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

The genome of the American aligator (Alligator mississippiensis).

Dataset type: Genomic
Data released on October 29, 2014

Green RE; Braun EL; Armstrong J; Earl D; Nguyen N; Hickey G; Vandewege MW; St John JA; Capella-Gutierrez S; Castoe TA; Kern C; Fujita MK; Opazo JC; Jurka J; Kojima KK; Caballero J; Hubley RM; Smit AF; Platt RN; Lavoie CA; Ramakodi MP; Finger Jr. JW; Suh A; Isberg SR; Miles L; Chong AY; Jaratlerdsiri W; Gongora J; Moran C; Iriarte A; McCormack J; Burgess SC; Edwards SV; Lyons E; Williams C; Breen M; Howard JT; Gresham CR; Peterson DG; Schmitz J; Pollock DD; Haussler D; Triplett EW; Zhang G; Irie N; Jarvis ED; Brochu CA; Schmidt CJ; McCarthy FM; Faircloth BC; Hoffmann FG; Glenn TC; Gabaldon T; Paten B; Ray DA (2014): The genome of the American aligator (Alligator mississippiensis). GigaScience Database. http://dx.doi.org/10.5524/100126

DOI10.5524/100126

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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Additional details

Read the peer-reviewed publication(s):

Green, R. E., Braun, E. L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., … Castoe, T. A. (2014). Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science, 346(6215), 1254449–1254449. 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:






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).




File NameSample IDData 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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