Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

[1]  Robert M. Waterhouse,et al.  Of Genes and Genomes: Mosquito Evolution and Diversity. , 2019, Trends in parasitology.

[2]  M. Sharakhova,et al.  Physical Genome Mapping Using Fluorescence In Situ Hybridization with Mosquito Chromosomes. , 2018, Methods in molecular biology.

[3]  Felipe A. Simão,et al.  Using BUSCO to Assess Insect Genomic Resources. , 2018, Methods in molecular biology.

[4]  Surya Saha,et al.  Long Range Sequencing and Validation of Insect Genome Assemblies. , 2018, Methods in molecular biology.

[5]  Richard Durbin,et al.  A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing , 2018, bioRxiv.

[6]  S. Koren,et al.  A chromosome-scale assembly of the major African malaria vector Anopheles funestus , 2018, bioRxiv.

[7]  Sergey Koren,et al.  Improved reference genome of Aedes aegypti informs arbovirus vector control , 2018, Nature.

[8]  Jun Yu,et al.  RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes , 2018, Genom. Proteom. Bioinform..

[9]  M. Sharakhova,et al.  The Development of Cytogenetic Maps for Malaria Mosquitoes , 2018, Insects.

[10]  Dmitry Antipov,et al.  Versatile genome assembly evaluation with QUAST-LG , 2018, Bioinform..

[11]  Christophe Klopp,et al.  D-GENIES: dot plot large genomes in an interactive, efficient and simple way , 2018, PeerJ.

[12]  Willem Takken,et al.  The Effect of Hybridization on Dosage Compensation in Member Species of the Anopheles gambiae Species Complex , 2018, bioRxiv.

[13]  Cédric Chauve,et al.  Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes , 2018, BMC Genomics.

[14]  A. N. Naumenko,et al.  Partial-arm translocations in evolution of malaria mosquitoes revealed by high-coverage physical mapping of the Anopheles atroparvus genome , 2018, BMC Genomics.

[15]  R. Scott Hawley,et al.  GENOME REPORT: High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing , 2018, bioRxiv.

[16]  Sergey Koren,et al.  Integrating Hi-C links with assembly graphs for chromosome-scale assembly , 2018, bioRxiv.

[17]  Martin Hunt,et al.  Inferring synteny between genome assemblies: a systematic evaluation , 2017, BMC Bioinformatics.

[18]  Ivan Liachko,et al.  Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly , 2017, The Journal of heredity.

[19]  B. White,et al.  Chromosome arm‐specific patterns of polymorphism associated with chromosomal inversions in the major African malaria vector, Anopheles funestus , 2017, Molecular ecology.

[20]  Robert M. Waterhouse,et al.  BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics , 2017, bioRxiv.

[21]  Robert M. Waterhouse,et al.  Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes , 2016, bioRxiv.

[22]  Jing Wang,et al.  Comparative physical genome mapping of malaria vectors Anopheles sinensis and Anopheles gambiae , 2017, Malaria Journal.

[23]  Bernardo J. Clavijo,et al.  Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data. , 2017, Genome research.

[24]  Joana Damas,et al.  Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set , 2017, Genome research.

[25]  Cedric Chauve,et al.  DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies , 2017, Genome biology and evolution.

[26]  John K. McCooke,et al.  A chromosome conformation capture ordered sequence of the barley genome , 2017, Nature.

[27]  S. Sim,et al.  A Chromosome-Scale Assembly of the Bactrocera cucurbitae Genome Provides Insight to the Genetic Basis of white pupae , 2017, G3: Genes, Genomes, Genetics.

[28]  Neva C. Durand,et al.  De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds , 2016, Science.

[29]  Evgeny M. Zdobnov,et al.  OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs , 2016, Nucleic Acids Res..

[30]  Michael F. Covington,et al.  Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population , 2016, G3: Genes, Genomes, Genetics.

[31]  Son K. Pham,et al.  Chromosome assembly of large and complex genomes using multiple references , 2016, bioRxiv.

[32]  Xiaofang Jiang,et al.  The Physical Genome Mapping of Anopheles albimanus Corrected Scaffold Misassemblies and Identified Interarm Rearrangements in Genus Anopheles , 2016, G3: Genes, Genomes, Genetics.

[33]  J. Doe,et al.  Fast‐Track Introgression of “QTL‐hotspot” for Root Traits and Other Drought Tolerance Traits in JG 11, an Elite and Leading Variety of Chickpea , 2016, The plant genome.

[34]  L. Florea,et al.  Rascaf: Improving Genome Assembly with RNA Sequencing Data , 2016, The plant genome.

