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Data released on October 29, 2014

The genome of the American aligator (Alligator mississippiensis).

Armstrong, J; Braun, E, L; Caballero, J; Capella-Gutierrez, S; Castoe, T, A; Chong, A, Y; Earl, D; Finger Jr., J, W; Fujita, M, K; Gongora, J; Green, R, E; Hickey, G; Hubley, R, M; Isberg, S, R; Jaratlerdsiri, W; Jurka, J; Kern, C; Kojima, K, K; Lavoie, C, A; Miles, L; Moran, C; Nguyen, N; Opazo, J, C; Platt, R, N; Ramakodi, M, P; Smit, A, F; St John, J, A; Suh, A; Vandewege, M, W; Burgess, S, C; Iriarte, A; McCormack, J; Edwards, S, V; Lyons, E; Breen, M; Williams, C; Howard, J, T; Gresham, C, R; Peterson, D, G; Schmitz, J; Pollock, D, D; Haussler, D; Triplett, E, W; Zhang, G; Irie, N; Jarvis, E, D; Brochu, C, A; Schmidt, C, J; McCarthy, F, M; Faircloth, B, C; Hoffmann, F, G; Glenn, T, C; Gabaldon, T; Paten, B; Ray, D, A (2014): The genome of the American aligator (Alligator mississippiensis). GigaScience Database. http://dx.doi.org/10.5524/100126 RIS BibTeX Text

The American alligator (Alligator mississippiensis)), as the name suggests, is endemic to North America, specifically to the South-East United States, where it inhabits wetlands on the Atlantic coast from North Carolina to Florida, and in the Northern Gulf of Mexico west to Texas.
These data have been produced as part of the Crocodilian Genomes Project. Genomic DNA was isolated using blood from two wild-caught individuals. Briefly, the alligator data consisted of Illumina sequences from five libraries ranging from 5.5 to 88.7x coverage. These reads were assembled using AllPaths-LG with default parameters. Legacy data from 21 fully sequenced BACs, 1309 BAC-end read pairs, and RNASeq data, were also used to aid the assembly.

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Related manuscripts:

doi:10.1126/science.1254449

Related datasets:

doi:10.5524/100126 IsPartOf doi:10.5524/100125

Genome browser:

http://crocgenome.hpc.msstate.edu/gb2/gbrowse/gator/

Accessions (data included in GigaDB):

PROJECT: PRJNA162735
SAMPLE: SAMN02981418

Projects:


Genomic

http://gigadb.org/images/data/cropped/aligator.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
amis8496 American alligatorAlligator mississippiensis Alternative accession-BioSample:SAMN02981418
Life stage:adult
Estimated genome size:unknown size
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Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
AnnotationUNKNOWN107.64 MB2014-10-21
Tabular dataUNKNOWN29.08 MB2014-10-21
amisSequence assemblyFASTA615.99 MB2014-10-30
Coding sequenceFASTA58.18 MB2014-10-21
Protein sequenceFASTA19.68 MB2014-10-21
ReadmeTEXT0.62 KB2014-10-21
Tabular dataUNKNOWN1.02 MB2014-10-21
Displaying 1-7 of 7 File(s).

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