Data Release: Zika-Susceptible Aedes aegypti De Novo Genome Assembly
Thursday, June 23, 2016
We are excited about the release of a new genome assembly for the mosquito Aedes aegypti, which we hope will aid scientists in studying vector-pathogen dynamics, including those of the rapidly spreading Zika virus. The Aedes aegypti Aag2 cell line genome sequence was generated by a joint effort between Raul Andino’s lab at The University of California, San Francisco and PacBio. This cell line was derived by Peleg in 1975 and adapted in 1991 by Lan and Fallon. It was selected for sequencing based on its susceptibility to infection by many arboviruses, including Dengue, Chikungunya, Zika, Sindbis, and Rift Valley Fever Virus, and for its use in molecular biology and virology experimentation. Genome sequencing was performed on genomic DNA purified from cells acquired from the Gamarnik lab at the Fundación Instituto Leloir. The Aag2 cell line is also persistently infected with Cell Fusing Agent Virus, an insect-specific Flavivirus.
The de novo assembly from ~58x shotgun SMRT Sequencing long-read coverage was performed using PacBio’s FALCON assembler, followed by polishing using the Quiver consensus caller. The assembly resulted in 3752 contigs, totaling 1.72 Gigabases, with a contig N50 of 1.42 Mb. The genome size of this cell line is significantly larger than that of the Liverpool assembly, likely due to the acquisition of a mini-chromosome.
The assembly has been publicly released through VectorBase. It is our hope that this new genome assembly will be of value to the scientific community in their efforts to understand the underlying mechanisms of arboviral infection and transmission in this critical disease-carrying vector.