{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T14:09:37Z","timestamp":1790863777489,"version":"4.1.0"},"reference-count":97,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,3,15]],"date-time":"2021-03-15T00:00:00Z","timestamp":1615766400000},"content-version":"vor","delay-in-days":14,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R21AI135298"],"award-info":[{"award-number":["R21AI135298"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture Hatch","doi-asserted-by":"crossref","award":["223822"],"award-info":[{"award-number":["223822"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Anopheles coluzzii and Anopheles arabiensis belong to the Anopheles gambiae complex and are among the major malaria vectors in sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Findings<\/jats:title>\n                    <jats:p>In this study, we produced de novo chromosome-level genome assemblies for A. coluzzii and A. arabiensis using the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. We obtained 273.4 and 256.8 Mb of the total assemblies for A. coluzzii and A. arabiensis, respectively. Each assembly consists of 3 chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species demonstrated that we obtained improved reference-quality genomes. The new assemblies allowed us to identify genomic coordinates for the breakpoint regions of fixed and polymorphic chromosomal inversions in A. coluzzii and A. arabiensis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The new chromosome-level assemblies will facilitate functional and population genomic studies in A. coluzzii and A. arabiensis. The presented assembly pipeline will accelerate progress toward creating high-quality genome references for other disease vectors.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/gigascience\/giab017","type":"journal-article","created":{"date-parts":[[2021,3,15]],"date-time":"2021-03-15T03:30:07Z","timestamp":1615779007000},"source":"Crossref","is-referenced-by-count":26,"title":["Chromosome-level genome assemblies of the malaria vectors\n                    <i>Anopheles coluzzii<\/i>\n                    and\n                    <i>Anopheles arabiensis<\/i>"],"prefix":"10.1093","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5402-1796","authenticated-orcid":false,"given":"Anton","family":"Zamyatin","sequence":"first","affiliation":[{"name":"Computer Technologies Laboratory, ITMO University , Kronverkskiy Prospekt 49-A, Saint Petersburg 197101,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7953-6259","authenticated-orcid":false,"given":"Pavel","family":"Avdeyev","sequence":"additional","affiliation":[{"name":"Department of Mathematics, The George Washington University , 801 22nd Street NW, Washington, DC 20052,","place":["USA"]},{"name":"Computational Biology Institute, Milken Institute School of Public Health, The George Washington University , 800 22nd Street NW, Washington, DC 20052,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8468-7457","authenticated-orcid":false,"given":"Jiangtao","family":"Liang","sequence":"additional","affiliation":[{"name":"Department of Entomology, Virginia Polytechnic Institute and State University , 170 Drillfield Drive, Blacksburg, VA 24061,","place":["USA"]},{"name":"Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University , 360 West Campus Drive, Blacksburg, VA 24061,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6299-7553","authenticated-orcid":false,"given":"Atashi","family":"Sharma","sequence":"additional","affiliation":[{"name":"Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University , 360 West Campus Drive, Blacksburg, VA 24061,","place":["USA"]},{"name":"Department of Biochemistry, Virginia Polytechnic Institute and State University , Blacksburg, VA 24061,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chujia","family":"Chen","sequence":"additional","affiliation":[{"name":"Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University , 360 West Campus Drive, Blacksburg, VA 24061,","place":["USA"]},{"name":"Department of Biochemistry, Virginia Polytechnic Institute and State University , Blacksburg, VA 24061,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1828-4721","authenticated-orcid":false,"given":"Varvara","family":"Lukyanchikova","sequence":"additional","affiliation":[{"name":"Department of Entomology, Virginia Polytechnic Institute and State University , 170 Drillfield Drive, Blacksburg, VA 24061,","place":["USA"]},{"name":"Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University , 360 West Campus Drive, Blacksburg, VA 24061,","place":["USA"]},{"name":"Institute of Cytology and Genetics the Siberian Division of the Russian Academy of Sciences , Prospekt Lavrentyeva 10, Novosibirsk 630090,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3415-9565","authenticated-orcid":false,"given":"Nikita","family":"Alexeev","sequence":"additional","affiliation":[{"name":"Computer