[35]  Max A. Alekseyev,et al.  CAMSA: a tool for comparative analysis and merging of scaffold assemblies , 2016, bioRxiv.

[36]  Yang Wang,et al.  Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. , 2016, Insect biochemistry and molecular biology.

[37]  Eleazar Eskin,et al.  The Genetic Basis of Host Preference and Resting Behavior in the Major African Malaria Vector, Anopheles arabiensis , 2016, PLoS genetics.

[38]  Gaik Tamazian,et al.  Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences , 2016, GigaScience.

[39]  Max A. Alekseyev,et al.  Multi-genome Scaffold Co-assembly Based on the Analysis of Gene Orders and Genomic Repeats , 2016, ISBRA.

[40]  Shuai Jiang,et al.  Reconstruction of ancestral genomes in presence of gene gain and loss , 2016, bioRxiv.

[41]  J. Mallet,et al.  Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution , 2015, G3: Genes, Genomes, Genetics.

[42]  Brendan L. O’Connell,et al.  Chromosome-scale shotgun assembly using an in vitro method for long-range linkage , 2015, Genome research.

[43]  Matthew W. Hahn,et al.  AGOUTI: improving genome assembly and annotation using transcriptome data , 2015, bioRxiv.

[44]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[45]  E. Baricheva,et al.  A standard photomap of ovarian nurse cell chromosomes in the European malaria vector Anopheles atroparvus , 2015, Medical and veterinary entomology.

[46]  Max A. Alekseyev,et al.  Scaffold assembly based on genome rearrangement analysis , 2015, Comput. Biol. Chem..

[47]  Annie Chateau,et al.  Ancestral gene synteny reconstruction improves extant species scaffolding , 2015, bioRxiv.

[48]  Janna L. Fierst,et al.  Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools , 2015, Front. Genet..

[49]  Xiaofang Jiang,et al.  Complete Dosage Compensation in Anopheles stephensi and the Evolution of Sex-Biased Genes in Mosquitoes , 2015, Genome biology and evolution.

[50]  H. A. Smith,et al.  Genome-wide QTL mapping of saltwater tolerance in sibling species of Anopheles (malaria vector) mosquitoes , 2015, Heredity.

[51]  D. Bachtrog,et al.  Numerous Transitions of Sex Chromosomes in Diptera , 2015, PLoS biology.

[52]  Michael C. Schatz,et al.  Metassembler: merging and optimizing de novo genome assemblies , 2015, bioRxiv.

[53]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[54]  Xiaofang Jiang,et al.  Extensive introgression in a malaria vector species complex revealed by phylogenomics , 2015, Science.

[55]  Sandra Gesing,et al.  VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases , 2014, Nucleic Acids Res..

[56]  James E. Allen,et al.  Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes , 2014, Science.

[57]  Tun-Wen Pai,et al.  Identification of conserved and polymorphic STRs for personal genomes , 2014, BMC Genomics.

[58]  I. Sharakhov Protocols for Cytogenetic Mapping of Arthropod Genomes , 2014 .

[59]  Xiaofang Jiang,et al.  Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi , 2014, Genome Biology.

[60]  Stephen J. Benkovic,et al.  Corrigendum: RecG and UvsW catalyse robust DNA rewinding critical for stalled DNA replication fork rescue , 2014, Nature Communications.

[61]  Liisa Holm,et al.  The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera , 2014, Nature Communications.

[62]  Lars Arvestad,et al.  BESST - Efficient scaffolding of large fragmented assemblies , 2014, BMC Bioinformatics.

[63]  Peter Rodgers,et al.  eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses , 2014, PloS one.

[64]  Michael J Sailor,et al.  Mesoporous silicon sponge as an anti-pulverization structure for high-performance lithium-ion battery anodes , 2014, Nature Communications.

[65]  S. Salzberg,et al.  Sequencing and Assembly of the 22-Gb Loblolly Pine Genome , 2014, Genetics.

[66]  Matthew W. Hahn,et al.  Sequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations , 2014, G3: Genes, Genomes, Genetics.

[67]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[68]  Yahya Al-Hazmi,et al.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) , 2014, ICPP 2014.

[69]  Kathleen Marchal,et al.  A network-based approach to identify substrate classes of bacterial glycosyltransferases , 2014, BMC Genomics.

[70]  Dan Graur,et al.  Finding the missing honey bee genes: lessons learned from a genome upgrade , 2014, BMC Genomics.

[71]  Lei Ma,et al.  Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites , 2014, BMC Genomics.

