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Pig Genome Newsletter #126
From: "Christopher K. Tuggle" <cktuggle@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #126
Date: Thu, 11 Oct 2018 14:59:20 -0500
Pig Genome Update # 126:
- PDF version is available at
http://www.animalgenome.org/pig/newsletter/pdf/No.126.pdf
- Web version is available at
http://www.animalgenome.org/pig/newsletter/No.126.html
- Plain text version is appended below:
P I G G E N O M E U P D A T E
_________________________________________________________________
A Periodic Newsletter of the U.S. Pig Genome Coordination Program
************** No. 126 **************
* *
* October 11, 2018 *
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1. Recent meetings summary
2. Update on USDA-NIFA-AFRI and new functional genomics project activities
3. Reminder on ISAFG2018, PAG2019, Midwest ASAS & ASAS-CSAS2019 deadlines
4. Neil A. Jorgenson Travel Award Opportunity
5. Upcoming additional meetings information
6. Update on projects supported by NRSP-8 funds- We want to hear from you!
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1. Recent meetings summary
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a. Biology of Genomes 2018 (Cold Spring Harbor Laboratory)
The use of CRISPR technology to edit genomes was widespread across many
talks at this meeting. Jef Boeke (NY Genome Center) discussed his
interesting work modifying large chunks of the yeast genome in synthetic
biology approaches, even to the point of creating whole
“neochromosomes”. Molly Gasperini (U. Washington) discussed high
multiplexing of guide RNAs to modify more than 1,000 sites in the human
genome to test function of predicted enhancers. High-dimensional, CRISPR-
based genome editing evaluation of 16,000+ SNPs in yeast was discussed by
Eilon Sharon (Stanford U.). Such techniques, impressive in their scope,
may be of interest in livestock functional genomics to test SNPs
associated with traits, especially those that can be scored in vitro.
Elaine Ostrander (NHGRI) discussed a strategic planning process for NHGRI
called Genomics 2020 (https://www.genome.gov/10001307/longrange-
planning/). She asked for suggestions on how to structure ther NIH grant
processs in the future. As the USDA is now working closely with NIH (i.e.,
on a Comparative Genomics joint call, see below #3): it could be ueful for
our community to engage with this discussion. Email this group at
genomics2020@mail.nih.gov with your suggestions!
Arang Rhie described the Vertebrate Genomes Project
(https://vertebrategenomesproject.org/), which had a full day Workshop at
PAG 2018. The VGP intends to exploit new technologies to assemble the
genome sequence of 10,000 or more vertebrate species (see more in the
report on Livestock Genomics meeting below). Rhie discussed a project
using a “trio-binning” approach with parental short-reads and
offspring long-reads to assemble parental haplotypes using data from a
Brahman cross with Angus
(https://www.biorxiv.org/content/early/2018/02/26/271486). This approach
could be useful in pigs as well, potentially to establish and use breed
haplotypes.
b. Genome Writer’s Guild meeting 2018
This interesting small meeting focused on all aspects of genome editing
(GE), technologies, uses and outcomes in agricultural (including pigs and
cattle) and biomedicine, and the societal implications of GE. Several
talks focused on engaging the public, to explain and discuss the science
and implications of GE, including presentations by Johnny Kung (Harvard
Medical School) and Charlie Arnot (Center for Food Integrity). Tammy Lee
(Recombinetics) described the process ahead for gaining approval for GE
pigs, including “castration-free” swine. Jeff Essner (Iowa State U.)
told the audience of new GE strategies to modify pig fibroblasts more
efficiently, in collaboration with Recombinetics.
c. Livestock Genomics 2018
This meeting is held every two years in the UK, organized by the European
Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI).
The meeting attracts European leaders in livestock genomics as well as
many speakers from around the globe. It is a smaller meeting with most
attendees providing a talk and/or a poster, thus providing excellent
opportunities to gain knowledge in livestock genomics thought leaders.
Twenty-two talks were presented at the meeting from 20-21 September 2018.
Six speakers and several poster presenters reported pig genome data, and
seven additional speakers covered results broader in scope but of
relevance to pig genomics.