Technologies Laboratory, ITMO University , Kronverkskiy Prospekt 49-A, Saint Petersburg 197101,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4227-3819","authenticated-orcid":false,"given":"Zhijian","family":"Tu","sequence":"additional","affiliation":[{"name":"Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University , 360 West Campus Drive, Blacksburg, VA 24061,","place":["USA"]},{"name":"Department of Biochemistry, Virginia Polytechnic Institute and State University , Blacksburg, VA 24061,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5140-8095","authenticated-orcid":false,"given":"Max A","family":"Alekseyev","sequence":"additional","affiliation":[{"name":"Department of Mathematics, The George Washington University , 801 22nd Street NW, Washington, DC 20052,","place":["USA"]},{"name":"Computational Biology Institute, Milken Institute School of Public Health, The George Washington University , 800 22nd Street NW, Washington, DC 20052,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0752-3747","authenticated-orcid":false,"given":"Igor V","family":"Sharakhov","sequence":"additional","affiliation":[{"name":"Department of Entomology, Virginia Polytechnic Institute and State University , 170 Drillfield Drive, Blacksburg, VA 24061,","place":["USA"]},{"name":"Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University , 360 West Campus Drive, Blacksburg, VA 24061,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,3,15]]},"reference":[{"key":"2024111606041770400_bib1","doi-asserted-by":"publisher","DOI":"10.1186\/1475-2875-10-80","article-title":"Increased proportions of outdoor feeding among residual malaria vector populations following increased use of insecticide-treated nets in rural Tanzania","volume":"10","author":"Russell","year":"2011","journal-title":"Malaria J"},{"issue":"2","key":"2024111606041770400_bib2","doi-asserted-by":"crossref","first-page":"229","DOI":"10.4269\/ajtmh.1992.46.229","article-title":"Intraspecific chromosomal polymorphism in the Anopheles gambiae complex as a factor affecting malaria transmission in the Kisumu area of Kenya","volume":"46","author":"Petrarca","year":"1992","journal-title":"Am J Trop Med Hyg"},{"issue":"9","key":"2024111606041770400_bib3","doi-asserted-by":"crossref","first-page":"e1006303","DOI":"10.1371\/journal.pgen.1006303","article-title":"The genetic basis of host preference and resting behavior in the major African malaria vector, Anopheles arabiensis","volume":"12","author":"Main","year":"2016","journal-title":"PLoS Genet"},{"key":"2024111606041770400_bib4","first-page":"211","article-title":"The Anopheles gambiae complex","volume-title":"Genetics of Insect Vectors of Disease","author":"Davidson","year":"1967"},{"issue":"1","key":"2024111606041770400_bib5","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1534\/genetics.167.1.275","article-title":"The genetics of inviability and male sterility in hybrids between Anopheles gambiae and An. arabiensi s","volume":"167","author":"Slotman","year":"2004","journal-title":"Genetics"},{"issue":"2","key":"2024111606041770400_bib6","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1534\/genetics.117.300221","article-title":"Cross-species Y chromosome function between malaria vectors of the Anopheles gambiae species complex","volume":"207","author":"Bernardini","year":"2017","journal-title":"Genetics"},{"issue":"6217","key":"2024111606041770400_bib7","doi-asserted-by":"crossref","first-page":"1258524","DOI":"10.1126\/science.1258524","article-title":"Extensive introgression in a malaria vector species complex revealed by phylogenomics","volume":"347","author":"Fontaine","year":"2015","journal-title":"Science"},{"issue":"10","key":"2024111606041770400_bib8","doi-asserted-by":"crossref","first-page":"2512","DOI":"10.1093\/molbev\/msy158","article-title":"Coalescent analysis of phylogenomic data confidently resolves the species relationships in the Anopheles gambiae species complex","volume":"35","author":"Thawornwattana","year":"2018","journal-title":"Mol Biol Evol"},{"issue":"4","key":"2024111606041770400_bib9","doi-asserted-by":"crossref","first-page":"e1005141","DOI":"10.1371\/journal.pgen.1005141","article-title":"Experimental swap of Anopheles gambia e's assortative mating preferences demonstrates key role of X-chromosome divergence island in incipient sympatric speciation","volume":"11","author":"Aboagye-Antwi","year":"2015","journal-title":"PLoS Genet"},{"issue":"1","key":"2024111606041770400_bib10","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1603\/0022-2585(2007)44[60:ETEOPI]2.0.CO;2","article-title":"Evaluating the effect of postmating isolation between molecular forms of Anopheles gambiae (Diptera: Culicidae)","volume":"44","author":"Diabate","year":"2007","journal-title":"J Med