Dear EUCAGEN members and genome paper collaborators,
This is a quick update on the status of the DOE-JGI E.
grandis genome project and the associated genome paper.
There has been some important developments that will affect the
genome analysis, the schedule of the genome paper and the
content of companion papers.
UPDATED ANNOTATION (V1.1)
The JGI has produced a new filtered annotation set (V1.1) of
the initial 8X mapped
Eucalyptus grandis BRASUZ1 genome
assembly. This version (1.1) is a subset of the initial
annotation (1.0) and was released together with Phytozome 8.0
(Jan 16, 2012). V1.1 was produced by filtering (out) 8620
low-confidence gene models from the original v1.0 annotation
using criteria described on Phytozome
http://www.phytozome.net/eucalyptus.php.
Most of the removed gene models are short, incomplete models
with little or no EST support and most form singletons in the
Phytozome gene cluster database (i.e. they do not cluster with
any other known proteins). In short, we consider this subset
(36,376 primary protein coding loci) a high confidence subset
and will report it as such in the main genome paper. Some
contributors have already indicated that they have expression
evidence for some removed gene models, or that they can find
full length versions of the gene models using their own gene
predictions. It is therefore likely that some legitimate gene
models are included in the filtered set, which is why V1.0 will
still be available in Phytozome (browser track and searchable).
My opinion is that the filtered set is an important part of the
genome biology of Eucalyptus - we see many pseudogenes and it is
possible that the genome is undergoing gene loss after
whole-genome duplication and high rates of tandem duplication.
The V1.1 annotation files are available for download at
ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v8.0/Egrandis/annotation/.
The low confidence, filtered set is also available for download
there.
We have decided to report gene numbers for the initial V1.0
annotation in the main genome paper and to report the
V1.1 subset as a "high confidence" subset. This means that
collaborators working on companion papers can keep V1.0 models
in figures and tables, and then provide summary data for the
high confidence models in their papers and supplementary
materials as needed. We would like people to rather highlight
the high confidence subset rather than the low confidence
filtered set.
GENOME PAPER DRAFT
I am at JGI this week working with Jerry Tuskan on the first
full draft of the main genome paper. By the end of the week, we
will have a much better idea of which contributed analyses,
figures and tables can be included. Some of the analyses done
for the genome paper (e.g. whole-genome duplication analysis)
will have to be rerun with V1.1. We will contact people directly
for updated results. In some cases we also need both a short and
a detailed version of the methods used to produce the
contributed results (for the Online Methods and Supplementary
Notes sections of the paper). We will contact people directly
for that. Please be ready to provide updated results (v1.1
numbers) and methods for the genome paper draft. At this stage
we are looking at producing a final draft by end of March/early
April and will circulate the first draft to core collaborators
as soon as possible.
COMPANION PAPERS
We have a list of draft companion paper abstracts that we
will use to motivate a special issue of New Phytologist. If
anybody wants to submit additional abstracts for consideration,
those can be emailed to me by the end of this week. An updated
list of submitted abstracts will be uploaded to the Eucalyptus
Genome Wiki on BOGAS (
http://bioinformatics.psb.ugent.be/webtools/bogas/)
At this stage, we would like companion papers to be in final
draft by mid April. Papers that do not get included in the New
Phytologist special issue can be submitted in other relevant
journals such as BMG Genomics and Tree Genetics and Genomes.
E. CAMALDULENSIS GENOME
KASUZA DNA Research Institute in Japan has decided to release
the E. camaldulensis genome sequence data which they have
produced via the genome database on Kazusa DNA Inst website,
http://www.kazusa.or.jp/eucaly/.
Details of the database construction will be published on the
Japanese Society for Plant Cell and Molecular Biology website
http://www.jspcmb.jp/english/pbcontents/index.html. We
are delighted about this development. The E. camaldulensis
genome data, together with the E. globulus genome data produced
by JGI and by collaborators in Australia will be very valuable
for comparative genomics among these three representatives of
the main sections of the subgenus Synphyomyrtus including most
of the commercially grown eucalypts. We encourage collaborators
to make use of the E. camaldulensis genome resource.
I hope that you find this information useful. Please email me
if you have any questions or suggestions for the main genome
paper or companion papers.
Kind regards
Zander Myburg
>>>
Highlights include:
JGI Genomes:
-preliminary assembly and annotation of Panicum
virgatum (switchgrass) and Phaseolus
vulgaris (common bean)
-assembly and annotation of the arabidopsis
comparator Capsella rubella
-Updated annotations of Aquilegia coerulea,
Eucalyptus grandis, and Volvox
carteri
External Genomes:
-updated annotations of Brachypodium
distachyon, Oryza sativa
(rice), Zea mays (maize)
-addition of Linum usitatissimum (flax),
Brassica rapa (napa cabbage), Malus
domestica (apple).
regards,
The JGI Phytozome Team
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