Two speakers discussed phylogeny of species in the suid ancestry (whole
genome sequence of pygmy hog, Langqing Li (Wageningen U.); amd African
genome assemblies, (Lel Eory, Roslin I.)). Transcripome-level analyses was
reported by the other four speakers. Chris Tuggle (Iowa State U.)
described the use of PacBio Isoseq data from nine tissues to improve the
annotation of the pig genome. Stefan Seeman (U. Copenhagen) described a
comparative study of X chromosome lncRNA between pig, human, and mouse.
Jun-mo Kim (Chung-Ang U.) used network analysis to elucidate the gene
expression changes during the estrous cycle in reproductive tissues, and
Martina Zappaterra (U. of Bologna) looked at differential expression in
muscles from pigs differing in intracellular fat content.
There were also talks on Ensembl tools relevant to livestock by EMBL-EBI
staff; including tools for analyzing GWAS associated variants (Daniel
Zerbino) and livestock species annotation (Kostas Billis), and an update
on the Data Coordinating Centre and FAANG metadata standards (Peter
Harrison). Paul Flicek (EMBL-EBI) concluded the meeting with an
interesting look on the status and aspirations of the Vertebrate Genome
Project. He introduced the metric of x.y.z score for each assembly, and
described the current stage of testing technologies to get to the goal of
a $10,000 assembly per species. 260 different species 50 million years
apart in evolution have been selected to represent vertebrates at the
ordinal level; 15 VGP genomes have been released thus far. Flicek
described the enormous efforts in coordination of data, metadata quality
control and annotation this inspiring project will demand, simply to make
the data useful and accessible.
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2. Update on USDA-NIFA-AFRI and new functional genomics project FAANG
activities
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As described in prior PG Updates, the FAANG Consortium has been organized
and held meetings and conference calls regularly. Some developments are
described below; for further information please see the FAANG website
(www.faang.org), which is hosted by www.animalgenome.org through the NRSP-
8 Bioinformatics Coordination team. A new webpage has been developed to
provide information on new funding opportunities for FAANG related
proposals (see also below; available on FAANG website, member’s area
page).
a) Three groups have been awarded substantial funding (totaling $6M) from
the USDA-NIFA-AFRI to create resources for functional analysis of animal
genomes (see:
https://www.news.iastate.edu/news/2018/06/13/swinegenomicscoe). These
include a group headed by Pablo Ross (UC-Davis) focused on cattle, and a
group headed by Yvonne Dreschler (Western University of Health Sciences)
focused on chicken. The third group is headed by Chris Tuggle, with a
focus on pigs, and includes ISU collaborators James Reecy and James
Koltes, as well as USDA-ARS-MARC (Dan Nonneman, Tim Smith), Michigan State
U (Cathy Ernst), UC-Davis (Huaijun Zhou, Pablo Ross), and USDA-ARS-NADC
(Crystal Loving). This group was awarded $2.5 M over 4 years to develop
data on the functional components of the pig genome in adult, fetal and
immune cells and tissues relevant to economically important traits. A
number of techniques will be used to generate RNA expression and
epigenetics data, and all data will be deposited in public databases as
soon as it is quality-controlled (prior to publication). The project
earned the distinction of being named a USDA “Center of Excellence”
for pig genomics, as well.
b) Lakshmi Matukumalli announced earlier this year that NIFA is partnering
with NIH to request proposals to work on comparative genomics. See
https://nifa.usda.gov/funding-opportunity/comparative-genomics-research-
program for details; there are several opportunities for funding in the
next year; however, the funding available may be fully committed before
all application deadlines are reached. Questions can be directed to the
contacts on the webpage.
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3. Reminder on ISAFG 2018, PAG 2019 **Short deadline**, Midwest ASAS-ADSA
2019, ASAS 2019 meeting registration deadlines.
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The 7th International Symposium on Animal Functional Genomics is being
held next month in Adelaide, Australia, 12-15 November 2018. The program
is now available at http://www.isafg2018.com/program.html, and looks to be
a great meeting on the functions of genomes for a number of animal
species. On-line registration is still available until the end of October
2018.