Entomol"},{"issue":"4","key":"2024111606041770400_bib11","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1111\/eva.12242","article-title":"Habitat segregation and ecological character displacement in cryptic African malaria mosquitoes","volume":"8","author":"Tene\u00a0Fossog","year":"2015","journal-title":"Evol Appl"},{"issue":"4","key":"2024111606041770400_bib12","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1093\/jmedent\/42.4.548","article-title":"Larval development of the molecular forms of Anopheles gambiae(Diptera: Culicidae) in different habitats: a transplantation experiment","volume":"42","author":"Diabate","year":"2005","journal-title":"J Med Entomol"},{"issue":"5","key":"2024111606041770400_bib13","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1093\/beheco\/arq114","article-title":"A behavioral mechanism underlying ecological divergence in the malaria mosquito Anopheles gambiae","volume":"21","author":"Gimonneau","year":"2010","journal-title":"Behav Ecol"},{"issue":"7531","key":"2024111606041770400_bib14","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/nature13987","article-title":"Signatures of aestivation and migration in Sahelian malaria mosquito populations","volume":"516","author":"Dao","year":"2014","journal-title":"Nature"},{"issue":"3","key":"2024111606041770400_bib15","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1111\/mec.15756","article-title":"A population genomic unveiling of a new cryptic mosquito taxon within the malaria-transmitting Anopheles gambiae complex","volume":"30","author":"Tennessen","year":"2021","journal-title":"Mol Ecol"},{"issue":"11","key":"2024111606041770400_bib16","doi-asserted-by":"crossref","first-page":"1925","DOI":"10.1101\/gr.094557.109","article-title":"Every genome sequence needs a good map","volume":"19","author":"Lewin","year":"2009","journal-title":"Genome Res"},{"key":"2024111606041770400_bib17","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.fgb.2015.08.010","article-title":"Mind the gap; seven reasons to close fragmented genome assemblies","volume":"90","author":"Thomma","year":"2016","journal-title":"Fungal Genet Biol"},{"issue":"6478","key":"2024111606041770400_bib18","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1126\/science.aay9847","article-title":"Mosquito heat seeking is driven by an ancestral cooling receptor","volume":"367","author":"Greppi","year":"2020","journal-title":"Science"},{"issue":"1","key":"2024111606041770400_bib19","doi-asserted-by":"crossref","first-page":"5656","DOI":"10.1038\/s41598-018-23987-y","article-title":"Characterization of chemosensory responses on the labellum of the malaria vector mosquito","volume":"8","author":"Saveer","year":"2018","journal-title":"Sci Rep"},{"issue":"5591","key":"2024111606041770400_bib20","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1126\/science.1076196","article-title":"G protein-coupled receptors in Anopheles gambiae","volume":"298","author":"Hill","year":"2002","journal-title":"Science"},{"key":"2024111606041770400_bib21","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1186\/1471-2148-11-72","article-title":"Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract","volume":"11","author":"Mancini","year":"2011","journal-title":"BMC Evol Biol"},{"key":"2024111606041770400_bib22","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1186\/1471-2148-11-292","article-title":"Molecular characterization and evolution of a gene family encoding male-specific reproductive proteins in the African malaria vectorAnopheles gambiae","volume":"11","author":"Mancini","year":"2011","journal-title":"BMC Evol Biol"},{"issue":"5591","key":"2024111606041770400_bib23","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1126\/science.1077136","article-title":"Immunity-related genes and gene families in Anopheles gambiae","volume":"298","author":"Christophides","year":"2002","journal-title":"Science"},{"issue":"51","key":"2024111606041770400_bib24","doi-asserted-by":"crossref","first-page":"25764","DOI":"10.1073\/pnas.1914633116","article-title":"Functional genetic validation of key genes conferring insecticide resistance in the major African malaria vector, Anopheles gambiae","volume":"116","author":"Adolfi","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"15","key":"2024111606041770400_bib25","doi-asserted-by":"crossref","first-page":"6062","DOI":"10.1073\/pnas.1102629108","article-title":"Aquaporin water channel AgAQP1 in the malaria vector mosquito Anopheles gambiae during blood feeding and humidity adaptation","volume":"108","author":"Liu","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5591","key":"2024111606041770400_bib26","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1126\/science.1076181","article-title":"The genome sequence of the malaria mosquito Anopheles