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Hyalella azteca

Summary

Tripal data table
Type	organism
Genus	Hyalella
Species	azteca
Genome Browser	JBrowse Viewer for Hyalella azteca
Description	Hyalella azteca is a freshwater epibenthic amphipod of interest to ecotoxicology and evolutionary biology. It is the primary invertebrate crustacean used in the U.S. for sediment toxicity testing and have been the subject of recent gene expression studies in ecotoxicogenomics. H. azteca is a species complex which has diverged in North America over the past 11 million years creating numerous ecotypes which are the subject of divergent and convergent evolutionary studies. Data were generated by the Baylor College of Medicine&#39s i5k pilot project. Genome update. Previously, the i5k Workspace@NAL hosted Hyalella azteca genome assembly Hazt_2.0.1 (GCA_000764305.3), NCBI Hyalella azteca Annotation Release 100, and Functional annotation of Hyalella azteca hyaazt OGSv1.2. The assembly and annotations have been updated to the most recent assembly, Hyalella azteca genome assembly Hazt_2.0.2(GCF_000764305.2) (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000764305.2/), NCBI Hyalella azteca Annotation Release 101 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Hyalella_azteca/101/), and Functional annotation of NCBI Hyalella azteca Annotation Release 101 (https://i5k.nal.usda.gov/data/Arthropoda/hyaazt-%28Hyalella_azteca%29/Hazt_2.0.2/2.Official%20or%20Primary%20Gene%20Set/).
Publication	Poynton HC, Hasenbein S, Benoit JB, Sepulveda MS, Poelchau MF, Hughes DST, Murali SC, Chen S, Glastad KM, Goodisman MAD, Werren JH, Vineis JH, Bowen JL, Friedrich M, Jones J, Robertson HM, Feyereisen R, Mechler-Hickson A, Mathers N, Lee CE, Colbourne JK, Biales A, Johnston JS, Wellborn GA, Rosendale AJ, Cridge AG, Munoz-Torres MC, Bain PA, Manny AR, Major KM, Lambert FN, Vulpe CD, Tuck P, Blalock BJ, Lin YY, Smith ME, Ochoa-Acuña H, Chen MM, Childers CP, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Gibbs RA, Richards S. The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology. . Environmental science & technology. 2018 05 15; 52(10):6009-6022. Thomas GWC, Dohmen E, Hughes DST, Murali SC, Poelchau M, Glastad K, Anstead CA, Ayoub NA, Batterham P, Bellair M, Binford GJ, Chao H, Chen YH, Childers C, Dinh H, Doddapaneni HV, Duan JJ, Dugan S, Esposito LA, Friedrich M, Garb J, Gasser RB, Goodisman MAD, Gundersen-Rindal DE, Han Y, Handler AM, Hatakeyama M, Hering L, Hunter WB, Ioannidis P, Jayaseelan JC, Kalra D, Khila A, Korhonen PK, Lee CE, Lee SL, Li Y, Lindsey ARI, Mayer G, McGregor AP, McKenna DD, Misof B, Munidasa M, Munoz-Torres M, Muzny DM, Niehuis O, Osuji-Lacy N, Palli SR, Panfilio KA, Pechmann M, Perry T, Peters RS, Poynton HC, Prpic NM, Qu J, Rotenberg D, Schal C, Schoville SD, Scully ED, Skinner E, Sloan DB, Stouthamer R, Strand MR, Szucsich NU, Wijeratne A, Young ND, Zattara EE, Benoit JB, Zdobnov EM, Pfrender ME, Hackett KJ, Werren JH, Worley KC, Gibbs RA, Chipman AD, Waterhouse RM, Bornberg-Bauer E, Hahn MW, Richards S. Gene content evolution in the arthropods. . Genome biology. 2020 01 23; 21(1):15.
Organism Image
Image Credit	Helen Poynton. Image license: CC-BY 4.0.

Assembly Stats

Tripal data table
Contig N50	112853
GC Content	38.87
Scaffold N50	213783

Other Information

Other Information Table
Community Contact	Helen C. Poynton, University of Massachusetts, Boston
Links	Hyalella azteca @ Baylor College of Medicine NCBI BioSample Download Data

Analyses

Tripal data table
Name	Program	Status Sort descending
Functional annotation of Hyalella azteca hyaazt OGSv1.2	AgBase functional annotation pipeline	Current
Functional annotation of NCBI Hyalella azteca Annotation Release 101	AgBase functional annotation pipeline	Current
NCBI Hyalella azteca Annotation Release 101	NCBI Eukaryotic Genome Annotation Pipeline	Current
Hyalella azteca genome assembly Hazt_2.0.2(GCF_000764305.2)	AllPathsLG v. 48744; Atlas Link v. 1.0; Atlas GapFill v. 2.2; Redundans v. 0.11b	Current
Hyalella azteca annotations OGSv1.3	Liftoff	Current
Hyalella azteca genome assembly Hazt_2.0.1 (GCA_000764305.3)	AllPathsLG v. 48744; Atlas Link v. 1.0; Atlas GapFill v. 2.2; Redundans v. 0.11b	Supressed
Hyalella azteca annotations OGSv1.1	remap-gff3 (NA)	Supressed
Hyalella azteca annotations OGSv1.2	remap-gff3; NCBI QC	Supressed
NCBI Hyalella azteca Annotation Release 100	NCBI Eukaryotic annotation pipeline	Supressed
Whole genome assembly of Hyalella azteca	Baylor College of Medicine genome assembly pipeline	Supressed
BCM annotation of the Hyalella azteca assembly using Maker and additional analyses	MAKER	Supressed
Hyalella azteca genome assembly Hazt_2.0 (GCF_000764305.1)	AllPathsLG v. 48744; Atlas Link v. 1.0; Atlas GapFill v. 2.2; Redundans v. 0.11b	Supressed
Hyalella azteca annotations OGSv1.0	MAKER2 and manual annotation	Supressed