De novo assembly of theAedes aegyptigenome using Hi-C yields chromosome-length scaffolds.
The Zika outbreak, spread by theAedes aegyptimosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective way. Here we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67× coverage). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectorsAeaegyptiandCulex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that almost all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, and accurate, and can be applied to many species.
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.|Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.|Center for Theoretical and Biological Physics, Rice University, Houston, TX 77030, USA.
Olga
0000-0001-9163-9544
O
Dudchenko
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.|Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
Sanjit S
SS
Batra
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.|Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
Arina D
AD
Omer
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.|Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
Sarah K
SK
Nyquist
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.|Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
Marie
0000-0002-7175-0736
M
Hoeger
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.|Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
Neva C
NC
Durand
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.|Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
Muhammad S
0000-0002-2600-5147
MS
Shamim
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.|Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
Ido
0000-0001-9042-2765
I
Machol
Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.|Department of Biology, MIT, Cambridge, MA 02139, USA.|Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
Eric S
0000-0003-2662-4631
ES
Lander
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.|Department of Bioengineering, Rice University, Houston, TX 77030, USA.|Department of Pediatrics, Texas Children's Hospital, Houston, TX 77030, USA.
Aviva Presser
0000-0002-5445-0969
AP
Aiden
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA. erez@erez.com.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.|Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.|Center for Theoretical and Biological Physics, Rice University, Houston, TX 77030, USA.|Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
Erez Lieberman
0000-0003-0634-6486
EL
Aiden
D000330:Aedes / Q000235:genetics*; D000818:Animals; D017124:Conserved Sequence; D020451:Contig Mapping / Q000379:methods*; D003465:Culex / Q000235:genetics; D015321:Gene Rearrangement; D049750:Genome, Insect; D006801:Humans; D009690:Nucleic Acid Conformation