gambiae","volume":"298","author":"Holt","year":"2002","journal-title":"Science"},{"issue":"1","key":"2024111606041770400_bib27","doi-asserted-by":"crossref","first-page":"R5","DOI":"10.1186\/gb-2007-8-1-r5","article-title":"Update of the Anopheles gambiae PEST genome assembly","volume":"8","author":"Sharakhova","year":"2007","journal-title":"Genome Biol"},{"issue":"4","key":"2024111606041770400_bib28","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.1534\/genetics.111.137794","article-title":"Ecological genomics of Anopheles gambiae along a latitudinal cline: a population-resequencing approach","volume":"190","author":"Cheng","year":"2012","journal-title":"Genetics"},{"issue":"22","key":"2024111606041770400_bib29","doi-asserted-by":"crossref","first-page":"5719","DOI":"10.1111\/mec.13840","article-title":"The last bastion? X chromosome genotyping of Anopheles gambiae species pair males from a hybrid zone reveals complex recombination within the major candidate \u2018genomic island of speciation\u2019","volume":"25","author":"Caputo","year":"2016","journal-title":"Mol Ecol"},{"issue":"7683","key":"2024111606041770400_bib30","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1038\/nature24995","article-title":"Genetic diversity of the African malaria vector Anopheles gambiae","volume":"552","author":"Miles","year":"2017","journal-title":"Nature"},{"key":"2024111606041770400_bib31","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1038\/s42003-019-0717-7","article-title":"Transcontinental dispersal of Anopheles gambiae occurred from West African origin via serial founder events","volume":"2","author":"Schmidt","year":"2019","journal-title":"Commun Biol"},{"issue":"9","key":"2024111606041770400_bib32","doi-asserted-by":"crossref","first-page":"2867","DOI":"10.1534\/g3.116.031906","article-title":"Genome-wide divergence in the West-African malaria vector Anopheles melas","volume":"6","author":"Deitz","year":"2016","journal-title":"G3 (Bethesda)"},{"issue":"6217","key":"2024111606041770400_bib33","doi-asserted-by":"crossref","first-page":"1258522","DOI":"10.1126\/science.1258522","article-title":"Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes","volume":"347","author":"Neafsey","year":"2015","journal-title":"Science"},{"issue":"6003","key":"2024111606041770400_bib34","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1126\/science.1195755","article-title":"Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences","volume":"330","author":"Lawniczak","year":"2010","journal-title":"Science"},{"issue":"1","key":"2024111606041770400_bib35","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-019-0728-3","article-title":"Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies","volume":"18","author":"Waterhouse","year":"2020","journal-title":"BMC Biol"},{"issue":"1","key":"2024111606041770400_bib36","doi-asserted-by":"publisher","DOI":"10.3390\/genes10010062","article-title":"A high-quality de novo genome assembly from a single mosquito using PacBio sequencing","volume":"10","author":"Kingan","year":"2019","journal-title":"Genes (Basel)"},{"key":"2024111606041770400_bib37","doi-asserted-by":"publisher","DOI":"10.1016\/j.cois.2015.02.013","article-title":"Best practices in insect genome sequencing: what works and what doesn't","volume":"7","author":"Richards","year":"2015","journal-title":"Curr Opin Insect Sci"},{"issue":"2","key":"2024111606041770400_bib38","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1016\/j.yexcr.2016.12.014","article-title":"The value of new genome references","volume":"358","author":"Worley","year":"2017","journal-title":"Exp Cell Res"},{"issue":"4","key":"2024111606041770400_bib39","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1038\/ng.3802","article-title":"Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome","volume":"49","author":"Bickhart","year":"2017","journal-title":"Nat Genet"},{"issue":"11","key":"2024111606041770400_bib40","doi-asserted-by":"crossref","first-page":"1750","DOI":"10.1101\/gr.191395.115","article-title":"Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome","volume":"25","author":"Goodwin","year":"2015","journal-title":"Genome Res"},{"issue":"1","key":"2024111606041770400_bib41","doi-asserted-by":"crossref","first-page":"5417","DOI":"10.1038\/s41598-018-23641-7","article-title":"Unbiased strain-typing of arbovirus directly from mosquitoes using Nanopore sequencing: A field-forward biosurveillance protocol","volume":"8","author":"Russell","year":"2018","journal-title":"Sci Rep"},{"issue":"22","key":"2024111606041770400_bib42","doi-asserted-by":"crossref","first-page":"5439","DOI":"10.1007\/s00216-018-0877-1","article-title":"Serogroup-level resolution of the \u201cSuper-7\u201d Shiga toxin-producing Escherichia coliusing nanopore single-molecule DNA sequencing","volume":"410","author":"Peritz","year":"2018","journal-title":"Anal Bioanal