A reminder that the 27th Plant and Animal Genome Meeting
(http://www.intlpag.org/), will be held January 11-16, 2019 in San Diego
CA (as usual, location is the Town and Country Hotel). This meeting will
include the Swine Genome Subcommittee Workshop on January 12, being
organized this year by the 2019 Chair, Christian Maltecca (North
Carolina). There will also be a FAANG Workshop held on January 11, 1-6
PM). The PAG27 early registration deadline is November 2, 2018
(http://www.intlpag.org/2019/attend/registration-and-fees), and the
poster/abstract submission deadline is October 26, 2018 (see:
http://www.intlpag.org/2019/abstracts/poster-submission). However, stay
tuned to an expected announcement in mid-late October for an extension of
the Abstract deadline.
The Midwest Section meeting of the ASAS and ADSA will be held March 11-13,
2019 in Omaha, NE. Registration for the Midwest ASAS-ADSA meeting will
open October 2018
(https://netforum.avectra.com/eweb/shopping/shopping.aspx?logoff=yes&site=
asas&cart=0&shopsearch=%25midwest&shopsearchCat=Event). Midwest ASAS-ADSA
2019 abstracts are due by 3:00 pm on November 8, 2018
(https://www.asas.org/taking-stock/blog-post/taking-stock/2018/09/16/2019-
midwestern-section-call-for-abstracts-and-early-registration ).
Check out: https://www.animalgenome.org/pig/community/meetings for meeting
information updates.
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4. Neil A. Jorgenson Travel Award Opportunity **Short deadline**
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A reminder that the NRSP-8 Swine Genome Coordinator can fund travel to the
PAG meeting for a student who presents their swine-genome related research
work there. If you or your graduate student is interested in applying for
the Neil Jorgensen Travel award, please send Chris Tuggle and Cathy Ernst
your application as soon as possible (see:
http://www.intlpag.org/2019/attend/travel-grants , scroll down to
Jorgenson Awards). Applications will be accepted until October 25, 2018,
not October 12 as stated on the PAG 27 website.
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5. Upcoming additional meetings information
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Besides the meetings discussed above, there are many other meetings of
relevance to the genomics community over the next 6-12 months, see:
http://www.animalgenome.org/pig/community/meetings). As mentioned above, a
reminder that the ISAG community will hold their next meeting in July 2019
at the University of Lleida in Spain. See https://www.isag.us/2019/ for
details. At time of writing, registration and abstraxt submission details
were not yet available.
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6. Update on projects supported by NRSP-8 funds - We want to hear from you!
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Update on PacBio Isoseq Data analysis: As described above, Chris Tuggle
presented the analysis of nine tissues of Iso-seq data at the Livestock
Genome meeting. There are plans to present updated results at the ISAFG
meeting in November 2019. Please email Chris Tuggle
(cktuggle@iastate.edu), Dan Nonneman (Dan.Nonneman@ARS.USDA.GOV, or Tim
Smith (Tim.Smith@ARS.USDA.GOV) with any questions.
The swine genome coordinators are always glad to hear from NRSP-8 members
and other readers about ways that the coordination effort can be improved
or provide resources that are needed. If you have items of general
interest to the swine genetics and genomics communities that can be
included in this newsletter please share. Our issues are now planned for
February and October each year. Any contribution should be sent to the
Coordinators one week prior to these dates.
<> <> <> <> <> <> <> <> <> <> <>
Joint Coordinators:
Christopher Tuggle Catherine Ernst
2255 Kildee Hall Anthony Hall, 474 S. Shaw Lane, Room 1205
Department of Animal Science Department of Animal Science
Iowa State University Michigan State University
Ames, IA 50011 East Lansing, MI 48824
Phone: 515-294-4252 Phone: 517-432-1941
Fax: 515-294-2401 Fax: 517-353-1699
Email: cktuggle@iastate.edu Email: ernstc@msu.edu
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Supported by Multi-State Research Funds to the National Research Service
Program (NRSP-8). National Animal Genome Research Program (NAGRP),
Lakshmi Matukumalli, NAGRP Director, NIFA, USDA
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Web: http://www.animalgenome.org/pig | Mail: angenmap@animalgenome.org
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