Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis
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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.
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Now published in GigaScience doi: 10.1093/gigascience/giab017
Anton Zamyatin 1Computer Technologies Laboratory, ITMO University, Saint Petersburg, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Anton ZamyatinPavel Avdeyev 2Department of Mathematics, The George Washington University, Washington, DC, USA3Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Pavel AvdeyevJiangtao Liang 4Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA5Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, …
Now published in GigaScience doi: 10.1093/gigascience/giab017
Anton Zamyatin 1Computer Technologies Laboratory, ITMO University, Saint Petersburg, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Anton ZamyatinPavel Avdeyev 2Department of Mathematics, The George Washington University, Washington, DC, USA3Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Pavel AvdeyevJiangtao Liang 4Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA5Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jiangtao LiangAtashi Sharma 5Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA6Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Atashi SharmaChujia Chen 5Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA6Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteVarvara Lukyanchikova 4Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA5Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA7Institute of Cytology and Genetics the Siberian Division of the Russian Academy of Sciences, Novosibirsk, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Varvara LukyanchikovaNikita Alexeev 1Computer Technologies Laboratory, ITMO University, Saint Petersburg, RussiaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nikita AlexeevZhijian Tu 5Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA6Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Zhijian TuMax A. Alekseyev 2Department of Mathematics, The George Washington University, Washington, DC, USA3Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA8Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Max A. AlekseyevIgor V. Sharakhov 4Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA5Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Igor V. SharakhovFor correspondence: igor@vt.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giab017 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102680 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102681
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