From listmaster animalgenome.org Tlistmaster Jan 28 21:29:09 2021
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From: "Bickhart, Derek" <derek.bickhartusda.gov>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: The Bovine Pangenome Consortium is accepting sample
submissions
Date: Thu, 28 Jan 2021 21:29:09 -0600
The Bovine Pangenome Consortium (BPC) would like to help you get a high-
quality genome assembly of your favorite cattle breed(s) or Bovidae
species! The BPC is soliciting samples from potential collaborators to
sequence as part of our international project plan. If you are interested
in participating in a consortium that seeks to sequence and assemble a
broad diversity of bovid species and breeds for full comparative genomic
analysis, please feel free to contact us for more details! If your
breed/species currently lacks a reference genome assembly, we will conduct
the sequencing and assembly of your sample. You maintain ownership of the
data and assembly; however, we will ask that your data be included in a
larger comparative genomics analysis effort that will include all members
and collaborators of the BPC at a later date.
Samples will be sequenced to a high depth of coverage on the Oxford
Nanopore PromethION sequencer and a team of Bioinformatics specialists
will create polished genome assemblies from the resulting reads. For
particularly interesting breeds/species, we can work with your group to
solicit additional datasets for scaffolding/analysis including – but not
limited to – Hi-C library preparation.
We are preferentially interested in sequencing samples that have the
following qualities (listed in order of decreasing importance):
1. An F1 cross of two cattle (or Bovid) breeds, and parental samples can
be taken for sequencing.
2. A sample from a rare or underrepresented breed of cattle
(preferentially, non-European breeds).
3. A sample that can be easily shipped to the US for sequencing (and does
not require special shipping permits).
Our larger collaborative network has already sequenced individuals from the
following species/breeds and has plans to sequence several more: Angus,
Ankole, Bison, Brahman, Chianina, Gaur, Hereford, Highland Cow, Holstein,
Jersey, NDama, Piedmontese, Sarda, Simmental, and Yak. For an example of
a collaborative project that resulted in a haplotype-resolved assembly of
the Simmental breed, please see our recent publication in the Journal of
Heredity: https://tinyurl.com/y22wo6ld . We are particularly interested in
working with partners that have access to samples from Asian or African
breeds of cattle.
For more information about our consortium, as well as information regarding
sample preparation and your rights as a prospective participant, please
visit our temporary webpage at the following link:
https://njdbickhart.github.io/
We look forward to working with you to sequence and assemble underrepresented
bovid species for comparative analysis!
Sincerely,
The BPC Co-chairs
Derek M Bickhart (derek.bickhartusda.gov)
Ben D Rosen (mailto:ben.rosenusda.gov)
Tim PL Smith (mailto:tim.smith2usda.gov)
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