genome Mapping ofAnopheles albimanusCorrected Scaffold Misassemblies and Identified Interarm Rearrangements in GenusAnopheles

inferredcites →https://doi.org/10.1534/g3.117.040170openalex-snapshot

A Chromosome-Scale Assembly of theBactrocera cucurbitaeGenome Provides Insight to the Genetic Basis ofwhite pupae

inferredcites →https://doi.org/10.1534/g3.117.043000openalex-snapshot

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

inferredcites →https://doi.org/10.1603/0022-2585(2006)43[861:ascpft]2.0.co;2openalex-snapshot

A Standard Cytogenetic Photomap for the Mosquito Anopheles stephensi (Diptera: Culicidae): Application for Physical Mapping

inferredcites →https://doi.org/10.3389/fgene.2015.00220openalex-snapshot

Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

inferredcites →https://doi.org/10.3390/genes10010062openalex-snapshot

A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing

inferredcites →https://doi.org/10.3390/insects9030121openalex-snapshot

The Development of Cytogenetic Maps for Malaria Mosquitoes

inferredcites →https://doi.org/10.4269/ajtmh.2010.10-0366openalex-snapshot

A Physical Map for an Asian Malaria Mosquito, Anopheles stephensi

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.pt.2018.10.003openalex-snapshot

Of Genes and Genomes: Mosquito Evolution and Diversity

inferred← citeshttps://doi.org/10.1093/gigascience/giz063openalex-snapshot

A chromosome-scale assembly of the major African malaria vector Anopheles funestus

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