 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 24, 2017 |
| Title |
De novo assembly of Aedes aegypti using Hi-C yields chromosome-length scaffolds |
| Platform organisms |
Aedes aegypti; Culex quinquefasciatus |
| Sample organisms |
Aedes aegypti; Culex quinquefasciatus; Homo sapiens |
| Experiment type |
Other
Third-party reanalysis
|
| Summary |
The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective fashion. 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 (67X coverage, Sample GSM1551550). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Aedes aegypti and Culex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that virtually all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, accurate, and can be applied to many species.
|
| |
|
| Overall design |
We use DNA proximity ligation (Hi-C) to create a genome assembly with chromosome-length scaffolds for the mosquito Aedes aegypti, principal vector of the Zika virus.
|
| |
|
| Contributor(s) |
Dudchenko O, Aiden EL |
| Citation(s) |
28336562 |
| Submission date |
Mar 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Olga Dudchenko |
| E-mail(s) |
Olga.Dudchenko@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL22030 |
Illumina NextSeq 500 (Aedes aegypti) |
| GPL22042 |
Illumina NextSeq 500 (Culex quinquefasciatus) |
|
| Samples (3) |
|
| Relations |
| Reanalysis of |
GSM1551550 |
| BioProject |
PRJNA378420 |
| SRA |
SRP101512 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE95797_AaegL2.mnd.txt.gz |
20.0 Gb |
(ftp)(http) |
TXT |
| GSE95797_AaegL4.fasta.gz |
397.1 Mb |
(ftp)(http) |
FASTA |
| GSE95797_CpipJ2.mnd.txt.gz |
16.0 Gb |
(ftp)(http) |
TXT |
| GSE95797_CpipJ3.fasta.gz |
158.6 Mb |
(ftp)(http) |
FASTA |
| GSE95797_Hs1.fasta.gz |
805.5 Mb |
(ftp)(http) |
FASTA |
| GSE95797_Hs1.mnd.txt.gz |
7.4 Gb |
(ftp)(http) |
TXT |
| GSE95797_Hs2-HiC.fasta.gz |
804.7 Mb |
(ftp)(http) |
FASTA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