Chem"},{"issue":"1","key":"2024111606041770400_bib43","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/s41467-018-03016-2","article-title":"High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell","volume":"9","author":"Michael","year":"2018","journal-title":"Nat Commun"},{"issue":"10","key":"2024111606041770400_bib44","doi-asserted-by":"crossref","first-page":"3131","DOI":"10.1534\/g3.118.200160","article-title":"Highly contiguous genome assemblies of 15 Drosophilaspecies generated using nanopore sequencing","volume":"8","author":"Miller","year":"2018","journal-title":"G3 (Bethesda)"},{"issue":"1","key":"2024111606041770400_bib45","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s13024-018-0274-4","article-title":"Long-read sequencing across the C9orf72 \u2018GGGGCC\u2019 repeat expansion: implications for clinical use and genetic discovery efforts in human disease","volume":"13","author":"Ebbert","year":"2018","journal-title":"Mol Neurodegener"},{"issue":"6","key":"2024111606041770400_bib46","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1093\/jhered\/esx058","article-title":"Improvement of the threespine stickleback genome using a Hi-C-based proximity-guided assembly","volume":"108","author":"Peichel","year":"2017","journal-title":"J Hered"},{"issue":"6333","key":"2024111606041770400_bib47","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1126\/science.aal3327","article-title":"De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds","volume":"356","author":"Dudchenko","year":"2017","journal-title":"Science"},{"issue":"7732","key":"2024111606041770400_bib48","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1038\/s41586-018-0692-z","article-title":"Improved reference genome of Aedes aegypti informs arbovirus vector control","volume":"563","author":"Matthews","year":"2018","journal-title":"Nature"},{"issue":"6","key":"2024111606041770400_bib49","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giz063","article-title":"A chromosome-scale assembly of the major African malaria vector Anopheles funestus","volume":"8","author":"Ghurye","year":"2019","journal-title":"Gigascience"},{"issue":"10","key":"2024111606041770400_bib50","doi-asserted-by":"crossref","first-page":"3811","DOI":"10.1534\/g3.120.401654","article-title":"The beginning of the end: a chromosomal assembly of the New World malaria mosquito ends with a novel telomere","volume":"10","author":"Compton","year":"2020","journal-title":"G3 (Bethesda)"},{"issue":"3","key":"2024111606041770400_bib51","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1534\/g3.119.400922","article-title":"Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome","volume":"10","author":"Bracewell","year":"2020","journal-title":"G3 (Bethesda)"},{"issue":"1","key":"2024111606041770400_bib52","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1093\/nar\/gkz1080","article-title":"Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster","volume":"48","author":"CE","year":"2020","journal-title":"Nucleic Acids Res"},{"issue":"18","key":"2024111606041770400_bib53","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"issue":"1","key":"2024111606041770400_bib54","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.ymeth.2013.06.027","article-title":"Kraken: a set of tools for quality control and analysis of high-throughput sequence data","volume":"63","author":"Davis","year":"2013","journal-title":"Methods"},{"issue":"2","key":"2024111606041770400_bib55","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41592-019-0669-3","article-title":"Fast and accurate long-read assembly with wtdbg2","volume":"17","author":"Ruan","year":"2020","journal-title":"Nat Methods"},{"issue":"5","key":"2024111606041770400_bib56","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"14","key":"2024111606041770400_bib57","doi-asserted-by":"crossref","first-page":"2103","DOI":"10.1093\/bioinformatics\/btw152","article-title":"Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences","volume":"32","author":"Li","year":"2016","journal-title":"Bioinformatics"},{"issue":"5","key":"2024111606041770400_bib58","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"Koren","year":"2017","journal-title":"Genome Res"},{"issue":"8","key":"2024111606041770400_bib59","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"issue":"6","key":"2024111606041770400_bib60","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1093\/bioinformatics\/btr011","article-title":"A fast, lock-free approach for efficient parallel counting of occurrences of k-mers","volume":"27","author":"Marcais","year":"2011","journal-title":"Bioinformatics"},{"issue":"19","key":"2024111606041770400_bib61","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Simao","year":"2015","journal-title":"Bioinformatics"},{"key":"2024111606041770400_bib62","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1007\/978-1-4939-9173-0_14","article-title":"BUSCO: assessing genome assembly and annotation