[72]  Andrew C. Adey,et al.  Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions , 2013, Nature Biotechnology.

[73]  Noam Kaplan,et al.  High-throughput genome scaffolding from in-vivo DNA interaction frequency , 2013, Nature Biotechnology.

[74]  Michal Levy-Sakin,et al.  Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy. , 2013, Current opinion in biotechnology.

[75]  Scott J. Emrich,et al.  The Evolution of the Anopheles 16 Genomes Project , 2013, G3: Genes, Genomes, Genetics.

[76]  Francisco Prosdocimi,et al.  The Genome of Anopheles darlingi, the main neotropical malaria vector , 2013, Nucleic acids research.

[77]  Douglas G. Scofield,et al.  The Norway spruce genome sequence and conifer genome evolution , 2013, Nature.

[78]  Loretta Auvil,et al.  Reference-assisted chromosome assembly , 2013, Proceedings of the National Academy of Sciences.

[79]  Sven Rahmann,et al.  Snakemake--a scalable bioinformatics workflow engine. , 2012, Bioinformatics.

[80]  Gergely J. Szöllosi,et al.  Evolution of gene neighborhoods within reconciled phylogenies , 2012, Bioinform..

[81]  Jian Ye,et al.  Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction , 2012, BMC Bioinformatics.

[82]  Etsuko N. Moriyama,et al.  Evolution of a Large, Conserved, and Syntenic Gene Family in Insects , 2012, G3: Genes | Genomes | Genetics.

[83]  Matthew W Hahn,et al.  Sex chromosomes evolved from independent ancestral linkage groups in winged insects. , 2012, Molecular biology and evolution.

[84]  Evgeny M Zdobnov,et al.  A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits , 2011, BMC Evolutionary Biology.

[85]  Walter Pirovano,et al.  BIOINFORMATICS APPLICATIONS , 2022 .

[86]  Ali Mortazavi,et al.  Scaffolding a Caenorhabditis nematode genome with RNA-seq. , 2010, Genome research.

[87]  Ai Xia,et al.  A physical map for an Asian malaria mosquito, Anopheles stephensi. , 2010, The American journal of tropical medicine and hygiene.

[88]  F. C. Kafatos,et al.  Widespread Divergence Between Incipient Anopheles gambiae Species Revealed by Whole Genome Sequences , 2010, Science.

[89]  Nikos Darzentas,et al.  Circoletto: visualizing sequence similarity with Circos , 2010, Bioinform..

[90]  Jeffrey A. Bailey,et al.  Genome Landscape and Evolutionary Plasticity of Chromosomes in Malaria Mosquitoes , 2010, PloS one.

[91]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[92]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[93]  K. Lindblad-Toh,et al.  Assisted assembly: how to improve a de novo genome assembly by using related species , 2009, Genome Biology.

[94]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[95]  P. Pevzner,et al.  Breakpoint graphs and ancestral genome reconstructions. , 2009, Genome research.

[96]  Robert M. Waterhouse,et al.  The Aedes aegypti genome: a comparative perspective , 2008, Insect molecular biology.

[97]  Denis Duboule,et al.  The rise and fall of Hox gene clusters , 2007, Development.

[98]  Robert S. Harris,et al.  Improved pairwise alignment of genomic dna , 2007 .

[99]  Ewan Birney,et al.  Update of the Anopheles gambiae PEST genome assembly , 2007, Genome Biology.

[100]  Ai Xia,et al.  A Standard Cytogenetic Photomap for the Mosquito Anopheles stephensi (Diptera: Culicidae): Application for Physical Mapping , 2006 .

[101]  M. Sharakhova,et al.  A standard cytogenetic photomap for the mosquito Anopheles stephensi (Diptera: Culicidae): application for physical mapping. , 2006, Journal of medical entomology.

[102]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[103]  N. Besansky,et al.  A microsatellite map of the African human malaria vector Anopheles funestus. , 2004, The Journal of heredity.

[104]  Jeanne Romero-Severson,et al.  Inversions and Gene Order Shuffling in Anopheles gambiae and A. funestus , 2002, Science.

[105]  Jian Wang,et al.  The Genome Sequence of the Malaria Mosquito Anopheles gambiae , 2002, Science.

[106]  A. della Torre,et al.  A Polytene Chromosome Analysis of the Anopheles gambiae Species Complex , 2002, Science.

[107]  J. Wiegant,et al.  A new method for fluorescence microscopical localization of specific DNA sequences by in situ hybridization of fluorochromelabelled RNA. , 1980, Experimental cell research.