Join NCBI at PAG in San Diego, January 12–16, 2019

Next week, NCBI staff will attend the Plant and Animal Genome (PAG) Conference. We have several activities planned, including 1 booth (#223), 4 workshops, 1 talk and 2 posters.

Read on to learn more about what you can look forward to if you’re attending PAG this year. (Note: The listed times are Pacific time.)

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500 organisms annotated with the Eukaryotic Genome Annotation Pipeline

This month, the NCBI Eukaryotic Genome Annotation Pipeline annotated its 500th organism! The lucky winner is Pocillopora damicornis, a stony reef-building coral frequently used as an experimental model, whose larval dispersal and development are affected by environmental changes in the oceans.

Stony coral (Pocillopora damicornis)

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

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

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

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

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).

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