Tag Archives: eukaryotic genome annotation

May – July annotations in RefSeq: ants, Chinese alligator & more

Posted on by
Reply

In recent months, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:

  • Alligator sinensis (Chinese alligator)
  • Athalia rosae (coleseed sawfly)
  • Bubalus bubalis (water buffalo)
  • Camponotus floridanus (Florida carpenter ant)
  • Canis lupus dingo (dingo)
  • Harpegnathos saltator (Jerdon’s jumping ant)
  • Melanaphis sacchari (aphid)
  • Pelodiscus sinensis (Chinese soft-shelled turtle)
  • Pogonomyrmex barbatus (red harvester ant)
  • Pomacea canaliculata (gastropod)
  • Sipha flava (yellow sugarcane aphid)
  • Theropithecus gelada (gelada)

See more details on the Eukaryotic RefSeq Genome Annotation Status page.

April and May annotations in RefSeq: cow, bonobo and more

Posted on by
1

In April and May, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:

  • Bos taurus (cattle)
  • Cephus cinctus (wheat stem sawfly)
  • Citrus sinensis (sweet orange)
  • Cynara cardunculus cardunculus (eudicot)
  • Cynoglossus semilaevis (tongue sole)
  • Gallus gallus (chicken)
  • Kryptolebias marmoratus (mangrove rivulus)
  • Macaca nemestrina (pig-tailed macaque)
  • Maylandia zebra (zebra mbuna)
  • Medicago truncatula (barrel medic)
  • Pan paniscus (pygmy chimpanzee)
  • Pteropus alecto (black flying fox)
  • Python bivittatus (Burmese python)
  • Ricinus communis (castor bean)
  • Temnothorax curvispinosus (ant)
  • Tetranychus urticae (two-spotted spider mite)
  • Ziziphus jujuba (common jujube)

See more details on the Eukaryotic RefSeq Genome Annotation Status page.

March & April annotations in RefSeq: chimpanzee, human & more

Posted on by
1

Chimpanzees_in_Uganda_(5984913059)The NCBI Eukaryotic Genome Annotation Pipeline has recently released new annotations in RefSeq for the following organisms:

  • Bombus impatiens (common eastern bumble bee)
  • Brachypodium distachyon (stiff brome)
  • Cimex lectularius (bed bug)
  • Desmodus rotundus (common vampire bat)
  • Halyomorpha halys (brown marmorated stink bug)
  • Homo sapiens (human, more information can be found here)
  • Lingula anatina (brachiopod)
  • Neophocaena asiaeorientalis asiaeorientalis (Yangtze finless porpoise)
  • Oncorhynchus tshawytscha (Chinook salmon)
  • Oryzias melastigma (Indian medaka)
  • Pan troglodytes (chimpanzee)
  • Physcomitrella patens (moss)
  • Populus trichocarpa (black cottonwood)
  • Rosa chinensis (China rose)
  • Selaginella moellendorffii (club-moss)
  • Terrapene mexicana triunguis (Three-toed box turtle)

See more details on the Eukaryotic RefSeq Genome Annotation Status page.

Human annotation release 109 for GRCh38.p12 is available in RefSeq

Posted on by
2

You can now download human annotation release 109 on FTP or explore it in the Genome Data Viewer, in the Gene database, and with BLAST.

Highlights in release 109:

  • A total of 20,203 protein-coding genes and 17,871 non-coding genes were annotated.
  • The number of annotated curated transcripts increased by 17% and genes with two or more curated alternative variants increased by 8%.
  • The annotation includes 6,862 features and 2,075 GeneIDs for non-genic functional elements, such as regulatory regions and known structural elements. For example, see the opsin locus control region (OPSIN-LCR).

Continue reading →

rRNA, snRNA and snoRNA models now predicted by the NCBI Eukaryotic Genome Annotation Pipeline

Posted on by
1

The NCBI Eukaryotic Genome Annotation Pipeline now includes the prediction of more non-coding RNAs. Starting with software release 8.0, rRNAs, snRNAs and snoRNAs are predicted by searching eukaryotic genomes with HMM models from RFAM. Below is an example of a rRNA cassette predicted in maize Annotation Release 102. These new small RNA types come in addition to the miRNAs and tRNAs that have long been annotated by the pipeline.

rRNA cassette on maize scaffold NW_017972167.1 of assembly B73 RefGen_v4

Fig.1: rRNA cassette on maize scaffold NW_017972167.1 of assembly B73 RefGen_v4. The top track displays the annotated 18S, 5.8S and 28S rRNA subunits in Annotation Release 102. These three genes were missing from the previous annotation, and replaced incorrect non-coding gene predictions (see Annotation Release 101, middle track). The bottom track shows the repeats identified by RepeatMasker. The boundaries of the rRNA repeats match precisely the predicted 18S and 28S rRNA genes.

See what we are annotating now on the Eukaryotic RefSeq Genome Annotation Status page.

Seventeen new NCBI annotations in RefSeq for cat, maize, clownfish, and more

Posted on by
1

In November and December, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:

  • Amphiprion ocellaris (clown anemonefish)
  • Centruroides sculpturatus (bark scorpion)
  • Ceratitis capitata (Mediterranean fruit fly)
  • Cucurbita maxima (winter squash)
  • Cucurbita moschata (crookneck pumpkin)
  • Drosophila hydei (fly)
  • Drosophila willistoni (fly)
  • Felis catus (domestic cat)
  • Leptinotarsa decemlineata (Colorado potato beetle)
  • Maylandia zebra (zebra mbuna)
  • Olea europaea sylvestris (wild olive)
  • Onthophagus taurus (beetle)
  • Piliocolobus tephrosceles (Ugandan red Colobus)
  • Seriola lalandi dorsalis (yellowtail amberjack)
  • Spodoptera litura (moth)
  • Xiphophorus maculatus (southern platyfish)
  • Zea mays (maize)

See more details on the Eukaryotic RefSeq Genome Annotation Status page.

Yellow fever mosquito, 6 other organisms in July RefSeq genome annotations

Posted on by
Reply

In July, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:

  • Papio anubis (olive baboon)
  • Prunus avium (sweet cherry)
  • Aedes aegypti (yellow fever mosquito)
  • Chenopodium quinoa (quinoa)
  • Hevea brasiliensis (a eudicot)
  • Manihot esculenta (cassava)
  • Carlito syrichta (Philippine tarsier)
Portrait of olive baboon

Papio anubis (olive or anubis baboon)
Source: United States Fish and Wildlife Service: Digital Library System

See more details on the Eukaryotic RefSeq Genome Annotation Status page.