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i5k Workspace@NAL
U.S. Department of Agriculture
  1. Organism
  2. Hyalella Azteca

Hyalella azteca

Summary
Type
organism
Genus
Hyalella
Species
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(link is external). 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/(link is external)), NCBI Hyalella azteca Annotation Release 101 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Hyalella_azteca/101/(link is external)), 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(link is external).
Assembly Stats
Contig N50
112853
GC Content
38.87
Scaffold N50
213783
Other Information
Community Contact
Helen C. Poynton, University of Massachusetts, Boston
Links
Hyalella azteca @ Baylor College of Medicine(link is external)
NCBI BioSample(link is external)
Download Data
Analyses
Name Program
BCM annotation of the Hyalella azteca assembly using Maker and additional analyses MAKER
NCBI Hyalella azteca Annotation Release 100 NCBI Eukaryotic annotation pipeline
Whole genome assembly of Hyalella azteca Baylor College of Medicine genome assembly pipeline
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
Functional annotation of Hyalella azteca hyaazt OGSv1.2 AgBase functional annotation pipeline
Hyalella azteca annotations OGSv1.3 Liftoff
Hyalella azteca annotations OGSv1.1 remap-gff3 (NA)
Functional annotation of NCBI Hyalella azteca Annotation Release 101 AgBase functional annotation pipeline
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
NCBI Hyalella azteca Annotation Release 101 NCBI Eukaryotic Genome Annotation Pipeline
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
Hyalella azteca annotations OGSv1.2 remap-gff3; NCBI QC
Hyalella azteca annotations OGSv1.0 MAKER2 and manual annotation