Anton Zamyatin1, Pavel Avdeyev2,3, Jiangtao Liang4,5, Atashi Sharma5,6, Chujia Chen5,6, Varvara Lukyanchikova4,5,7, Nikita Alexeev1, Zhijian Tu5,6, Max A Alekseyev2,3, Igor V Sharakhov4,5. 1. Computer Technologies Laboratory, ITMO University, Kronverkskiy Prospekt 49-A, Saint Petersburg 197101, Russia. 2. Department of Mathematics, The George Washington University, 801 22nd Street NW, Washington, DC 20052, USA. 3. Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, 800 22nd Street NW, Washington, DC 20052, USA. 4. Department of Entomology, Virginia Polytechnic Institute and State University, 170 Drillfield Drive, Blacksburg, VA 24061, USA. 5. Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA. 6. Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. 7. Institute of Cytology and Genetics the Siberian Division of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia.
Abstract
BACKGROUND: 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. FINDINGS: 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. CONCLUSION: 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.
BACKGROUND: 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. FINDINGS: 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. CONCLUSION: 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.
Authors: Neil F Lobo; Djibril M Sangaré; Allison A Regier; Kyanne R Reidenbach; David A Bretz; Maria V Sharakhova; Scott J Emrich; Sekou F Traore; Carlo Costantini; Nora J Besansky; Frank H Collins Journal: Malar J Date: 2010-10-25 Impact factor: 2.979
Authors: Nicholas H Putnam; Brendan L O'Connell; Jonathan C Stites; Brandon J Rice; Marco Blanchette; Robert Calef; Christopher J Troll; Andrew Fields; Paul D Hartley; Charles W Sugnet; David Haussler; Daniel S Rokhsar; Richard E Green Journal: Genome Res Date: 2016-02-04 Impact factor: 9.043
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Authors: Andrew Brantley Hall; Yumin Qi; Vladimir Timoshevskiy; Maria V Sharakhova; Igor V Sharakhov; Zhijian Tu Journal: BMC Genomics Date: 2013-04-23 Impact factor: 3.969
Authors: Federica Bernardini; Roberto Galizi; Mariana Wunderlich; Chrysanthi Taxiarchi; Nace Kranjc; Kyros Kyrou; Andrew Hammond; Tony Nolan; Mara N K Lawniczak; Philippos Aris Papathanos; Andrea Crisanti; Nikolai Windbichler Journal: Genetics Date: 2017-08-31 Impact factor: 4.562