completeness","volume":"1962","author":"Seppey","year":"2019","journal-title":"Methods Mol Biol"},{"issue":"5","key":"2024111606041770400_bib63","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1101\/gr.214270.116","article-title":"Fast and accurate de novo genome assembly from long uncorrected reads","volume":"27","author":"Vaser","year":"2017","journal-title":"Genome Res"},{"key":"2024111606041770400_bib64","journal-title":"medaka: Sequence correction provided by ONT Research"},{"issue":"4","key":"2024111606041770400_bib65","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nbt.4060","article-title":"Nanopore sequencing and assembly of a human genome with ultra-long reads","volume":"36","author":"Jain","year":"2018","journal-title":"Nat Biotechnol"},{"issue":"11","key":"2024111606041770400_bib66","doi-asserted-by":"crossref","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PLoS One"},{"issue":"1","key":"2024111606041770400_bib67","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","article-title":"Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst"},{"issue":"12","key":"2024111606041770400_bib68","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1038\/nbt.2768","article-title":"High-throughput genome scaffolding from in vivo DNA interaction frequency","volume":"31","author":"Kaplan","year":"2013","journal-title":"Nat Biotechnol"},{"issue":"12","key":"2024111606041770400_bib69","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1038\/nbt.2727","article-title":"Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions","volume":"31","author":"Burton","year":"2013","journal-title":"Nat Biotechnol"},{"key":"2024111606041770400_bib70","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms6695","article-title":"High-quality genome (re) assembly using chromosomal contact data","volume":"5","author":"Marie-Nelly","year":"2014","journal-title":"Nat Commun"},{"issue":"3","key":"2024111606041770400_bib71","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1101\/gr.193474.115","article-title":"Chromosome-scale shotgun assembly using an in vitro method for long-range linkage","volume":"26","author":"Putnam","year":"2016","journal-title":"Genome Res"},{"issue":"21\u201322","key":"2024111606041770400_bib72","doi-asserted-by":"crossref","first-page":"1591","DOI":"10.1101\/gad.328971.119","article-title":"Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling","volume":"33","author":"Renschler","year":"2019","journal-title":"Genes Dev"},{"issue":"8","key":"2024111606041770400_bib73","doi-asserted-by":"crossref","first-page":"e1007273","DOI":"10.1371\/journal.pcbi.1007273","article-title":"Integrating Hi-C links with assembly graphs for chromosome-scale assembly","volume":"15","author":"Ghurye","year":"2019","journal-title":"PLoS Comput Biol"},{"key":"2024111606041770400_bib74","article-title":"The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000","author":"Dudchenko","year":"2018","journal-title":"bioRxiv"},{"issue":"1","key":"2024111606041770400_bib75","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1186\/s12859-018-2485-7","article-title":"Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies","volume":"19","author":"Roach","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2024111606041770400_bib76","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1186\/1471-2164-14-273","article-title":"Six novel Y chromosome genes in Anophelesmosquitoes discovered by independently sequencing males and females","volume":"14","author":"Hall","year":"2013","journal-title":"BMC Genomics"},{"issue":"15","key":"2024111606041770400_bib77","doi-asserted-by":"crossref","first-page":"E2114","DOI":"10.1073\/pnas.1525164113","article-title":"Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes","volume":"113","author":"Hall","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"2024111606041770400_bib78","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1534\/genetics.104.034264","article-title":"Satellite DNA from the Y chromosome of the malaria vector Anopheles gambiae","volume":"169","author":"Krzywinski","year":"2005","journal-title":"Genetics"},{"issue":"1","key":"2024111606041770400_bib79","doi-asserted-by":"crossref","first-page":"R10","DOI":"10.1186\/gb-2013-14-1-r10","article-title":"Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution","volume":"14","author":"Melters","year":"2013","journal-title":"Genome Biol"},{"issue":"1","key":"2024111606041770400_bib80","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1093\/jmedent\/29.1.125","article-title":"Reassociation kinetics of Anopheles gambiae (Diptera: Culicidae) DNA","volume":"29","author":"Besansky","year":"1992","journal-title":"J Med Entomol"},{"issue":"3","key":"2024111606041770400_bib81","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic Local Alignment Search Tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"2024111606041770400_bib82","doi-asserted-by":"crossref","first-page":"e4958","DOI":"10.7717\/peerj.4958","article-title":"D-GENIES: dot plot large genomes in an interactive, efficient and simple way","volume":"6","author":"Cabanettes","year":"2018","journal-title":"PeerJ"},{"issue":"3","key":"2024111606041770400_bib83","doi-asserted-by":"publisher","DOI":"10.3390\/genes11030327","article-title":"Structural variation of the X chromosome heterochromatin in the Anopheles gambiaecomplex","volume":"11","author":"Sharma","year":"2020","journal-title":"Genes (Basel)"},{"issue":"18","key":"2024111606041770400_bib84","doi-asserted-by":"crossref","first-page":"2334","DOI":"10.1093\/bioinformatics\/btq413","article-title":"genoPlotR: comparative gene and genome visualization in R","volume":"26","author":"Guy","year":"2010","journal-title":"Bioinformatics"},{"issue":"1","key":"2024111606041770400_bib85","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1186\/s13059-019-1911-0","article-title":"SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies","volume":"20","author":"Goel","year":"2019","journal-title":"Genome Biol"},{"issue":"5597","key":"2024111606041770400_bib86","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1126\/science.1077769","article-title":"A polytene chromosome analysis of the Anopheles gambiaespecies complex","volume":"298","author":"Coluzzi","year":"2002","journal-title":"Science"},{"key":"2024111606041770400_bib87","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1186\/1475-2875-9-293","article-title":"Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion","volume":"9","author":"Lobo","year":"2010","journal-title":"Malar J"},{"issue":"16","key":"2024111606041770400_bib88","doi-asserted-by":"crossref","first-page":"6258","DOI":"10.1073\/pnas.0509683103","article-title":"Breakpoint structure reveals the unique origin of an interspecific chromosomal inversion (2La) in the Anopheles gambiae complex","volume":"103","author":"Sharakhov","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024111606041770400_bib89","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1186\/1471-2164-11-459","article-title":"Genome mapping and characterization of the Anopheles gambiaeheterochromatin","volume":"11","author":"Sharakhova","year":"2010","journal-title":"BMC Genomics"},{"key":"2024111606041770400_bib90","article-title":"Anophelesmosquitoes revealed new principles of 3D genome organization in insects","author":"Lukyanchikova","year":"2020","journal-title":"bioRxiv"},{"issue":"15","key":"2024111606041770400_bib91","doi-asserted-by":"crossref","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","article-title":"NanoPack: visualizing and processing long-read sequencing data","volume":"34","author":"De\u00a0Coster","year":"2018","journal-title":"Bioinformatics"},{"issue":"6","key":"2024111606041770400_bib92","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1093\/bioinformatics\/btr010","article-title":"A novel hybrid gene prediction method employing protein multiple sequence alignments","volume":"27","author":"Keller","year":"2011","journal-title":"Bioinformatics"},{"issue":"17","key":"2024111606041770400_bib93","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2024111606041770400_bib94","author":"Genome Size Estimation Tutorial"},{"key":"2024111606041770400_bib95","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013"},{"key":"2024111606041770400_bib96","unstructured":"Zamyatin A, Avdeyev P, Liang J, et al. \u00a0Supporting data for the chromosome-level genome assembly of the malaria vector Anopheles arabiensis. GigaScience Database. 2021. 10.5524\/100860."},{"key":"2024111606041770400_bib97","doi-asserted-by":"crossref","unstructured":"Zamyatin A, Avdeyev P, Liang J, et al. \u00a0Supporting data for the chromosome-level genome assembly of the malaria vectors Anopheles coluzzii. GigaScience Database. 2021. 10.5524\/100861.","DOI":"10.1101\/2020.09.29.318477"}],"container-title":["GigaScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/10\/3\/giab017\/60688753\/giab017.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/10\/3\/giab017\/60688753\/giab017.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,16]],"date-time":"2024-11-16T01:05:25Z","timestamp":1731719125000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gigascience\/article\/doi\/10.1093\/gigascience\/giab017\/6170950"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,3]]},"references-count":97,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2021,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/gigascience\/giab017","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.09.29.318477","asserted-by":"object"}]},"ISSN":["2047-217X"],"issn-type":[{"value":"2047-217X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,3]]},"published":{"date-parts":[[2021,3]]},"article-number":"giab017"}}