From listmaster animalgenome.org Wed Sep 16 12:28:35 2020
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From: Dawson@animalgenome.org, Harry <harry.dawsonusda.gov>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: Update to our Porcine Translational Research
Database
Date: Wed, 16 Sep 2020 12:28:35 -0500
Hello All,
We have released a major update to our Porcine Translational Research
Database ( http://tinyurl.com/hxxq3ur). As of March 2020, the database has
been online for 15 years. It is used by research scientists working with
pigs worldwide as well as commercial and public developers of new reagents.
This database is the largest manually curated database for any agriculture
species. It is referenced in more than 90 manuscripts or websites and used
as an information resource for several reagent vendors.
What is new?
1. Content
The database currently has 17,880 entries (pig, mouse and/or human) and
transcript information for 11,547 pig genes. This represents an increase of
1,848 entries from the previous update. 4,747 entries have also been
updated in that time frame. Each entry now has 103 data fields. We have
also added 2 dimensional, and on a limited basis, 3-dimensional structural
comparisons between the 3 species (pig, mouse, and human). The database now
contains 3,327 real-time PCR assay (Taqman and SYBR green). The database
also contains antibody or protein assay data for 965 proteins including 982
monoclonal antibodies, 994 polyclonal antibodies and 450 enzyme-linked
immunosorbent assays.
2. Splice variant analysis
We have numbered pig splice variants according to their human counterpart
when possible. Although splice variant conservation of major isoforms is
generally conserved, our comparison of 7,822 splice variants revealed that
pigs lack the exon to make 9.3% of human splice variants. Possible
differences in the functional capabilities of splice variants have also
been added to our notes field.
3. Error determination
Information in the database identifies and corrects > 7,000 errors (gene
duplications artifacts, mis-assemblies, mis-annotations, and incorrect
species assignments) in the current genome builds (NCBI and Ensembl build
11.1). Our analysis of 6,518 Ensembl locus reveals that only 46.1% are
correctly assembled and annotated. We have recently extended this analysis
to the Ensembl assembly of MARC 1.0. An error analysis of the 150 largest
proteins show that the percentage correctly assembled genes for NCBI build
11.1, Ensembl build 11.1 and Ensembl MARC build is, respectively, 37%, 20%
and 18%. Our preliminary analysis of 1,032 genes from the Ensembl assembly
of MARC build 1.0 also reveals 61 genes that are not annotated and 52 genes
that are missing from chromosomes 1, 2, 3, 7 and 13.
4. Porcine Immunome
The 7th and 8th comparative genome manuscripts were published in 2019-2020.
One describing porcine CD markers (PMID: 29518710) and another describing
porcine cytokines, chemokine and growth factors (PMID: 32442727). The
latter paper fills in certain gaps in sequence information (chemokines, IL-
1 Family) in the porcine genome necessary for understanding inflammation.
To date, we have identified 3,696 genes (or their paralogs) that have a
documented role in the immune or inflammatory response. We have identified
3,163 of these genes in pigs. Three species (pig, mouse, human) comparisons
(presence/absence, splice variant and structural domain conservation) have
been made for 17 recently described families of genes (B7-related MG
Family, Butyrophilins, C-type Lectins, Chckpoint Receptors and Ligands,
Chitinases, Complement-Related Genes, DeAD Box helicases, Defensins and
Antimicrobial Peptides, IAP and IAP-Related Genes, Immunity-related
GTPases, Immunoglobulin Receptors, Intelectins, Non-coding RNA, Ly49
Superfamily, LY9 Superfamily, PYHIN Superfamily and SIRPs). The number of
genes identified and annotated are more than twice the number found in our
previous immunome investigation (PMID: 23676093).
5. Porcine Nutrigenome
To date, we have identified 3,426 genes (or their paralogs) associated with
porcine, murine, and human macro and micronutrient metabolism, including Zn
metalloproteins. Preliminary analysis reveal that pigs have roughly 4-fold
fewer unique genes than the mouse and human. The great majority of these
unique genes were zinc-containing members of the KRAB-A box Transcription
Factor Superfamily. An analysis of 142 non-orthologous genes revealed that
these genes were about 10 times more likely to be present in only pigs and
humans (120) than only in mice and humans (17). Genes involved in vitamin A
and lipid metabolism were more highly conserved between pigs and humans.
Notable, differences were found between humans and pigs in regard to genes
encoding digestive enzymes and nutrient sensing genes. In some cases,
mechanistic data were obtained to explain for previously described
differences in physiology. For example, the lack of porcine salivary lipase
and amylase activities is likely related to the absence of these genes in
the pig. An analysis of 888 orthologous proteins indicated a greater pig-
human protein similarity for almost every gene examined.
The sequences in this database (and associated informatics) are available
(in bulk) to extramural laboratories, via MTA, that are looking to
supplement their analysis of the porcine genome. Please contact us if you
are interested in this.
All the Best,
Harry
Harry Dawson, Ph.D.
Diet, Genomics, Immunology Laboratory
Rm 224, Bld 307C
Beltsville Human Nutrition Research Center
United States Department of Agriculture
BARC-East
10300 Baltimore Ave.
Beltsville, MD 20705
Phone: (301) 504-9412
Fax: (301) 504-9062
--
Website:
http://www.ars.usda.gov/...e.htm?personid=21984
LinkedIn:
https://www.linkedin.com/...rry-dawson-aba07212/
Google Scholar:
https://scholar.google.com/...r=D0fHRaAAAAAJ&hl=en
ResearchGate:
https://www.researchgate.net/...rofile/Harry_Dawson2
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